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5
.gitignore vendored
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/install/
/build/
!/scripts/
.DS_Store

24
generic_install.sh Normal file
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#!/bin/bash
BUILD_LOCATION=/avfs/backend
INSTALL_LOCATION=/avfs/projects/ops
mkdir -p ${BUILD_LOCATION}
mkdir -p ${INSTALL_LOCATION}
## INSTALL ${PROGRAM} FROM SOURCE
PROGRAM_BUILD_DIR=${BUILD_LOCATION}/${PROGRAM}
PROGRAM_INSTALL_DIR=${INSTALL_LOCATION}/${PROGRAM}
mkdir -p ${PROGRAM_BUILD_DIR}
mkdir -p ${PROGRAM_INSTALL_DIR}
PROGRAM_VERSION=1.1.1w
cd ${PROGRAM_BUILD_DIR}
wget -c [website]
tar -xf ${PROGRAM}-${PROGRAM_VERSION}.tar.gz
cd ${PROGRAM}-${PROGRAM_VERSION}
mkdir build && cd build
../config --prefix=${PROGRAM_INSTALL_DIR}/${PROGRAM_VERSION}
make -j$(nproc)
make -j$(nproc) test
make install

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install_script.sh Normal file
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#!/bin/bash
# ------------------------------------------------------------------------
# PACKAGE LIST: register all new dependent tools and libs here. Order
# is important, the first in the list gets installed first
# ------------------------------------------------------------------------
tool_list="gcc intel cmake"
mpi_list="mpich openmpi intelmpi"
math_list="mkl acml openblas"
lib_list="fftw libint libxc libgrpp libxsmm cosma scalapack elpa cusolvermp plumed \
spfft spla ptscotch superlu pexsi quip gsl spglib hdf5 libvdwxc sirius
libvori libtorch deepmd"
package_list="${tool_list} ${mpi_list} ${math_list} ${lib_list}"
# ------------------------------------------------------------------------
# first set everything to __DONTUSE__
for ii in ${package_list}; do
eval with_${ii}="__DONTUSE__"
done
# ------------------------------------------------------------------------
# Work out default settings
# ------------------------------------------------------------------------
# tools to turn on by default:
with_gcc="__SYSTEM__"
if [ "COMPILER" = intel ]; then
./install_intel.sh
elif [ "COMPILER" = llvm ]; then
./install_llvm.sh
elif [ "COMPILER" = clang]; then
./install_llvm.sh
else
./install_gcc.sh
fi

1011
install_toolchain.sh
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268
make_cluster.sh Normal file
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#!/bin/bash
if [[ "$BASH_SOURCE" == "$0" ]]; then
echo "This script is the top-level bash file being run."
echo "Setting up the environment for the cluster."
BUILD_LOCATION=/avfs/backend
INSTALL_LOCATION=/avfs/projects/ops
mkdir -p ${BUILD_LOCATION}
mkdir -p ${INSTALL_LOCATION}
echo "Build location: ${BUILD_LOCATION}"
echo "Install location: ${INSTALL_LOCATION}"
else
echo "This script is not the top-level bash file being run."
fi
./scripts/install_gcc.sh
./scripts/install_env-modules.sh
./scripts/install_openssl.sh
./scripts/stage0/install_qt.sh
./scripts/stage0/install_cmake.sh
./scripts/stage0/install_git.sh
./scripts/stage0/install_llvm.sh
## INSTALL OPENMPI FROM SOURCE
module load gcc/${GCC_VERSION} cmake/${CMAKE_VERSION}
OPENMPI_BUILD_DIR=${BUILD_LOCATION}/openmpi
OPENMPI_INSTALL_DIR=${INSTALL_LOCATION}/openmpi
mkdir -p ${OPENMPI_BUILD_DIR}
mkdir -p ${OPENMPI_INSTALL_DIR}
OPENMPI_VERSION=4.1.1
cd ${OPENMPI_BUILD_DIR}
wget -c https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION%.*}/openmpi-${OPENMPI_VERSION}.tar.gz
tar -xf openmpi-${OPENMPI_VERSION}.tar.gz
cd openmpi-${OPENMPI_VERSION}
mkdir build && cd build
if [ $(command -v srun) ]; then
echo "Slurm installation found. OpenMPI will be configured with --with-pmi."
EXTRA_CONFIGURE_FLAGS="--with-pmi"
else
EXTRA_CONFIGURE_FLAGS=""
fi
pkg_install_dir=${OPENMPI_INSTALL_DIR}/${OPENMPI_VERSION}/${AVFS_COMPILER}/${AVFS_COMPILER_VERSION}
../configure CFLAGS="${CFLAGS}" \
--prefix=${pkg_install_dir} \
--libdir="${pkg_install_dir}/lib" \
--enable-mpi1-compatibility \
${EXTRA_CONFIGURE_FLAGS}
make -j$(nproc)
make -j$(nproc) install
## INSTALL MPICH FROM SOURCE
module load gcc/${GCC_VERSION} cmake/${CMAKE_VERSION}
MPICH_BUILD_DIR=${BUILD_LOCATION}/mpich
MPICH_INSTALL_DIR=${INSTALL_LOCATION}/mpich
mkdir -p ${MPICH_BUILD_DIR}
mkdir -p ${MPICH_INSTALL_DIR}
MPICH_VERSION=4.0.3
cd ${MPICH_BUILD_DIR}
wget -c https://mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz
tar -xf mpich-${MPICH_VERSION}.tar.gz
cd mpich-${MPICH_VERSION}
mkdir build && cd build
if ("${FC}" --version | grep -q 'GNU'); then
compat_flag=$(allowed_gfortran_flags "-fallow-argument-mismatch")
else
compat_flag=""
fi
pkg_install_dir=${MPICH_INSTALL_DIR}/${MPICH_VERSION}/${AVFS_COMPILER}/${AVFS_COMPILER_VERSION}
../configure \
--prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
MPICC="" \
FFLAGS="${FCFLAGS} ${compat_flag}" \
FCFLAGS="${FCFLAGS} ${compat_flag}" \
--without-x \
--enable-gl=no \
--with-device=${MPICH_DEVICE}
make -j$(nproc)
make -j$(nproc) install
MPIRUN="${pkg_install_dir}/bin/mpiexec"
MPICC="${pkg_install_dir}/bin/mpicc"
MPICXX="${pkg_install_dir}/bin/mpicxx"
MPIFC="${pkg_install_dir}/bin/mpifort"
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
MPICH_CFLAGS="-I'${pkg_install_dir}/include'"
MPICH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
export MPI_MODE="${MPI_MODE}"
export MPIRUN="${MPIRUN}"
export MPICC="${MPICC}"
export MPICXX="${MPICXX}"
export MPIFC="${MPIFC}"
export MPIFORT="${MPIFORT}"
export MPIF77="${MPIF77}"
export MPICH_CFLAGS="${MPICH_CFLAGS}"
export MPICH_LDFLAGS="${MPICH_LDFLAGS}"
export MPICH_LIBS="${MPICH_LIBS}"
export MPI_CFLAGS="${MPICH_CFLAGS}"
export MPI_LDFLAGS="${MPICH_LDFLAGS}"
export MPI_LIBS="${MPICH_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__parallel|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${MPICH_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${MPICH_LDFLAGS}|)"
export CP_LIBS="\${CP_LIBS} IF_MPI(${MPICH_LIBS}|)"
## INSTALL OPENBLAS FROM SOURCE
OPENBLAS_BUILD_DIR=${BUILD_LOCATION}/openblas
OPENBLAS_INSTALL_DIR=${INSTALL_LOCATION}/openblas
mkdir -p ${OPENBLAS_BUILD_DIR}
mkdir -p ${OPENBLAS_INSTALL_DIR}
OPENBLAS_VERSION=0.3.18
cd ${OPENBLAS_BUILD_DIR}
wget -c https://github.com/OpenMathLib/OpenBLAS/releases/download/v${OPENBLAS_VERSION}/OpenBLAS-${OPENBLAS_VERSION}.tar.gz
tar -xf OpenBLAS-${OPENBLAS_VERSION}.tar.gz
cd OpenBLAS-${OPENBLAS_VERSION}
pkg_install_dir=${OPENBLAS_INSTALL_DIR}/${OPENBLAS_VERSION}
make -j$(nproc) \
MAKE_NB_JOBS=0 \
TARGET=${TARGET} \
NUM_THREADS=128 \
USE_THREAD=1 \
USE_OPENMP=1 \
NO_AFFINITY=1 \
CC="${CC}" \
FC="${FC}" \
PREFIX="${pkg_install_dir}"
make -j$(nproc) \
MAKE_NB_JOBS=0 \
TARGET=${TARGET} \
NUM_THREADS=128 \
USE_THREAD=1 \
USE_OPENMP=1 \
NO_AFFINITY=1 \
CC="${CC}" \
FC="${FC}" \
PREFIX="${pkg_install_dir}" install
## INSTALL FFTW FROM SOURCE
./scripts/install_fftw.sh
## INSTALL HDF5 FROM SOURCE
module load gcc/8.1.0 openmpi/4.1.4 cmake/3.21.3
# Check if MPI is enabled
if [ -n "$MPI_ENABLED" ]; then
MPI_ENABLED=true
else
MPI_ENABLED=false
fi
HDF5_BUILD_DIR=${BUILD_LOCATION}/hdf5
HDF5_VERSION=1.12.1
# Use the MPI_ENABLED variable in your script
if [ "$MPI_ENABLED" = true ]; then
# MPI is enabled, do something
echo "MPI is enabled"
HDF5_INSTALL_DIR=${INSTALL_LOCATION}/hdf5-withmpi/${HDF5_VERSION}/${COMPILER}/${COMPILER_VERSION}/${MPI_NAME}/${MPI_VERSION}
else
# MPI is not enabled, do something else
echo "MPI is not enabled"
HDF5_INSTALL_DIR=${INSTALL_LOCATION}/hdf5/${HDF5_VERSION}/${COMPILER}/${COMPILER_VERSION}
fi
## INSTALL NETCDF FROM SOURCE
## INSTALL OPENMC FROM SOURCE
module load gcc/8.1.0 cmake/3.21.3 python/3.11.5 git/2.11.3
OPENMC_BUILD_DIR=${BUILD_LOCATION}/openmc
OPENMC_INSTALL_DIR=${INSTALL_LOCATION}/openmc
mkdir -p ${OPENMC_BUILD_DIR}
mkdir -p ${OPENMC_INSTALL_DIR}
PROJECT_FOLDER=/avfs/projects/openmc
cd ${PROJECT_FOLDER}
python3 -m venv .venv
OPENMC_VERSION=0.14.0
cd ${OPENMC_BUILD_DIR}
git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
cd openmc
git checkout v${OPENMC_VERSION}
mkdir build && cd build
if [ "$MPI_ENABLED" = true ]; then
# MPI is enabled, do something
# HDF5_ROOT=/avfs/projects/hdf5-withmpi/gcc/8.1.0/openmpi/4.1.4 \
# CC=/avfs/projects/openmpi/4.1.4/gcc/8.1.0/bin/mpicc \
# CXX=/avfs/projects/openmpi/4.1.4/gcc/8.1.0/bin/mpicxx \
module load hdf5-withmpi openmpi/4.1.4
HDF5_ROOT=${HDF5_ROOT} CC=mpicc CXX=mpicxx \
cmake .. -DCMAKE_INSTALL_PREFIX=${OPENMC_INSTALL_DIR}/${OPENMC_VERSION} -DOPENMC_USE_MPI=ON -DOPENMC_USE_OPENMP=ON -DCMAKE_BUILD_TYPE=Release
else
# MPI is not enabled, do something else
module load hdf5
HDF5_ROOT=${HDF5_ROOT}
cmake .. -DCMAKE_INSTALL_PREFIX=${OPENMC_INSTALL_DIR}/${OPENMC_VERSION} -DOPENMC_USE_MPI=OFF -DOPENMC_USE_OPENMP=ON -DCMAKE_BUILD_TYPE=Release
fi
make -j20
make install
cd ..
source ${PROJECT_FOLDER}/.venv/bin/activate
if [ "$MPI_ENABLED" = true ]; then
# MPI is enabled, do something
MPICC=/avfs/projects/openmpi/4.1.4/gcc/8.1.0/bin/mpicc \
/avfs/projects/python/3.11.5/bin/python3 -m pip install mpi4py
CC=/avfs/projects/openmpi/4.1.4/gcc/8.1.0/bin/mpicc HDF5_MPI=ON \
HDF5_DIR=/avfs/projects/hdf5-withmpi/gcc/8.1.0/openmpi/4.1.4 \
${PROJECT_FOLDER}/.venv/bin/python3 -m pip install --no-binary=h5py h5py
${PROJECT_FOLDER}/.venv/bin/python3 -m pip install .
else
# MPI is not enabled, do something else
HDF5_DIR=${HDF5_ROOT}
${PROJECT_FOLDER}/.venv/bin/python3 -m pip install .
fi
# HDF5_ROOT=/share/apps/hdf5-withmpi/gcc/8.1.0/openmpi/4.1.4 CC=/share/apps/openmpi/4.1.4/gcc/8.1.0/bin/mpicc CXX=/share/apps/openmpi/4.1.4/gcc/8.1.0/bin/mpicxx cmake .. -DCMAKE_INSTALL_PREFIX=/qfs/people/parl703/openmc -DOPENMC_USE_MPI=ON -DOPENMC_USE_OPENMP=ON -DCMAKE_BUILD_TYPE=Release
# make -j20
# make install
# cd ..
# MPICC=/share/apps/openmpi/4.1.4/gcc/8.1.0/bin/mpicc /share/apps/python/3.11.5/bin/python3 -m pip install mpi4py
# CC=/share/apps/openmpi/4.1.4/gcc/8.1.0/bin/mpicc HDF5_MPI=ON HDF5_DIR=/share/apps/hdf5-withmpi/gcc/8.1.0/openmpi/4.1.4 /rcfs/projects/sherlock/openmc/dwnld/.venv/bin/python3 -m pip install --no-binary=h5py h5py
# /rcfs/projects/sherlock/openmc/dwnld/.venv/bin/python3 -m pip install .

2
scripts/VERSION
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# version file to force a rebuild of the entire toolchain
VERSION="2019.1"

35
scripts/common_vars.sh
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# Common variables used by the installation scripts
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
# shellcheck shell=bash
# directories and files used by the installer
ROOTDIR=${ROOTDIR:-"$(pwd -P)"}
SCRIPTDIR=${SCRIPTDIR:-"${ROOTDIR}/scripts"}
INSTALLDIR=${INSTALLDIR:-"${ROOTDIR}/install"}
BUILDDIR=${BUILDDIR:-"${ROOTDIR}/build"}
SETUPFILE=${SETUPFILE:-"${INSTALLDIR}/setup"}
ARCH_FILE_TEMPLATE=${ARCH_FILE_TEMPLATE:-"${SCRIPTDIR}/arch_base.tmpl"}
VERSION_FILE=${VERSION_FILE:-"${SCRIPTDIR}/VERSION"}
# system arch gotten from OpenBLAS prebuild
OPENBLAS_ARCH=${OPENBLAS_ARCH:-"x86_64"}
OPENBLAS_LIBCORE=${OPENBLAS_LIBCORE:-''}
# search paths
SYS_INCLUDE_PATH=${SYS_INCLUDE_PATH:-'/usr/local/include:/usr/include'}
SYS_LIB_PATH=${SYS_LIB_PATHS:-'/usr/local/lib64:/usr/local/lib:/usr/lib64:/usr/lib:/lib64:/lib'}
INCLUDE_PATHS=${INCLUDE_PATHS:-"CPATH SYS_INCLUDE_PATH"}
LIB_PATHS=${LIB_PATHS:-'LD_LIBRARY_PATH LIBRARY_PATH LD_RUN_PATH SYS_LIB_PATH'}
# mode flags
ENABLE_OMP=${ENABLE_OMP:-"__TRUE__"}
ENABLE_CUDA=${ENABLE_CUDA:-"__FALSE__"}
ENABLE_HIP=${ENABLE_HIP:-"__FALSE__"}
ENABLE_OPENCL=${ENABLE_OPENCL:-"__FALSE__"}
ENABLE_CRAY=${ENABLE_CRAY:-"__FALSE__"}
MPI_MODE=${MPI_MODE:-openmpi}
MATH_MODE=${MATH_MODE:-openblas}
export NVCC=${NVCC:-nvcc}

61
scripts/get_openblas_arch.sh
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#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"
openblas_ver="0.3.25" # Keep in sync with install_openblas.sh
openblas_sha256="4c25cb30c4bb23eddca05d7d0a85997b8db6144f5464ba7f8c09ce91e2f35543"
openblas_pkg="OpenBLAS-${openblas_ver}.tar.gz"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
find_openblas_dir() {
local __dir=''
for __dir in *OpenBLAS*; do
if [ -d "$__dir" ]; then
echo "$__dir"
return 0
fi
done
echo ''
}
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
echo "==================== Getting proc arch info using OpenBLAS tools ===================="
# find existing openblas source dir
openblas_dir="$(find_openblas_dir)"
# if cannot find openblas source dir, try download one
if ! [ "$openblas_dir" ]; then
if [ -f ${openblas_pkg} ]; then
echo "${openblas_pkg} is found"
else
download_pkg_from_cp2k_org "${openblas_sha256}" "${openblas_pkg}"
fi
tar -xzf ${openblas_pkg}
openblas_dir="$(find_openblas_dir)"
fi
openblas_conf="${openblas_dir}/Makefile.conf"
# try find Makefile.config, if not then generate one with make lapack_prebuild
if ! [ -f "$openblas_conf" ]; then
cd "$openblas_dir"
make lapack_prebuild
cd ..
fi
OPENBLAS_LIBCORE="$(grep 'LIBCORE=' $openblas_conf | cut -f2 -d=)"
OPENBLAS_ARCH="$(grep 'ARCH=' $openblas_conf | cut -f2 -d=)"
echo "OpenBLAS detected LIBCORE = $OPENBLAS_LIBCORE"
echo "OpenBLAS detected ARCH = $OPENBLAS_ARCH"
# output setup file
cat << EOF > "${BUILDDIR}/openblas_arch"
export OPENBLAS_LIBCORE="${OPENBLAS_LIBCORE}"
export OPENBLAS_ARCH="${OPENBLAS_ARCH}"
EOF

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scripts/parse_if.py
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#!/usr/bin/env python3
import sys
import argparse
class Parser:
"Parser for files with IF_XYZ(A|B) constructs"
def __init__(self, switches):
self.mSwitches = switches
def Switches(self):
"outputs the switches used by parser"
return self.mSwitches
def SetSwitch(self, key, val):
"Set or add a (key,val) switch"
self.mSwitches[key] = val
def ParseSingleIf(self, string, switch):
"""
switch should be a tuple (key, val)
ParseSingleIf(string, switch) will replace in string the
first occurrence of IF_key(A|B) with A if val = True;
B if val = False
"""
init = string.find("IF_" + switch[0])
start = init
end = len(string)
mark = end
counter = 0
ind = start
# determine the correct location for '|'
for cc in string[init:]:
if cc == "(":
if counter == 0:
start = ind
counter += 1
elif cc == ")":
counter -= 1
if counter == 0:
end = ind
break
elif cc == "|" and counter == 1:
mark = ind
ind += 1
# resolve the option
if switch[1]:
result = (
string[0:init]
+ string[start + 1 : mark]
+ string[end + 1 : len(string)]
)
else:
result = (
string[0:init] + string[mark + 1 : end] + string[end + 1 : len(string)]
)
return result
def ParseIf(self, string, switch):
"""
ParseIf(string, switch) will replace in string recursively
occurance of IF_key(A|B) statements with A if val = True;
B if val = False
"""
result = string
while result.find("IF_" + switch[0]) > -1:
result = self.ParseSingleIf(result, switch)
return result
def ParseString(self, string):
"""
ParseString(string) will parse in string recursively
all of IF_key(A|B) statements for all (key, val) pairs
in dictionary self.mSwitches
"""
result = string
for switch in self.mSwitches.items():
result = self.ParseIf(result, switch)
return result
def ParseDocument(self, input_file, output_file):
"""
ParseDocument(input_file, output_fiel) will replace recursively
all of IF_key(A|B) statements for all (key, val) pairs
in dictionary self.mSwitches in the input_file stream and output
to the output_file stream.
"""
output = []
for line in input_file:
output.append(self.ParseString(line))
if input_file == output_file:
output_file.seek(0)
output_file.truncate()
# write to the same file
for line in output:
output_file.write(line)
# ------------------------------------------------------------------------
# main program
# ------------------------------------------------------------------------
if __name__ == "__main__":
argparser = argparse.ArgumentParser(
description="Resolve IF_*() macros based on given tags"
)
argparser.add_argument(
"-f",
"--file",
metavar="FILENAME",
type=str,
help="read from given file instead of stdin",
)
argparser.add_argument(
"-i",
"--inplace",
action="store_true",
help="do in-place replacement for the given file instead of echo to stdout",
)
argparser.add_argument("--selftest", action="store_true", help="run self test")
argparser.add_argument(
"flags",
metavar="FLAG",
type=str,
nargs="*",
help="specified flags are set to true",
)
args = argparser.parse_args()
# default list of switches used by the parser
switches = {
"MPI": False,
"CUDA": False,
"HIP": False,
"OPENCL": False,
"WARNALL": False,
"DEBUG": False,
"ASAN": False,
"STATIC": False,
"VALGRIND": False,
"COVERAGE": False,
}
parser = Parser(switches)
# set the list of switches given on the command line to True
for flag in args.flags:
parser.SetSwitch(flag, True)
if args.selftest:
sys.exit(0) # TODO implement selftest
# do parsing
if not args.file:
parser.ParseDocument(sys.stdin, sys.stdout)
else:
if args.inplace:
with open(args.file, mode="r+") as fhandle:
parser.ParseDocument(fhandle, fhandle)
else:
with open(args.file, mode="r") as fhandle:
parser.ParseDocument(fhandle, sys.stdout)

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scripts/signal_trap.sh
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# signal trapping
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
# shellcheck shell=bash
trap 'error_handler ${LINENO}' ERR

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scripts/stage0/install_beegfs.sh Executable file
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#!/bin/bash
# node01: Management Server
# node02: Metadata Server
# node03: Storage Server
# node04: Client
alias node01='172.17.2.101'
alias node02='172.17.2.102'
alias node03='172.17.2.103'
alias node04='172.17.2.104'
for ((i = 1 ; i < 5 ; i++)); do
ssh-copy-id -i ~/.ssh/id_rsa root@node0$i
ssh root@node0$i
yum install -y wget fio
hostnamectl set-hostname node0$i
wget -O /etc/yum.repos.d/beegfs_rhel8.repo https://www.beegfs.io/release/beegfs_7.4.3/dists/beegfs-rhel8.repo
systemctl disable firewalld
systemctl stop firewalld
sed -i 's/SELINUX=enforcing/SELINUX=disabled/g' /etc/sysconfig/selinux
sed -i 's/SELINUX=enforcing/SELINUX=disabled/g' /etc/selinux/config
cat <<EOF >> /etc/hosts
10.0.1.2 node01
10.0.1.3 node02
10.0.1.4 node03
10.0.1.5 node04
EOF
reboot now
done
ssh root@node01 yum install -y beegfs-mgmtd # management service
ssh root@node02 yum install -y beegfs-meta #libbeegfs-ib # metadata service; libbeegfs-ib is only required for RDMA
ssh root@node03 yum install -y beegfs-storage #libbeegfs-ib # storage service; libbeegfs-ib is only required for RDMA
ssh root@node04 yum install -y kernel-devel beegfs-client beegfs-helperd beegfs-utils # client and command-line utils
ssh root@node01
/opt/beegfs/sbin/beegfs-setup-mgmtd -p /data/beegfs/beegfs_mgmtd
systemctl start beegfs-mgmtd
systemctl status beegfs-mgmtd
ssh root@node02
/opt/beegfs/sbin/beegfs-setup-meta -p /data/beegfs/beegfs_meta -s 2 -m node01
systemctl start beegfs-meta
systemctl status beegfs-meta
ssh root@node03
mkdir -p /data/beegfs_storage{1..3}
mkfs.ext4 /dev/disk/by-id/scsi-0Linode_Volume_node01
mkfs.ext4 /dev/disk/by-id/scsi-0Linode_Volume_node02
mkfs.ext4 /dev/disk/by-id/scsi-0Linode_Volume_node03
mount /dev/disk/by-id/scsi-0Linode_Volume_node01 /data/beegfs_storage1
mount /dev/disk/by-id/scsi-0Linode_Volume_node02 /data/beegfs_storage2
mount /dev/disk/by-id/scsi-0Linode_Volume_node03 /data/beegfs_storage3
cat "/dev/disk/by-id/scsi-0Linode_Volume_node01 /data/beegfs_storage1" >> /etc/fstab
cat "/dev/disk/by-id/scsi-0Linode_Volume_node02 /data/beegfs_storage2" >> /etc/fstab
cat "/dev/disk/by-id/scsi-0Linode_Volume_node03 /data/beegfs_storage3" >> /etc/fstab
/opt/beegfs/sbin/beegfs-setup-storage -p /data/beegfs_storage1 -s 3 -i 301 -m node01
/opt/beegfs/sbin/beegfs-setup-storage -p /data/beegfs_storage2 -s 3 -i 302
/opt/beegfs/sbin/beegfs-setup-storage -p /data/beegfs_storage3 -s 3 -i 303
systemctl start beegfs-storage
systemctl status beegfs-storage
ssh root@node04
/opt/beegfs/sbin/beegfs-setup-client -m node01
systemctl start beegfs-helperd
systemctl status beegfs-helperd
systemctl start beegfs-client
systemctl status beegfs-client
vim /etc/beegfs/beegfs-mounts.conf
# set connDisableAuthentication to true on all nodes.
ssh node04
beegfs-ctl --listnodes --nodetype=meta --nicdetails
beegfs-ctl --listnodes --nodetype=storage --nicdetails
beegfs-ctl --listnodes --nodetype=client --nicdetails
beegfs-net # Displays connections the client is actually using
beegfs-check-servers # Displays possible connectivity of the services
beegfs-df # Displays free space and inodes of storage and metadata targets
ssh root@node01
fio --name=test --group_report --filename=/mnt/beegfs/testfile1 --ioengine=posixaio --time_based --runtime=180 --startdelay=10 --nrfiles=1 --size=1G --numjobs=1 --bs=128K --rw=read
ssh root@node04
fio --name=test --group_report --filename=/mnt/beegfs/testfile2 --ioengine=posixaio --time_based --runtime=180 --startdelay=10 --nrfiles=1 --size=1G --numjobs=1 --bs=128K --rw=read

5
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@ -0,0 +1,5 @@
BINUTILS_VERSION=2.35
wget -c https://ftp.gnu.org/gnu/binutils/binutils-${BINUTILS_VERSION}.tar.gz
tar -xf binutils-${BINUTILS_VERSION}.tar.gz

120
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@ -1,100 +1,26 @@
#!/bin/bash -e ## INSTALL CMAKE FROM SOURCE
CMAKE_BUILD_DIR=${BUILD_LOCATION}/cmake
CMAKE_INSTALL_DIR=${INSTALL_LOCATION}/cmake
mkdir -p ${CMAKE_BUILD_DIR}
mkdir -p ${CMAKE_INSTALL_DIR}
# TODO: Review and if possible fix shellcheck errors. VERSIONS=(3.5.2
# shellcheck disable=all 3.12.4
3.17.5
3.21.3
3.24.4
3.28.1)
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0 OPENSSL_ROOT_DIR=${SSL_INSTALL_DIR}/${SSL_VERSION}
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)" for CMAKE_VERSION in "${strings[@]}"; do
# CMAKE_VERSION=3.21.3
CMAKE_MAJOR_VERSION=$(echo ${CMAKE_VERSION} | cut -d. -f1-2)
cd ${CMAKE_BUILD_DIR}
wget -c http://www.cmake.org/files/v${CMAKE_MAJOR_VERSION}/cmake-${CMAKE_VERSION}.tar.gz
tar -xf cmake-${CMAKE_VERSION}.tar.gz
mkdir -p cmake-${CMAKE_VERSION}/build && cd cmake-${CMAKE_VERSION}/build
source "${SCRIPT_DIR}"/common_vars.sh ../configure --prefix=${CMAKE_INSTALL_DIR}/${CMAKE_VERSION} --parallel=$(nproc)
source "${SCRIPT_DIR}"/tool_kit.sh make -j$(nproc)
source "${SCRIPT_DIR}"/signal_trap.sh make install
source "${INSTALLDIR}"/toolchain.conf done
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_cmake" ] && rm "${BUILDDIR}/setup_cmake"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_cmake}" in
__INSTALL__)
echo "==================== Installing CMake ===================="
cmake_ver="3.28.1"
if [ "${OPENBLAS_ARCH}" = "arm64" ]; then
cmake_arch="linux-aarch64"
cmake_sha256="4ecba78ef9499a973d012a83feab5f888e86fc5388e9a768037ab4f7232cab16"
elif [ "${OPENBLAS_ARCH}" = "x86_64" ]; then
cmake_arch="linux-x86_64"
cmake_sha256="ada6a46be9da5f8cbeb00b9523ffe45ee6b36172eb81aaa5bdc6a2a8231b677c"
else
report_error ${LINENO} \
"cmake installation for ARCH=${ARCH} is not supported. You can try to use the system installation using the flag --with-cmake=system instead."
exit 1
fi
pkg_install_dir="${INSTALLDIR}/cmake/${cmake_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "cmake-${cmake_ver} is already installed, skipping it."
else
if [ -f cmake-${cmake_ver}-${cmake_arch}.sh ]; then
echo "cmake-${cmake_ver}-${cmake_arch}.sh is found"
else
download_pkg_from_cp2k_org "${cmake_sha256}" "cmake-${cmake_ver}-${cmake_arch}.sh"
fi
echo "Installing from scratch into ${pkg_install_dir}"
mkdir -p ${pkg_install_dir}
/bin/sh cmake-${cmake_ver}-${cmake_arch}.sh --prefix=${pkg_install_dir} --skip-license > install.log 2>&1 || tail -n ${LOG_LINES} install.log
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
fi
;;
__SYSTEM__)
echo "==================== Finding CMake from system paths ===================="
check_command cmake "cmake"
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking CMake to user paths ===================="
pkg_install_dir="$with_cmake"
check_dir "${with_cmake}/bin"
;;
esac
if [ "${with_cmake}" != "__DONTUSE__" ]; then
if [ "${with_cmake}" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_cmake"
prepend_path PATH "${pkg_install_dir}/bin"
EOF
mkdir -p "${MODULEDIR}/tools/cmake"
cat << EOF > "${MODULEDIR}"/tools/cmake/${cmake_ver}
#%Module1.0
##
## CMake modulefile
##
proc ModulesHelp { } {
global version
puts stderr "\tThis loads the cmake environment."
puts stderr "\tModifies: PATH"
}
module-whatis "load cmake environment"
module-whatis "Modifies: PATH"
# for Tcl script use only
set cmake_root ${pkg_install_dir}
setenv CMAKE "\$cmake_root"
prepend-path PATH "\$cmake_root/bin"
EOF
cat "${BUILDDIR}/setup_cmake" >> $SETUPFILE
fi
fi
load "${BUILDDIR}/setup_cmake"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "cmake"

276
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@ -1,253 +1,45 @@
#!/bin/bash -e #!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)" SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
gcc_ver="13.2.0" VERSIONS=(4.4.7
gcc_sha256="8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078" 4.6.2
4.8.5
4.9.3
5.1.0
5.2.0
5.4.0
6.1.0
6.3.0
7.1.0
7.5.0
8.4.0
9.1.0
10.2.0
10.3.0
11.2.0
12.3.0
13.1.0)
source "${SCRIPT_DIR}"/common_vars.sh source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_gcc" ] && rm "${BUILDDIR}/setup_gcc" GCC_VERSION=7.5.0
GCC_LDFLAGS="" GCC_BUILD_DIR=${BUILD_LOCATION}/gcc
GCC_CFLAGS="" GCC_INSTALL_DIR=${INSTALL_LOCATION}/gcc
TSANFLAGS="" mkdir -p ${GCC_INSTALL_DIR}
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}" mkdir gcc-${GCC_VERSION}-build
cd "${BUILDDIR}"
case "${with_gcc}" in cd ${GCC_BUILD_DIR}
__INSTALL__)
echo "==================== Installing GCC ===================="
pkg_install_dir="${INSTALLDIR}/gcc/${gcc_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "gcc-${gcc_ver} is already installed, skipping it."
else
if [ -f gcc-${gcc_ver}.tar.gz ]; then
echo "gcc-${gcc_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${gcc_sha256}" "gcc-${gcc_ver}.tar.gz"
fi
[ -d gcc-${gcc_ver} ] && rm -rf gcc-${gcc_ver}
tar -xzf gcc-${gcc_ver}.tar.gz
echo "Installing GCC from scratch into ${pkg_install_dir}" wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCC_VERSION}/gcc-${GCC_VERSION}.tar.gz
cd gcc-${gcc_ver} tar -xf gcc-${GCC_VERSION}.tar.gz
mv gcc-${GCC_VERSION} gcc-${GCC_VERSION}-source
# Download prerequisites from cp2k.org because gcc.gnu.org returns 403 when queried from GCP. cd gcc-${GCC_VERSION}-source
sed -i 's|http://gcc.gnu.org/pub/gcc/infrastructure/|https://cp2k.org/static/downloads/|' ./contrib/download_prerequisites ./contrib/download_prerequisites
./contrib/download_prerequisites > prereq.log 2>&1 || tail -n ${LOG_LINES} prereq.log cd ../gcc-${GCC_VERSION}-build
GCCROOT=${PWD} ${GCC_BUILD_DIR}/gcc-${GCC_VERSION}-source/configure --prefix=${GCC_INSTALL_DIR}/${GCC_VERSION} --enable-languages=c,c++,fortran,go --enable-lto --disable-multilib --enable-checking=release --enable-threads=posix --enable-libstdcxx-debug --enable-__cxa_atexit --enable-plugins --enable-bootstrap
mkdir obj make -j$(nproc)
cd obj make -j$(nproc) check
# TODO: Maybe use --disable-libquadmath-support to improve static linking: make install
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=46539
#
# TODO: Maybe use --disable-gnu-unique-object to improve static linking:
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60348#c13
# https://stackoverflow.com/questions/11931420
#
# TODO: Unfortunately, we can not simply use --disable-shared, because
# it would break OpenBLAS build and probably others too.
COMMON_FLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g"
CFLAGS="${COMMON_FLAGS} -std=gnu99"
CXXFLAGS="${CFLAGS}"
FCFLAGS="${COMMON_FLAGS} -fbacktrace"
${GCCROOT}/configure --prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
--enable-languages=c,c++,fortran \
--disable-multilib --disable-bootstrap \
--enable-lto \
--enable-plugins \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
FCFLAGS="${FCFLAGS}" \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
# thread sanitizer
if [ ${ENABLE_TSAN} = "__TRUE__" ]; then
# now the tricky bit... we need to recompile in particular
# libgomp with -fsanitize=thread.. there is not configure
# option for this (as far as I know). we need to go in
# the build tree and recompile / reinstall with proper
# options... this is likely to break for later version of
# gcc, tested with 5.1.0 based on
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=55374#c10
cd x86_64*/libgfortran
make clean > clean.log 2>&1 || tail -n ${LOG_LINES} clean.log
CFLAGS="${CFLAGS} -fsanitize=thread"
CXXFLAGS="${CXXFLAGS} -fsanitize=thread"
FCFLAGS="${FCFLAGS} -fsanitize=thread"
make -j $(get_nprocs) \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
FCFLAGS="${FCFLAGS}" \
LDFLAGS="-B$(pwd)/../libsanitizer/tsan/.libs/ -Wl,-rpath,$(pwd)/../libsanitizer/tsan/.libs/ -fsanitize=thread" \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ../libgomp
make clean > clean.log 2>&1 || tail -n ${LOG_LINES} clean.log
make -j $(get_nprocs) \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
FCFLAGS="${FCFLAGS}" \
LDFLAGS="-B$(pwd)/../libsanitizer/tsan/.libs/ -Wl,-rpath,$(pwd)/../libsanitizer/tsan/.libs/ -fsanitize=thread" \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ${GCCROOT}/obj/
fi
cd ../..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
fi
check_install ${pkg_install_dir}/bin/gcc "gcc" && CC="${pkg_install_dir}/bin/gcc" || exit 1
check_install ${pkg_install_dir}/bin/g++ "gcc" && CXX="${pkg_install_dir}/bin/g++" || exit 1
check_install ${pkg_install_dir}/bin/gfortran "gcc" && FC="${pkg_install_dir}/bin/gfortran" || exit 1
F90="${FC}"
F77="${FC}"
GCC_CFLAGS="-I'${pkg_install_dir}/include'"
GCC_LDFLAGS="-L'${pkg_install_dir}/lib64' -L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib64' -Wl,-rpath,'${pkg_install_dir}/lib64'"
;;
__SYSTEM__)
echo "==================== Finding GCC from system paths ===================="
check_command gcc "gcc" && CC="$(command -v gcc)" || exit 1
check_command g++ "gcc" && CXX="$(command -v g++)" || exit 1
check_command gfortran "gcc" && FC="$(command -v gfortran)" || exit 1
F90="${FC}"
F77="${FC}"
add_include_from_paths -p GCC_CFLAGS "c++" ${INCLUDE_PATHS}
add_lib_from_paths GCC_LDFLAGS "libgfortran.*" ${LIB_PATHS}
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking GCC to user paths ===================="
pkg_install_dir="${with_gcc}"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/lib64"
check_dir "${pkg_install_dir}/include"
check_command ${pkg_install_dir}/bin/gcc "gcc" && CC="${pkg_install_dir}/bin/gcc" || exit 1
check_command ${pkg_install_dir}/bin/g++ "gcc" && CXX="${pkg_install_dir}/bin/g++" || exit 1
check_command ${pkg_install_dir}/bin/gfortran "gcc" && FC="${pkg_install_dir}/bin/gfortran" || exit 1
F90="${FC}"
F77="${FC}"
GCC_CFLAGS="-I'${pkg_install_dir}/include'"
GCC_LDFLAGS="-L'${pkg_install_dir}/lib64' -L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib64' -Wl,-rpath,'${pkg_install_dir}/lib64'"
;;
esac
if [ "${ENABLE_TSAN}" = "__TRUE__" ]; then
TSANFLAGS="-fsanitize=thread"
else
TSANFLAGS=""
fi
if [ "${with_gcc}" != "__DONTUSE__" ]; then
cat << EOF > "${BUILDDIR}/setup_gcc"
export CC="${CC}"
export CXX="${CXX}"
export FC="${FC}"
export F90="${F90}"
export F77="${F77}"
export AVFS_COMPILER="gcc"
export AVFS_COMPILER_VERSION="${gcc_ver}"
EOF
if [ "${with_gcc}" != "__SYSTEM__" ]; then
cat << EOF >> "${BUILDDIR}/setup_gcc"
# needs full path for mpich/openmpi builds, triggers openblas bug
prepend_path PATH "${pkg_install_dir}/bin"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib64"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib64"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib64"
prepend_path CPATH "${pkg_install_dir}/include"
EOF
mkdir -p "${MODULEDIR}/compilers/gcc"
cat << EOF > "${MODULEDIR}/compilers/gcc/${gcc_ver}"
#%Module1.0#####################################################################
##
## GNU compiler modulefile
##
proc ModulesHelp { } {
global version
puts stderr "\tSets up GNU compiler environment"
puts stderr "\tModifies: MANPATH, LD_LIBRARY_PATH, PATH"
}
module-whatis "load gnu environment"
module-whatis "Modifies: MANPATH, PATH, LD_LIBRARY_PATH"
# for Tcl script use only
setenv AVFS_COMPILER "gcc"
setenv AVFS_COMPILER_VERSION "${gcc_ver}"
set gcc_root ${pkg_install_dir}
prepend-path PATH "\$gcc_root/bin"
prepend-path LD_LIBRARY_PATH "\$gcc_root/lib:\$gcc_root/lib64"
prepend-path MANPATH "\$gcc_root/share/man"
setenv CC gcc
setenv FC gfortran
setenv F90 gfortran
setenv CXX g++
setenv F77 gfortran
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_gcc"
export GCC_CFLAGS="${GCC_CFLAGS}"
export GCC_LDFLAGS="${GCC_LDFLAGS}"
export TSANFLAGS="${TSANFLAGS}"
EOF
cat "${BUILDDIR}/setup_gcc" >> ${SETUPFILE}
fi
# ----------------------------------------------------------------------
# Suppress reporting of known leaks
# ----------------------------------------------------------------------
# this might need to be adjusted for the versions of the software
# employed
cat << EOF >> ${INSTALLDIR}/lsan.supp
# known leak either related to mpi or scalapack (e.g. showing randomly for Fist/regtest-7-2/UO2-2x2x2-genpot_units.inp)
leak:__cp_fm_types_MOD_cp_fm_write_unformatted
# leak related to mpi or scalapack triggers sometimes for regtest-kp-2/cc2.inp
leak:Cblacs_gridmap
leak:blacs_gridmap_
# leak due to compiler bug triggered by combination of OOP and ALLOCATABLE
leak:__dbcsr_tensor_types_MOD___copy_dbcsr_tensor_types_Dbcsr_tas_dist_t
leak:__dbcsr_tensor_types_MOD___copy_dbcsr_tensor_types_Dbcsr_tas_blk_size_t
EOF
cat << EOF >> ${INSTALLDIR}/tsan.supp
# tsan bugs likely related to gcc
# PR66756
deadlock:_gfortran_st_open
mutex:_gfortran_st_open
# bugs related to removing/filtering blocks in DBCSR.. to be fixed
race:__dbcsr_block_access_MOD_dbcsr_remove_block
race:__dbcsr_operations_MOD_dbcsr_filter_anytype
race:__dbcsr_transformations_MOD_dbcsr_make_untransposed_blocks
EOF
# need to also link to the .supp file in setup file
cat << EOF >> ${SETUPFILE}
export LSAN_OPTIONS=suppressions=${INSTALLDIR}/lsan.supp
export TSAN_OPTIONS=suppressions=${INSTALLDIR}/tsan.supp
EOF
load "${BUILDDIR}/setup_gcc"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "gcc"

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## INSTALL GIT FROM SOURCE
GIT_BUILD_DIR=${BUILD_LOCATION}/git
GIT_INSTALL_DIR=${INSTALL_LOCATION}/git
mkdir -p ${GIT_BUILD_DIR}
mkdir -p ${GIT_INSTALL_DIR}
GIT_VERSION=2.11.3
cd ${GIT_BUILD_DIR}
wget -c https://mirrors.edge.kernel.org/pub/software/scm/git/git-${GIT_VERSION}.tar.gz
tar -xzf git-${GIT_VERSION}.tar.gz
cd git-${GIT_VERSION}
make configure
./configure --prefix=${GIT_INSTALL_DIR}/${GIT_VERSION}
make -j$(nproc)
make -j$(nproc) test
make install

105
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@ -6,94 +6,39 @@
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0} [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0}
SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)" SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_intel" ] && rm "${BUILDDIR}/setup_intel"
INTEL_CFLAGS="" INTEL_CFLAGS=""
INTEL_LDFLAGS="" INTEL_LDFLAGS=""
INTEL_LIBS="" INTEL_LIBS=""
mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_intel}" in echo "==================== Finding Intel compiler from system paths ===================="
__INSTALL__) if [ "${intel_classic}" = "yes" ]; then
echo "==================== Installing the Intel compiler ====================" check_command icc "intel" && CC="$(realpath $(command -v icc))" || exit 1
echo "__INSTALL__ is not supported; please install the Intel compiler manually" check_command icpc "intel" && CXX="$(realpath $(command -v icpc))" || exit 1
exit 1 check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1
;; else
__SYSTEM__) check_command icx "intel" && CC="$(realpath $(command -v icx))" || exit 1
echo "==================== Finding Intel compiler from system paths ====================" check_command icpx "intel" && CXX="$(realpath $(command -v icpx))" || exit 1
if [ "${intel_classic}" = "yes" ]; then check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1
check_command icc "intel" && CC="$(realpath $(command -v icc))" || exit 1 fi
check_command icpc "intel" && CXX="$(realpath $(command -v icpc))" || exit 1 F90="${FC}"
check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1 F77="${FC}"
else
check_command icx "intel" && CC="$(realpath $(command -v icx))" || exit 1 echo "CC is ${CC}"
check_command icpx "intel" && CXX="$(realpath $(command -v icpx))" || exit 1 echo "CXX is ${CXX}"
check_command ifort "intel" && FC="$(realpath $(command -v ifort))" || exit 1 echo "FC is ${FC}"
fi
F90="${FC}"
F77="${FC}"
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking Intel compiler to user paths ===================="
pkg_install_dir="${with_intel}"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
if [ "${intel_classic}" = "yes" ]; then
check_command ${pkg_install_dir}/bin/icc "intel" && CC="${pkg_install_dir}/bin/icc" || exit 1
check_command ${pkg_install_dir}/bin/icpc "intel" && CXX="${pkg_install_dir}/bin/icpc" || exit 1
check_command ${pkg_install_dir}/bin/ifort "intel" && FC="${pkg_install_dir}/bin/ifort" || exit 1
else
check_command ${pkg_install_dir}/bin/icx "intel" && CC="${pkg_install_dir}/bin/icx" || exit 1
check_command ${pkg_install_dir}/bin/icpx "intel" && CXX="${pkg_install_dir}/bin/icpx" || exit 1
check_command ${pkg_install_dir}/bin/ifort "intel" && FC="${pkg_install_dir}/bin/ifort" || exit 1
fi
F90="${FC}"
F77="${FC}"
INTEL_CFLAGS="-I'${pkg_install_dir}/include'"
INTEL_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_intel}" != "__DONTUSE__" ]; then
echo "CC is ${CC}"
echo "CXX is ${CXX}"
echo "FC is ${FC}"
cat << EOF > "${BUILDDIR}/setup_intel"
export CC="${CC}" export CC="${CC}"
export CXX="${CXX}" export CXX="${CXX}"
export FC="${FC}" export FC="${FC}"
export F90="${F90}" export F90="${F90}"
export F77="${F77}" export F77="${F77}"
EOF
if [ "${with_intel}" != "__SYSTEM__" ]; then export PATH=${pkg_install_dir}/bin:${PATH}
cat << EOF >> "${BUILDDIR}/setup_intel" export LD_LIBRARY_PATH=${pkg_install_dir}/lib:${LD_LIBRARY_PATH}
prepend_path PATH "${pkg_install_dir}/bin" export LD_RUN_PATH=${pkg_install_dir}/lib:${LD_RUN_PATH}
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib" export LIBRARY_PATH=${pkg_install_dir}/lib:${LIBRARY_PATH}
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib" export CPATH=${pkg_install_dir}/include:${CPATH}
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path CPATH "${pkg_install_dir}/include"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_intel"
export INTEL_CFLAGS="${INTEL_CFLAGS}" export INTEL_CFLAGS="${INTEL_CFLAGS}"
export INTEL_LDFLAGS="${INTEL_LDFLAGS}" export INTEL_LDFLAGS="${INTEL_LDFLAGS}"
export INTEL_LIBS="${INTEL_LIBS}" export INTEL_LIBS="${INTEL_LIBS}"
EOF
cat "${BUILDDIR}/setup_intel" >> ${SETUPFILE}
fi
load "${BUILDDIR}/setup_intel"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "intel"

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@ -0,0 +1,18 @@
## INSTALL LLVM FROM SOURCE
LLVM_BUILD_DIR=${BUILD_LOCATION}/llvm
LLVM_INSTALL_DIR=${INSTALL_LOCATION}/llvm
mkdir -p ${LLVM_BUILD_DIR}
mkdir -p ${LLVM_INSTALL_DIR}
LLVM_VERSION=13.0.0
git clone https://github.com/llvm/llvm-project.git ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
cd ${LLVM_BUILD_DIR}/llvm-${LLVM_VERSION}
git checkout llvmorg-${LLVM_VERSION}
mkdir build && cd build
cmake -S llvm -B build -G "Unix Makefiles" \
-DLLVM_ENABLE_PROJECTS="clang;clang-tools-extra;compiler-rt;libcxx;libcxxabi;libunwind;lld;lldb;openmp;parallel-libs;polly" \
-DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${LLVM_INSTALL_DIR}/${LLVM_VERSION} \
-DLLVM_INSTALL_UTILS=ON llvm
make -j$(nproc)
make install

26
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@ -0,0 +1,26 @@
#!/bin/bash -e
LUA_VERSION=5.1.4.9
wget https://sourceforge.net/projects/lmod/files/lua-${LUA_VERSION}.tar.bz2
tar -xf lua-${LUA_VERSION}.tar.bz2
cd lua-X.Y.Z
./configure --prefix=/avfs/projects/ops/lua/${LUA_VERSION}
make -j4
make install
cd /avfs/projects/ops/lua
ln -s ${LUA_VERSION} lua
LMOD_VERSION=8.7.37
wget https://sourceforge.net/projects/lmod/files/Lmod-${LMOD_VERSION}.tar.bz2
tar -xf Lmod-${LMOD_VERSION}.tar.bz2
# wget https://github.com/TACC/Lmod/archive/refs/tags/${LMOD_VERSION}.tar.gz
# tar -xf ${LMOD_VERSION}.tar.gz
cd Lmod-${LMOD_VERSION}
PATH=$PATH:/avfs/projects/ops/lua/lua/bin ./configure --prefix=/avfs/projects/ops/ \
--with-spiderCacheDir=/avfs/projects/ops/lmod/cacheDir \
--with-updateSystemFn=/avfs/projects/ops/lmod/cacheDir/system.txt
make install
ln -s /avfs/projects/ops/lmod/lmod/init/profile /etc/profile.d/z00_lmod.sh
ln -s /avfs/projects/ops/lmod/lmod/init/cshrc /etc/profile.d/z00_lmod.csh

94
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@ -3,84 +3,20 @@
# TODO: Review and if possible fix shellcheck errors. # TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all # shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0 MODULES_VERSION=5.3.1
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
modules_ver="3.2.10" MODULES_BUILD_DIR=${BUILD_LOCATION}
modules_sha256="fb05c82a83477805a1d97737a9f0ca0db23f69b7bce504f1609ba99477b03955" MODULES_INSTALL_DIR=${INSTALL_LOCATION}/modules
#modules_ver="5.3.1" mkdir -p ${MODULES_BUILD_DIR}
#modules_sha256="d02f9ce4f8baf6c99edceb7c73bfdd1e97d77bcc4725810b86efed9f58dda962" mkdir -p ${MODULES_INSTALL_DIR}
source "${SCRIPT_DIR}"/common_vars.sh cd ${MODULES_BUILD_DIR}
source "${SCRIPT_DIR}"/tool_kit.sh curl -LJO https://github.com/cea-hpc/modules/releases/download/v${MODULES_VERSION}/modules-${MODULES_VERSION}.tar.gz
source "${SCRIPT_DIR}"/signal_trap.sh tar -xf modules-${MODULES_VERSION}.tar.gz
source "${INSTALLDIR}"/toolchain.conf cd modules-${MODULES_VERSION}
source "${INSTALLDIR}"/toolchain.env mkdir build && cd build
./configure --prefix=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION} --modulefilesdir=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/modulefiles
[ -f "${BUILDDIR}/setup_modules" ] && rm "${BUILDDIR}/setup_modules" make -j$(nproc)
make install
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}" ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.sh /etc/profile.d/modules.sh
cd "${BUILDDIR}" ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.csh /etc/profile.d/modules.csh
case "${with_modules}" in
__INSTALL__)
echo "============ Installing Environment Modules ============"
pkg_install_dir="${INSTALLDIR}/modules/Modules/${modules_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "modules-${modules_ver} is already installed, skipping it."
else
if [ -f modules-${modules_ver}.tar.gz ]; then
echo "modules-${modules_ver}.tar.gz is found"
else
wget -c https://github.com/cea-hpc/modules/releases/download/v${modules_ver}/modules-${modules_ver}.tar.gz
fi
[ -d modules-${modules_ver} ] && rm -rf modules-${modules_ver}
tar -xzf modules-${modules_ver}.tar.gz
echo "Installing Environment Modules from scratch into ${pkg_install_dir}"
cd modules-${modules_ver}
./configure --prefix="${pkg_install_dir}" \
--modulefilesdir="${pkg_install_dir}/modulefiles" \
--enable-example-modulefiles \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
ln -s ${pkg_install_dir}/init/profile.sh /etc/profile.d/modules.sh
ln -s ${pkg_install_dir}/init/profile.csh /etc/profile.d/modules.csh
mkdir "${pkg_install_dir}/modulefiles/apps"
mkdir "${pkg_install_dir}/modulefiles/compilers"
mkdir "${pkg_install_dir}/modulefiles/mpi"
mkdir "${pkg_install_dir}/modulefiles/science"
mkdir "${pkg_install_dir}/modulefiles/tools"
cd ../..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
fi
# check_install ${pkg_install_dir}/bin/gcc "gcc" && CC="${pkg_install_dir}/bin/gcc" || exit 1
;;
__SYSTEM__)
echo "==================== Finding GCC from system paths ===================="
;;
__DONTUSE__)
# Nothing to do
;;
*)
;;
esac
cat << EOF > "${BUILDDIR}/setup_modules"
export MODULEDIR=/avfs/projects/ops/modules/Modules/4.0.0/modulefiles
EOF
cat "${BUILDDIR}/setup_modules" >> ${SETUPFILE}
load "${BUILDDIR}/setup_modules"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "modules"

16
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@ -0,0 +1,16 @@
SSL_VERSION=1.1.1w
SSL_BUILD_DIR=${BUILD_LOCATION}/openssl
SSL_INSTALL_DIR=${INSTALL_LOCATION}/openssl
mkdir -p ${SSL_BUILD_DIR}
mkdir -p ${SSL_INSTALL_DIR}
cd ${SSL_BUILD_DIR}
wget -c https://www.openssl.org/source/openssl-${SSL_VERSION}.tar.gz
tar -xf openssl-${SSL_VERSION}.tar.gz
cd openssl-${SSL_VERSION}
mkdir build && cd build
../config --prefix=${SSL_INSTALL_DIR}/${SSL_VERSION} --openssldir=${SSL_INSTALL_DIR}/${SSL_VERSION}
make -j$(nproc)
make -j$(nproc) test
make install

108
scripts/stage0/install_python.sh
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@ -1,108 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
python_ver="3.11.7"
python_sha256="d96c7e134c35a8c46236f8a0e566b69c"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_python" ] && rm "${BUILDDIR}/setup_python"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_python}" in
__INSTALL__)
echo "================= Installing Python ===================="
pkg_install_dir="${INSTALLDIR}/python/${python_ver}"
install_lock_file="${pkg_install_dir}/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "python-${python_ver} is already installed, skipping it."
else
if [ -f Python-${python_ver}.tar.xz ]; then
echo "Python-${python_ver}.tar.xz is found"
else
wget -c https://www.python.org/ftp/python/${python_ver}/Python-${python_ver}.tar.xz
fi
[ -d Python-${python_ver} ] && rm -rf Python-${python_ver}
tar -xf Python-${python_ver}.tar.xz
echo "Installing Python from scratch into ${pkg_install_dir}"
cd Python-${python_ver}
./configure --prefix="${pkg_install_dir}" \
--enable-optimizations \
--with-ensurepip \
--with-openssl=${SSLBASE} \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install \
> install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ../..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
fi
check_install ${pkg_install_dir}/bin/python3 "python3" || exit 1
check_install ${pkg_install_dir}/bin/pip3 "pip3" || exit 1
;;
__SYSTEM__)
echo "================== Finding Python from system paths ==================="
check_command python3 "python3" || exit 1
check_command pip3 "pip3" || exit 1
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "================== Linking Python to user paths ==================="
esac
if [ "${with_python}" != "__DONTUSE__" ]; then
cat << EOF > "${BUILDDIR}/setup_python"
export PYTHONHOME="${pkg_install_dir}"
export PATH="\${PYTHONHOME}/bin:\${PATH}"
export LD_LIBRARY_PATH="\${PYTHONHOME}/lib:\${LD_LIBRARY_PATH}"
EOF
if [ "${with_python}" != "__SYSTEM__" ]; then
mkdir -p "${MODULEDIR}/tools/python"
cat <<EOF > "${MODULEDIR}/tools/python/${python_ver}"
#%Module1.0#####################################################################
##
## Python ${python_ver} modulefile
##
proc ModulesHelp { } {
puts stderr "\tSets up environment for Python v${python_ver}"
}
module-whatis "sets up python environment"
module-whatis "Modifies: MANPATH, PATH, PYTHONHOME, LD_LIBRARY_PATH"
# for Tcl script use only
set python_root ${pkg_install_dir}
setenv PYTHONHOME "\$python_root"
prepend-path PATH \$python_root/bin
prepend-path LD_LIBRARY_PATH \$python_root/lib
prepend-path MANPATH \$python_root/man
conflict python
EOF
fi
fi
load "${BUILDDIR}/setup_python"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "python"

21
scripts/stage0/install_qt.sh Normal file
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@ -0,0 +1,21 @@
## INSTALL Qt FOR CMAKE-GUI
QT_BUILD_DIR=${BUILD_LOCATION}/qt
QT_INSTALL_DIR=${INSTALL_LOCATION}/qt
mkdir -p ${QT_BUILD_DIR}
mkdir -p ${QT_INSTALL_DIR}
## SOME COMBINATION WILL INSTALL GL
# install build-essential libgl1-mesa-dev libglu1-mesa-dev libglut-dev libgl2-mesa-dev libdrm-dev
# wget -c https://qt.mirror.constant.com/archive/online_installers/4.6/qt-unified-linux-x64-4.6.1-online.run
QT_VERSION=5.15.12
QT_MAJOR_VERSION=$(echo ${QT_VERSION} | cut -d. -f1-2)
cd ${QT_BUILD_DIR}
wget -c https://download.qt.io/official_releases/qt/${QT_MAJOR_VERSION}/${QT_VERSION}/single/qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
tar -xf qt-everywhere-opensource-src-${QT_VERSION}.tar.xz
cd qt-everywhere-opensource-src-${QT_VERSION}
mkdir build && cd build
../configure -prefix ${QT_INSTALL_DIR}/${QT_VERSION} -make tests -release -opensource -confirm-license
##### THIS COMMAND NEEDS TO BE FINISHED#####

101
scripts/stage0/install_ssl.sh
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@ -1,101 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
ssl_ver="1.1.1w"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_ssl" ] && rm "${BUILDDIR}/setup_ssl"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_ssl}" in
__INSTALL__)
echo "================== Installing OpenSSL =================="
pkg_install_dir="${INSTALLDIR}/openssl/${ssl_ver}"
install_lock_file="${pkg_install_dir}/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "openssl-${ssl_ver} is already installed, skipping it."
else
if [ -f openssl-${ssl_ver}.tar.xz ]; then
echo "openssl-${ssl_ver}.tar.xz is found"
else
wget -c https://www.openssl.org/source/openssl-${ssl_ver}.tar.gz
fi
[ -d openssl-${ssl_ver} ] && rm -rf openssl-${ssl_ver}
tar -xf openssl-${ssl_ver}.tar.gz
echo "Installing OpenSSL from scratch into ${pkg_install_dir}"
cd openssl-${ssl_ver}
./config --prefix="${pkg_install_dir}" \
--openssldir=${pkg_install_dir} \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) test
make -j $(get_nprocs) install \
> install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ../..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
fi
check_install ${pkg_install_dir}/bin/openssl "openssl" || exit 1
;;
__SYSTEM__)
check_command openssl "openssl" || exit 1
;;
__DONTUSE__)
# Nothing to do
;;
*)
esac
if [ "${with_ssl}" != "__DONTUSE__" ]; then
if [ "${with_python}" != "__SYSTEM__" ]; then
mkdir -p "${MODULEDIR}/tools/openssl"
cat << EOF > "${MODULEDIR}/tools/openssl/${ssl_ver}"
#%Module1.0#####################################################################
##
## OpenSSL ${ssl_ver} modulefile
##
proc ModulesHelp { } {
puts stderr "\tSets up environment for OpenSSL v${ssl_ver}"
}
module-whatis "sets up python environment"
module-whatis "Modifies: MANPATH, PATH, PYTHONHOME, LD_LIBRARY_PATH"
# for Tcl script use only
set openssl_root ${pkg_install_dir}
setenv SSLHOME \$openssl_root
prepend-path PATH \$openssl_root/bin
prepend-path LD_LIBRARY_PATH \$openssl_root/lib
conflict openssl
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_ssl"
export PATH="${pkg_install_dir}/bin:\${PATH}"
export LD_LIBRARY_PATH="${pkg_install_dir}/lib:\${LD_LIBRARY_PATH}"
export SSLBASE="${pkg_install_dir}"
EOF
cat "${BUILDDIR}/setup_ssl" >> ${SETUPFILE}
fi
load "${BUILDDIR}/setup_ssl"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "openssl"

12
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@ -3,12 +3,16 @@
# TODO: Review and if possible fix shellcheck errors. # TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all # shellcheck disable=all
./scripts/stage0/install_modules.sh
./scripts/stage0/install_gcc.sh ./scripts/stage0/install_gcc.sh
./scripts/stage0/install_beegfs.sh
./scripts/stage0/install_modules.sh
./scripts/stage0/install_binutils.sh
./scripts/stage0/install_llvm.sh
./scripts/stage0/install_intel.sh ./scripts/stage0/install_intel.sh
./scripts/stage0/setup_buildtools.sh ./scripts/stage0/setup_buildtools.sh
./scripts/stage0/install_openssl.sh
./scripts/stage0/install_git.sh
./scripts/stage0/install_qt.sh
./scripts/stage0/install_cmake.sh ./scripts/stage0/install_cmake.sh
./scripts/stage0/install_ssl.sh
./scripts/stage0/install_python.sh
#EOF #EOF

2
scripts/stage0/setup_buildtools.sh Executable file → Normal file
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@ -69,4 +69,4 @@ load "${BUILDDIR}/openblas_arch"
write_toolchain_env "${INSTALLDIR}" write_toolchain_env "${INSTALLDIR}"
#EOF #EOF

129
scripts/stage1/install_intelmpi.sh
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@ -1,129 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ ${MPI_MODE} != "intelmpi" ] && exit 0
rm -f "${BUILDDIR}/setup_intelmpi"
INTELMPI_CFLAGS=""
INTELMPI_LDFLAGS=""
INTELMPI_LIBS=""
mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_intelmpi}" in
__INSTALL__)
echo "==================== Installing Intel MPI ===================="
echo '__INSTALL__ is not supported; please manually install Intel MPI'
exit 1
;;
__SYSTEM__)
echo "==================== Finding Intel MPI from system paths ===================="
check_command mpiexec "intelmpi" && MPIRUN="$(realpath $(command -v mpiexec))"
if [ "${with_intel}" != "__DONTUSE__" ]; then
check_command mpiicc "intelmpi" && MPICC="$(realpath $(command -v mpiicc))" || exit 1
check_command mpiicpc "intelmpi" && MPICXX="$(realpath $(command -v mpiicpc))" || exit 1
check_command mpiifort "intelmpi" && MPIFC="$(realpath $(command -v mpiifort))" || exit 1
else
echo "The use of Intel MPI is only supported with the Intel compiler"
exit 1
fi
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
# include path is already handled by compiler wrapper scripts (can cause wrong mpi.mod with GNU Fortran)
# add_include_from_paths INTELMPI_CFLAGS "mpi.h" $INCLUDE_PATHS
add_lib_from_paths INTELMPI_LDFLAGS "libmpi.*" $LIB_PATHS
check_lib -lmpi "intelmpi"
check_lib -lmpicxx "intelmpi"
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking INTELMPI to user paths ===================="
pkg_install_dir="${with_intelmpi}"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
check_command ${pkg_install_dir}/bin/mpiexec "intel" && MPIRUN="${pkg_install_dir}/bin/mpiexec" || exit 1
if [ "${with_intel}" != "__DONTUSE__" ]; then
check_command ${pkg_install_dir}/bin/mpiicc "intel" && MPICC="${pkg_install_dir}/bin/mpiicc" || exit 1
check_command ${pkg_install_dir}/bin/mpiicpc "intel" && MPICXX="${pkg_install_dir}/bin/mpiicpc" || exit 1
check_command ${pkg_install_dir}/bin/mpiifort "intel" && MPIFC="${pkg_install_dir}/bin/mpiifort" || exit 1
else
echo "The use of Intel MPI is only supported with the Intel compiler"
exit 1
fi
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
# include path is already handled by compiler wrapper scripts (can cause wrong mpi.mod with GNU Fortran)
#INTELMPI_CFLAGS="-I'${pkg_install_dir}/include'"
INTELMPI_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_intelmpi}" != "__DONTUSE__" ]; then
if [ "${intel_classic}" = "yes" ]; then
I_MPI_CXX="icpc"
I_MPI_CC="icc"
I_MPI_FC="ifort"
else
I_MPI_CXX="icpx"
I_MPI_CC="icx"
I_MPI_FC="ifort"
fi
INTELMPI_LIBS="-lmpi -lmpicxx"
echo "I_MPI_CXX is ${I_MPI_CXX}"
echo "I_MPI_CC is ${I_MPI_CC}"
echo "I_MPI_FC is ${I_MPI_FC}"
echo "MPICXX is ${MPICXX}"
echo "MPICC is ${MPICC}"
echo "MPIFC is ${MPIFC}"
cat << EOF > "${BUILDDIR}/setup_intelmpi"
export I_MPI_CXX="${I_MPI_CXX}"
export I_MPI_CC="${I_MPI_CC}"
export I_MPI_FC="${I_MPI_FC}"
export MPI_MODE="${MPI_MODE}"
export MPIRUN="${MPIRUN}"
export MPICC="${MPICC}"
export MPICXX="${MPICXX}"
export MPIFC="${MPIFC}"
export MPIFORT="${MPIFORT}"
export MPIF77="${MPIF77}"
export INTELMPI_CFLAGS="${INTELMPI_CFLAGS}"
export INTELMPI_LDFLAGS="${INTELMPI_LDFLAGS}"
export INTELMPI_LIBS="${INTELMPI_LIBS}"
export MPI_CFLAGS="${INTELMPI_CFLAGS}"
export MPI_LDFLAGS="${INTELMPI_LDFLAGS}"
export MPI_LIBS="${INTELMPI_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__parallel -D__MPI_F08|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${INTELMPI_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${INTELMPI_LDFLAGS}|)"
export CP_LIBS="\${CP_LIBS} IF_MPI(${INTELMPI_LIBS}|)"
EOF
if [ "${with_intelmpi}" != "__SYSTEM__" ]; then
cat << EOF >> "${BUILDDIR}/setup_intelmpi"
prepend_path PATH "${pkg_install_dir}/bin"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path CPATH "${pkg_install_dir}/include"
EOF
fi
cat "${BUILDDIR}/setup_intelmpi" >> ${SETUPFILE}
fi
load "${BUILDDIR}/setup_intelmpi"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "intelmpi"

213
scripts/stage1/install_mpich.sh
View file

@ -1,213 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
mpich_ver="4.0.3"
mpich_sha256="17406ea90a6ed4ecd5be39c9ddcbfac9343e6ab4f77ac4e8c5ebe4a3e3b6c501"
mpich_pkg="mpich-${mpich_ver}.tar.gz"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ ${MPI_MODE} != "mpich" ] && exit 0
[ -f "${BUILDDIR}/setup_mpich" ] && rm "${BUILDDIR}/setup_mpich"
MPICH_CFLAGS=""
MPICH_LDFLAGS=""
MPICH_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_mpich}" in
__INSTALL__)
echo "==================== Installing MPICH ===================="
pkg_install_dir="${INSTALLDIR}/mpich/${mpich_ver}/${AVFS_COMPILER}/${AVFS_COMPILER_VERSION}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "mpich-${mpich_ver} is already installed, skipping it."
else
if [ -f ${mpich_pkg} ]; then
echo "${mpich_pkg} is found"
else
download_pkg_from_cp2k_org "${mpich_sha256}" "${mpich_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir} for MPICH device ${MPICH_DEVICE}"
[ -d mpich-${mpich_ver} ] && rm -rf mpich-${mpich_ver}
tar -xzf ${mpich_pkg}
cd mpich-${mpich_ver}
unset F90
unset F90FLAGS
# workaround for compilation with GCC >= 10, until properly fixed:
# https://github.com/pmodels/mpich/issues/4300
if ("${FC}" --version | grep -q 'GNU'); then
compat_flag=$(allowed_gfortran_flags "-fallow-argument-mismatch")
fi
./configure \
--prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
MPICC="" \
FFLAGS="${FCFLAGS} ${compat_flag}" \
FCFLAGS="${FCFLAGS} ${compat_flag}" \
--without-x \
--enable-gl=no \
--with-device=${MPICH_DEVICE} \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage1/$(basename ${SCRIPT_NAME})"
fi
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
check_install ${pkg_install_dir}/bin/mpiexec "mpich" && MPIRUN="${pkg_install_dir}/bin/mpiexec" || exit 1
check_install ${pkg_install_dir}/bin/mpicc "mpich" && MPICC="${pkg_install_dir}/bin/mpicc" || exit 1
check_install ${pkg_install_dir}/bin/mpicxx "mpich" && MPICXX="${pkg_install_dir}/bin/mpicxx" || exit 1
check_install ${pkg_install_dir}/bin/mpifort "mpich" && MPIFC="${pkg_install_dir}/bin/mpifort" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
MPICH_CFLAGS="-I'${pkg_install_dir}/include'"
MPICH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding MPICH from system paths ===================="
check_command mpiexec "mpich" && MPIRUN="$(command -v mpiexec)"
check_command mpicc "mpich" && MPICC="$(command -v mpicc)" || exit 1
if [ $(command -v mpic++ > /dev/null 2>&1) ]; then
check_command mpic++ "mpich" && MPICXX="$(command -v mpic++)" || exit 1
else
check_command mpicxx "mpich" && MPICXX="$(command -v mpicxx)" || exit 1
fi
check_command mpifort "mpich" && MPIFC="$(command -v mpifort)" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
check_lib -lmpifort "mpich"
check_lib -lmpicxx "mpich"
check_lib -lmpi "mpich"
add_include_from_paths MPICH_CFLAGS "mpi.h" ${INCLUDE_PATHS}
add_lib_from_paths MPICH_LDFLAGS "libmpi.*" ${LIB_PATHS}
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking MPICH to user paths ===================="
pkg_install_dir="${with_mpich}"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
check_command ${pkg_install_dir}/bin/mpiexec "mpich" && MPIRUN="${pkg_install_dir}/bin/mpiexec" || exit 1
check_command ${pkg_install_dir}/bin/mpicc "mpich" && MPICC="${pkg_install_dir}/bin/mpicc" || exit 1
check_command ${pkg_install_dir}/bin/mpicxx "mpich" && MPICXX="${pkg_install_dir}/bin/mpicxx" || exit 1
check_command ${pkg_install_dir}/bin/mpifort "mpich" && MPIFC="${pkg_install_dir}/bin/mpifort" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
MPICH_CFLAGS="-I'${pkg_install_dir}/include'"
MPICH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_mpich}" != "__DONTUSE__" ]; then
if [ "${with_mpich}" != "__SYSTEM__" ]; then
mpi_bin="${pkg_install_dir}/bin/mpiexec"
else
mpi_bin="mpiexec"
fi
MPICH_LIBS="-lmpifort -lmpicxx -lmpi"
cat << EOF > "${BUILDDIR}/setup_mpich"
export MPI_MODE="${MPI_MODE}"
export MPIRUN="${MPIRUN}"
export MPICC="${MPICC}"
export MPICXX="${MPICXX}"
export MPIFC="${MPIFC}"
export MPIFORT="${MPIFORT}"
export MPIF77="${MPIF77}"
export MPICH_CFLAGS="${MPICH_CFLAGS}"
export MPICH_LDFLAGS="${MPICH_LDFLAGS}"
export MPICH_LIBS="${MPICH_LIBS}"
export MPI_CFLAGS="${MPICH_CFLAGS}"
export MPI_LDFLAGS="${MPICH_LDFLAGS}"
export MPI_LIBS="${MPICH_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__parallel|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${MPICH_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${MPICH_LDFLAGS}|)"
export CP_LIBS="\${CP_LIBS} IF_MPI(${MPICH_LIBS}|)"
EOF
if [ "${with_mpich}" != "__SYSTEM__" ]; then
# Using append_path instead of prepend_path for compatibility with Shifter.
# See http://github.com/cp2k/cp2k/issues/2058
cat << EOF >> "${BUILDDIR}/setup_mpich"
append_path PATH "${pkg_install_dir}/bin"
append_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
append_path LD_RUN_PATH "${pkg_install_dir}/lib"
append_path LIBRARY_PATH "${pkg_install_dir}/lib"
append_path CPATH "${pkg_install_dir}/include"
EOF
mkdir -p "${MODULEDIR}/mpi/mpich"
cat << EOF > "${MODULEDIR}/mpi/mpich/${mpich_ver}"
#%Module1.0
##
## MPICH ${mpich_ver} modulefile
##
proc ModulesHelp { } {
global version
puts stderr "\tThis loads the MPICH ${mpich_ver} environment."
puts stderr "\tModifies: MPI_ROOT, MANPATH, PATH, LD_LIBRARY_PATH, AVFS_MPI, AVFS_MPI_VERSION, IBV_FORK_SAFE"
}
module-whatis "load MPICH${mpich_ver} environment"
module-whatis "Modifies: MPI_ROOT, MANPATH, PATH, LD_LIBRARY_PATH, AVFS_MPI, AVFS_MPI_VERSION, IBV_FORK_SAFE"
# for Tcl script use only
if { [info exists env(AVFS_COMPILER) ] } {
set compiler_type \$env(AVFS_COMPILER)
} else {
puts stderr "\tNo compiler loaded."
exit
}
if { [info exists env(AVFS_COMPILER_VERSION) ] } {
set compiler_version \$env(AVFS_COMPILER_VERSION)
} else {
puts stderr "\tError in \$compiler_type module: AVFS_COMPILER_VERSION not set, please notify administrator"
exit
}
set mpi_root "${INSTALLDIR}/mpich/${mpich_ver}/\${compiler_type}/\${compiler_version}"
if { ! [file exists \$mpi_root ] } {
puts stderr "\t The combination of compiler and MPI does not appear to be built yet"
exit
}
setenv MPI_ROOT "\$mpi_root"
setenv AVFS_MPI "mvapich2"
setenv AVFS_MPI_VERSION "${mpich_ver}"
setenv IBV_FORK_SAFE 1
prepend-path PATH "\$mpi_root/bin"
prepend-path LD_LIBRARY_PATH "\$mpi_root/lib"
prepend-path MANPATH "\$mpi_root/share/man"
EOF
fi
cat "${BUILDDIR}/setup_mpich" >> ${SETUPFILE}
fi
# Update leak suppression file
cat << EOF >> ${INSTALLDIR}/lsan.supp
# MPICH 3.3.2 with GCC 10.3.0
leak:MPIR_Find_local_and_external
leak:MPIU_Find_local_and_external
EOF
load "${BUILDDIR}/setup_mpich"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "mpich"

321
scripts/stage1/install_openmpi.sh Executable file → Normal file
View file

@ -1,285 +1,46 @@
#!/bin/bash -e #!/bin/bash
# TODO: Review and if possible fix shellcheck errors. if [[ "$BASH_SOURCE" == "$0" ]]; then
# shellcheck disable=all BUILD_LOCATION=${PWD}
INSTALL_LOCATION=/people/parl703
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0 TARGET_CPU="native"
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)" CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g -march=${TARGET_CPU} -mtune=${TARGET_CPU}"
FFLAGS="${CFLAGS} -fbacktrace"
openmpi_ver="4.1.5" CXXFLAGS="${CFLAGS}"
openmpi_sha256="c018b127619d2a2a30c1931f316fc8a245926d0f5b4ebed4711f9695e7f70925" F77FLAGS="${FFLAGS}"
openmpi_pkg="openmpi-${openmpi_ver}.tar.gz" F90FLAGS="${FFLAGS}"
FCFLAGS="${FFLAGS}"
source "${SCRIPT_DIR}"/common_vars.sh LOG_LINES=200
source "${SCRIPT_DIR}"/tool_kit.sh else
source "${SCRIPT_DIR}"/signal_trap.sh source ${BUILD_LOCATION}/build.env
source "${INSTALLDIR}"/toolchain.conf ROOT=${PWD}
source "${INSTALLDIR}"/toolchain.env
[ ${MPI_MODE} != "openmpi" ] && exit 0
[ -f "${BUILDDIR}/setup_openmpi" ] && rm "${BUILDDIR}/setup_openmpi"
OPENMPI_CFLAGS=""
OPENMPI_LDFLAGS=""
OPENMPI_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_openmpi}" in
__INSTALL__)
echo "==================== Installing OpenMPI ===================="
pkg_install_dir="${INSTALLDIR}/openmpi/${openmpi_ver}/${AVFS_COMPILER}/${AVFS_COMPILER_VERSION}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "openmpi-${openmpi_ver} is already installed, skipping it."
else
if [ -f ${openmpi_pkg} ]; then
echo "${openmpi_pkg} is found"
else
download_pkg_from_cp2k_org "${openmpi_sha256}" "${openmpi_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d openmpi-${openmpi_ver} ] && rm -rf openmpi-${openmpi_ver}
tar -xzf ${openmpi_pkg}
cd openmpi-${openmpi_ver}
if [ "${OPENBLAS_ARCH}" = "x86_64" ]; then
# can have issue with older glibc libraries, in which case
# we need to add the -fgnu89-inline to CFLAGS. We can check
# the version of glibc using ldd --version, as ldd is part of
# glibc package
glibc_version=$(ldd --version | awk '/ldd/{print $NF}')
glibc_major_ver=${glibc_version%%.*}
glibc_minor_ver=${glibc_version##*.}
if [ $glibc_major_ver -lt 2 ] ||
[ $glibc_major_ver -eq 2 -a $glibc_minor_ver -lt 12 ]; then
CFLAGS="${CFLAGS} -fgnu89-inline"
fi
fi
if [ $(command -v srun) ]; then
echo "Slurm installation found. OpenMPI will be configured with --with-pmi."
EXTRA_CONFIGURE_FLAGS="--with-pmi"
else
EXTRA_CONFIGURE_FLAGS=""
fi
# We still require MPI-1.0-compatability for PTSCOTCH
./configure CFLAGS="${CFLAGS}" \
--prefix=${pkg_install_dir} \
--libdir="${pkg_install_dir}/lib" \
--enable-mpi1-compatibility \
${EXTRA_CONFIGURE_FLAGS} \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage1/$(basename ${SCRIPT_NAME})"
fi
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
check_install ${pkg_install_dir}/bin/mpiexec "openmpi" && MPIRUN="${pkg_install_dir}/bin/mpiexec" || exit 1
check_install ${pkg_install_dir}/bin/mpicc "openmpi" && MPICC="${pkg_install_dir}/bin/mpicc" || exit 1
check_install ${pkg_install_dir}/bin/mpicxx "openmpi" && MPICXX="${pkg_install_dir}/bin/mpicxx" || exit 1
check_install ${pkg_install_dir}/bin/mpifort "openmpi" && MPIFC="${pkg_install_dir}/bin/mpifort" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
OPENMPI_CFLAGS="-I'${pkg_install_dir}/include'"
OPENMPI_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding OpenMPI from system paths ===================="
check_command mpiexec "openmpi" && MPIRUN="$(command -v mpiexec)"
check_command mpicc "openmpi" && MPICC="$(command -v mpicc)" || exit 1
check_command mpic++ "openmpi" && MPICXX="$(command -v mpic++)" || exit 1
check_command mpifort "openmpi" && MPIFC="$(command -v mpifort)" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
# Fortran code in CP2K is built via the mpifort wrapper, but we may need additional
# libraries and linker flags for C/C++-based MPI codepaths, pull them in at this point.
OPENMPI_CFLAGS="$(mpicxx --showme:compile)"
OPENMPI_LDFLAGS="$(mpicxx --showme:link)"
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking OpenMPI to user paths ===================="
pkg_install_dir="${with_openmpi}"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
check_command ${pkg_install_dir}/bin/mpiexec "openmpi" && MPIRUN="${pkg_install_dir}/bin/mpiexec" || exit 1
check_command ${pkg_install_dir}/bin/mpicc "openmpi" && MPICC="${pkg_install_dir}/bin/mpicc" || exit 1
check_command ${pkg_install_dir}/bin/mpic++ "openmpi" && MPICXX="${pkg_install_dir}/bin/mpic++" || exit 1
check_command ${pkg_install_dir}/bin/mpifort "openmpi" && MPIFC="${pkg_install_dir}/bin/mpifort" || exit 1
MPIFORT="${MPIFC}"
MPIF77="${MPIFC}"
OPENMPI_CFLAGS="-I'${pkg_install_dir}/include'"
OPENMPI_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_openmpi}" != "__DONTUSE__" ]; then
if [ "${with_openmpi}" != "__SYSTEM__" ]; then
mpi_bin="${pkg_install_dir}/bin/mpiexec"
mpicxx_bin="${pkg_install_dir}/bin/mpicxx"
else
mpi_bin="mpiexec"
mpicxx_bin="mpicxx"
fi
# check openmpi version as reported by mpiexec
raw_version=$(${mpi_bin} --version 2>&1 |
grep "(Open MPI)" | awk '{print $4}')
major_version=$(echo ${raw_version} | cut -d '.' -f 1)
minor_version=$(echo ${raw_version} | cut -d '.' -f 2)
OPENMPI_LIBS=""
# grab additional runtime libs (for C/C++) from the mpicxx wrapper,
# and remove them from the LDFLAGS if present
for lib in $("${mpicxx_bin}" --showme:libs); do
OPENMPI_LIBS+=" -l${lib}"
OPENMPI_LDFLAGS="${OPENMPI_LDFLAGS//-l${lib}/}"
done
cat << EOF > "${BUILDDIR}/setup_openmpi"
export MPI_MODE="${MPI_MODE}"
export MPIRUN="${MPIRUN}"
export MPICC="${MPICC}"
export MPICXX="${MPICXX}"
export MPIFC="${MPIFC}"
export MPIFORT="${MPIFORT}"
export MPIF77="${MPIF77}"
export OPENMPI_CFLAGS="${OPENMPI_CFLAGS}"
export OPENMPI_LDFLAGS="${OPENMPI_LDFLAGS}"
export OPENMPI_LIBS="${OPENMPI_LIBS}"
export MPI_CFLAGS="${OPENMPI_CFLAGS}"
export MPI_LDFLAGS="${OPENMPI_LDFLAGS}"
export MPI_LIBS="${OPENMPI_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__parallel|)"
# For proper mpi_f08 support, we need at least GCC version 9 (asynchronous keyword)
# Other compilers should work
if ! [ "$(gfortran -dumpversion | cut -d. -f1)" -lt 9 ]; then
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__MPI_F08|)"
fi
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${OPENMPI_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${OPENMPI_LDFLAGS}|)"
export CP_LIBS="\${CP_LIBS} IF_MPI(${OPENMPI_LIBS}|)"
EOF
if [ "${with_openmpi}" != "__SYSTEM__" ]; then
cat << EOF >> "${BUILDDIR}/setup_openmpi"
prepend_path PATH "${pkg_install_dir}/bin"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path CPATH "${pkg_install_dir}/include"
EOF
mkdir -p "${MODULEDIR}/mpi/openmpi"
cat << EOF > "${MODULEDIR}/mpi/openmpi/${openmpi_ver}"
#%Module1.0
##
## OpenMPI ${openmpi_ver} modulefile
##
proc ModulesHelp { } {
global version
puts stderr "\tThis loads the OpenMPI ${openmpi_ver} environment."
puts stderr "\tModifies: MPI_ROOT, MANPATH, PATH, LD_LIBRARY_PATH, AVFS_MPI, AVFS_MPI_VERSION, IBV_FORK_SAFE"
}
module-whatis "load OPENMPI${openmpi_ver} environment"
module-whatis "Modifies: MPI_ROOT, MANPATH, PATH, LD_LIBRARY_PATH, AVFS_MPI, AVFS_MPI_VERSION, IBV_FORK_SAFE"
# for Tcl script use only
if { [info exists env(AVFS_COMPILER) ] } {
set compiler_type \$env(AVFS_COMPILER)
} else {
puts stderr "\tNo compiler loaded."
exit
}
if { [info exists env(AVFS_COMPILER_VERSION) ] } {
set compiler_version \$env(AVFS_COMPILER_VERSION)
} else {
puts stderr "\tError in \$compiler_type module: AVFS_COMPILER_VERSION not set, please notify administrator"
exit
}
set mpi_root "${INSTALLDIR}/openmpi/${openmpi_ver}/\${compiler_type}/\${compiler_version}"
if { ! [file exists \$mpi_root ] } {
puts stderr "\t The combination of compiler and MPI does not appear to be built yet"
exit
}
setenv MPI_ROOT "\$mpi_root"
setenv AVFS_MPI "openmpi"
setenv AVFS_MPI_VERSION "${openmpi_ver}"
setenv IBV_FORK_SAFE 1
prepend-path PATH "\$mpi_root/bin"
prepend-path LD_LIBRARY_PATH "\$mpi_root/lib"
prepend-path MANPATH "\$mpi_root/share/man"
EOF
fi
cat "${BUILDDIR}/setup_openmpi" >> ${SETUPFILE}
fi fi
# ---------------------------------------------------------------------- MPI_VERSION=4.1.5
# Suppress reporting of known leaks
# ----------------------------------------------------------------------
cat << EOF >> ${INSTALLDIR}/valgrind.supp
{
<BuggyOpenMPI_1>
Memcheck:Leak
...
fun:*alloc
...
fun:ompi_mpi_init
}
{
<BuggyOpenMPI_2>
Memcheck:Leak
...
fun:*alloc
...
fun:ompi_mpi_finalize
}
{
<BuggyOpenMPI_3>
Memcheck:Leak
...
fun:malloc
fun:opal_free_list_grow_st
...
fun:mpi_alloc_mem
}
{
<BuggyOpenMPI_4>
Memcheck:Leak
...
fun:malloc
...
fun:progress_engine
...
fun:clone
}
{
<BuggyOpenMPI_5>
Memcheck:Leak
...
fun:malloc
...
fun:query_2_0_0
...
fun:ompi_comm_activate
}
EOF
cat << EOF >> ${INSTALLDIR}/lsan.supp
# leaks related to OpenMPI
leak:query_2_0_0
leak:ompi_init_f
leak:ompi_finalize_f
leak:ompi_file_open_f
leak:progress_engine
leak:__GI___strdup
EOF
load "${BUILDDIR}/setup_openmpi" OPENMPI_BUILD_DIR=${BUILD_LOCATION}/openmpi
write_toolchain_env "${INSTALLDIR}" OPENMPI_INSTALL_DIR=${INSTALL_LOCATION}/openmpi/${MPI_VERSION}
mkdir -p ${OPENMPI_BUILD_DIR}
mkdir -p ${OPENMPI_INSTALL_DIR}
cd "${ROOTDIR}" cd ${OPENMPI_BUILD_DIR}
report_timing "openmpi" wget -c https://www.openmpi.org/openmpi-${MPI_VERSION}.tar.gz
tar -xf openmpi-${MPI_VERSION}.tar.gz
cd openmpi-${MPI_VERSION}
mkdir build && cd build
if [ "MPI_ENABLED" = false ]; then
exit 1
fi
echo ${FFTW_INSTALL_DIR}
./configure --prefix=${FFTW_INSTALL_DIR} ${FFTW_FLAGS}
make -j$(nproc)
make -j$(nproc) check > check.log 2>&1 || tail -n ${LOG_LINES} check.log
make -j$(nproc) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
if [[ "$BASH_SOURCE" != "$0" ]]; then
cd ${ROOT}
else
echo "Exiting ..."
fi

10
scripts/stage1/install_stage1.sh
View file

@ -1,10 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage1/install_mpich.sh
./scripts/stage1/install_openmpi.sh
./scripts/stage1/install_intelmpi.sh
#EOF

70
scripts/stage2/install_acml.sh
View file

@ -1,70 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_acml" ] && rm "${BUILDDIR}/setup_acml"
ACML_CFLAGS=''
ACML_LDFLAGS=''
ACML_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_acml" in
__INSTALL__)
echo "==================== Installing ACML ===================="
report_error $LINENO "To install ACML you should either contact your system administrator or go to https://developer.amd.com/tools-and-sdks/archive/amd-core-math-library-acml/acml-downloads-resources/ and download the correct version for your system."
exit 1
;;
__SYSTEM__)
echo "==================== Finding ACML from system paths ===================="
check_lib -lacml "ACML"
add_include_from_paths ACML_CFLAGS "acml.h" $INCLUDE_PATHS
add_lib_from_paths ACML_LDFLAGS "libacml.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking ACML to user paths ===================="
pkg_install_dir="$with_acml"
check_dir "${pkg_install_dir}/lib"
ACML_CFLAGS="-I'${pkg_install_dir}/include'"
ACML_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_acml" != "__DONTUSE__" ]; then
ACML_LIBS="-lacml"
if [ "$with_acml" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_acml"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
EOF
cat "${BUILDDIR}/setup_acml" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_acml"
export ACML_CFLAGS="${ACML_CFLAGS}"
export ACML_LDFLAGS="${ACML_LDFLAGS}"
export ACML_LIBS="${ACML_LIBS}"
export MATH_CFLAGS="\${MATH_CFLAGS} ${ACML_CFLAGS}"
export MATH_LDFLAGS="\${MATH_LDFLAGS} ${ACML_LDFLAGS}"
export MATH_LIBS="\${MATH_LIBS} ${ACML_LIBS}"
EOF
fi
load "${BUILDDIR}/setup_acml"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "acml"

48
scripts/stage2/install_mathlibs.sh
View file

@ -1,48 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
export MATH_CFLAGS=''
export MATH_LDFLAGS=''
export MATH_LIBS=''
write_toolchain_env "${INSTALLDIR}"
case "$MATH_MODE" in
mkl)
"${SCRIPTDIR}"/stage2/install_mkl.sh "${with_mkl}"
load "${BUILDDIR}/setup_mkl"
;;
acml)
"${SCRIPTDIR}"/stage2/install_acml.sh "${with_acml}"
load "${BUILDDIR}/setup_acml"
;;
openblas)
"${SCRIPTDIR}"/stage2/install_openblas.sh "${with_openblas}"
load "${BUILDDIR}/setup_openblas"
;;
cray)
# note the space is intentional so that the variable is
# non-empty and can pass require_env checks
export MATH_LDFLAGS="${MATH_LDFLAGS} "
export MATH_LIBS="${MATH_LIBS} ${CRAY_EXTRA_LIBS}"
;;
esac
export CP_CFLAGS="${CP_CFLAGS} ${MATH_CFLAGS}"
export CP_LDFLAGS="${CP_LDFLAGS} ${MATH_LDFLAGS}"
export CP_LIBS="${CP_LIBS} ${MATH_LIBS}"
write_toolchain_env "${INSTALLDIR}"
#EOF

139
scripts/stage2/install_mkl.sh
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@ -1,139 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_mkl" ] && rm "${BUILDDIR}/setup_mkl"
MKL_CFLAGS=""
MKL_LDFLAGS=""
MKL_LIBS=""
MKL_FFTW="yes"
if [ "${with_libvdwxc}" != "__DONTUSE__" ] && [ "${MPI_MODE}" != "no" ]; then
report_warning ${LINENO} "MKL FFTW3 interface is present, but FFTW library is needed for FFTW-MPI wrappers."
MKL_FFTW="no"
fi
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_mkl}" in
__INSTALL__)
echo "==================== Installing MKL ===================="
report_error ${LINENO} "To install MKL, please contact your system administrator."
exit 1
;;
__SYSTEM__)
echo "==================== Finding MKL from system paths ===================="
if ! [ -z "${MKLROOT}" ]; then
echo "MKLROOT is found to be ${MKLROOT}"
else
report_error ${LINENO} "Cannot find env variable MKLROOT, the script relies on it being set. Please check in MKL installation and use --with-mkl=<location> to pass the path to MKL root directory to this script."
exit 1
fi
check_lib -lm
check_lib -ldl
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking MKL to user paths ===================="
check_dir "${with_mkl}"
MKLROOT="${with_mkl}"
;;
esac
if [ "${with_mkl}" != "__DONTUSE__" ]; then
case ${OPENBLAS_ARCH} in
x86_64)
mkl_arch_dir="intel64"
MKL_CFLAGS="-m64"
;;
i386)
mkl_arch_dir="ia32"
MKL_CFLAGS="-m32"
;;
*)
report_error $LINENO "MKL only supports intel64 (x86_64) and ia32 (i386) at the moment, and your arch obtained from OpenBLAS prebuild is $OPENBLAS_ARCH"
exit 1
;;
esac
mkl_lib_dir="${MKLROOT}/lib/${mkl_arch_dir}"
# check we have required libraries
mkl_required_libs="libmkl_gf_lp64.so libmkl_sequential.so libmkl_core.so"
for ii in $mkl_required_libs; do
if [ ! -f "$mkl_lib_dir/${ii}" ]; then
report_error $LINENO "missing MKL library ${ii}"
exit 1
fi
done
case ${MPI_MODE} in
intelmpi | mpich)
mkl_scalapack_lib="IF_MPI(-lmkl_scalapack_lp64|)"
mkl_blacs_lib="IF_MPI(-lmkl_blacs_intelmpi_lp64|)"
;;
openmpi)
mkl_scalapack_lib="IF_MPI(-lmkl_scalapack_lp64|)"
mkl_blacs_lib="IF_MPI(-lmkl_blacs_openmpi_lp64|)"
;;
*)
echo "Not using MKL provided ScaLAPACK and BLACS"
mkl_scalapack_lib=""
mkl_blacs_lib=""
;;
esac
# set the correct lib flags from MLK link adviser
MKL_LIBS="-L${mkl_lib_dir} -Wl,-rpath,${mkl_lib_dir} ${mkl_scalapack_lib}"
MKL_LIBS+=" -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential -lmkl_core"
MKL_LIBS+=" ${mkl_blacs_lib} -Wl,--end-group -lpthread -lm -ldl"
# setup_mkl disables using separate FFTW library (see below)
MKL_CFLAGS="${MKL_CFLAGS} -I${MKLROOT}/include"
if [ "${MKL_FFTW}" != "no" ]; then
MKL_CFLAGS+=" -I${MKLROOT}/include/fftw"
fi
# write setup files
cat << EOF > "${BUILDDIR}/setup_mkl"
export MKLROOT="${MKLROOT}"
export MKL_CFLAGS="${MKL_CFLAGS}"
export MKL_LIBS="${MKL_LIBS}"
export MATH_CFLAGS="\${MATH_CFLAGS} ${MKL_CFLAGS}"
export MATH_LIBS="\${MATH_LIBS} ${MKL_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__MKL -D__FFTW3 IF_COVERAGE(IF_MPI(|-U__FFTW3)|)"
EOF
if [ -n "${mkl_scalapack_lib}" ]; then
cat << EOF >> "${BUILDDIR}/setup_mkl"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__SCALAPACK|)"
export with_scalapack="__DONTUSE__"
EOF
fi
if [ "${MKL_FFTW}" != "no" ]; then
cat << EOF >> "${BUILDDIR}/setup_mkl"
export with_fftw="__DONTUSE__"
export FFTW3_INCLUDES="${MKL_CFLAGS}"
export FFTW3_LIBS="${MKL_LIBS}"
export FFTW_CFLAGS="${MKL_CFLAGS}"
export FFTW_LDFLAGS="${MKL_LDFLAGS}"
export FFTW_LIBS="${MKL_LIBS}"
EOF
fi
cat "${BUILDDIR}/setup_mkl" >> ${SETUPFILE}
fi
load "${BUILDDIR}/setup_mkl"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "mkl"

184
scripts/stage2/install_openblas.sh
View file

@ -1,184 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
openblas_ver="0.3.25" # Keep in sync with get_openblas_arch.sh
openblas_sha256="4c25cb30c4bb23eddca05d7d0a85997b8db6144f5464ba7f8c09ce91e2f35543"
openblas_pkg="OpenBLAS-${openblas_ver}.tar.gz"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_openblas" ] && rm "${BUILDDIR}/setup_openblas"
OPENBLAS_CFLAGS=""
OPENBLAS_LDFLAGS=""
OPENBLAS_LIBS=""
OPENBLAS_ROOT=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_openblas}" in
__INSTALL__)
echo "==================== Installing OpenBLAS ===================="
pkg_install_dir="${INSTALLDIR}/openblas/${openblas_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "openblas-${openblas_ver} is already installed, skipping it."
else
if [ -f ${openblas_pkg} ]; then
echo "${openblas_pkg} is found"
else
download_pkg_from_cp2k_org "${openblas_sha256}" "${openblas_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d OpenBLAS-${openblas_ver} ] && rm -rf OpenBLAS-${openblas_ver}
tar -zxf ${openblas_pkg}
cd OpenBLAS-${openblas_ver}
# First attempt to make openblas using auto detected
# TARGET, if this fails, then make with forced
# TARGET=NEHALEM
#
# wrt NUM_THREADS=128: this is what the most common Linux distros seem to choose atm
# for a good compromise between memory usage and scalability
#
# Unfortunately, NO_SHARED=1 breaks ScaLAPACK build.
case "${TARGET_CPU}" in
"generic")
TARGET="NEHALEM"
;;
"native")
TARGET=${OPENBLAS_LIBCORE}
;;
"broadwell" | "skylake")
TARGET="HASWELL"
;;
"skylake-avx512")
TARGET="SKYLAKEX"
;;
"znver*")
TARGET="ZEN"
;;
*)
TARGET=${TARGET_CPU}
;;
esac
TARGET=$(echo ${TARGET} | tr '[:lower:]' '[:upper:]')
echo "Installing OpenBLAS library for target ${TARGET}"
(
make -j $(get_nprocs) \
MAKE_NB_JOBS=0 \
TARGET=${TARGET} \
NUM_THREADS=128 \
USE_THREAD=1 \
USE_OPENMP=1 \
NO_AFFINITY=1 \
CC="${CC}" \
FC="${FC}" \
PREFIX="${pkg_install_dir}" \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
) || (
make -j $(get_nprocs) \
MAKE_NB_JOBS=0 \
TARGET=NEHALEM \
NUM_THREADS=128 \
USE_THREAD=1 \
USE_OPENMP=1 \
NO_AFFINITY=1 \
CC="${CC}" \
FC="${FC}" \
PREFIX="${pkg_install_dir}" \
> make.nehalem.log 2>&1 || tail -n ${LOG_LINES} make.nehalem.log
)
make -j $(get_nprocs) \
MAKE_NB_JOBS=0 \
TARGET=${TARGET} \
NUM_THREADS=128 \
USE_THREAD=1 \
USE_OPENMP=1 \
NO_AFFINITY=1 \
CC="${CC}" \
FC="${FC}" \
PREFIX="${pkg_install_dir}" \
install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage2/$(basename ${SCRIPT_NAME})"
fi
OPENBLAS_CFLAGS="-I'${pkg_install_dir}/include'"
OPENBLAS_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
OPENBLAS_ROOT="${pkg_install_dir}"
# Prefer static library if available
if [ -f "${pkg_install_dir}/lib/libopenblas.a" ]; then
OPENBLAS_LIBS="-l:libopenblas.a"
else
OPENBLAS_LIBS="-lopenblas"
fi
;;
__SYSTEM__)
echo "==================== Finding LAPACK from system paths ===================="
# assume that system openblas is threaded
check_lib -lopenblas "OpenBLAS"
OPENBLAS_LIBS="-lopenblas"
# detect separate omp builds
check_lib -lopenblas_openmp 2> /dev/null && OPENBLAS_LIBS="-lopenblas_openmp"
check_lib -lopenblas_omp 2> /dev/null && OPENBLAS_LIBS="-lopenblas_omp"
add_include_from_paths OPENBLAS_CFLAGS "openblas_config.h" $INCLUDE_PATHS
add_lib_from_paths OPENBLAS_LDFLAGS "libopenblas.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking LAPACK to user paths ===================="
pkg_install_dir="$with_openblas"
check_dir "${pkg_install_dir}/include"
check_dir "${pkg_install_dir}/lib"
OPENBLAS_CFLAGS="-I'${pkg_install_dir}/include'"
OPENBLAS_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
OPENBLAS_LIBS="-lopenblas"
# detect separate omp builds
(__libdir="${pkg_install_dir}/lib" LIB_PATHS="__libdir" check_lib -lopenblas_openmp 2> /dev/null) &&
OPENBLAS_LIBS="-lopenblas_openmp"
(__libdir="${pkg_install_dir}/lib" LIB_PATHS="__libdir" check_lib -lopenblas_omp 2> /dev/null) &&
OPENBLAS_LIBS="-lopenblas_omp"
;;
esac
if [ "$with_openblas" != "__DONTUSE__" ]; then
if [ "$with_openblas" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_openblas"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
prepend_path CPATH "$pkg_install_dir/include"
export OPENBLAS_ROOT=${pkg_install_dir}
EOF
cat "${BUILDDIR}/setup_openblas" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_openblas"
export OPENBLAS_ROOT="${pkg_install_dir}"
export OPENBLAS_CFLAGS="${OPENBLAS_CFLAGS}"
export OPENBLAS_LDFLAGS="${OPENBLAS_LDFLAGS}"
export OPENBLAS_LIBS="${OPENBLAS_LIBS}"
export MATH_CFLAGS="\${MATH_CFLAGS} ${OPENBLAS_CFLAGS}"
export MATH_LDFLAGS="\${MATH_LDFLAGS} ${OPENBLAS_LDFLAGS}"
export MATH_LIBS="\${MATH_LIBS} ${OPENBLAS_LIBS}"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
load "${BUILDDIR}/setup_openblas"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "openblas"

8
scripts/stage2/install_stage2.sh
View file

@ -1,8 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage2/install_mathlibs.sh
#EOF

202
scripts/stage3/install_fftw.sh Executable file → Normal file
View file

@ -1,136 +1,76 @@
#!/bin/bash -e #!/bin/bash
# TODO: Review and if possible fix shellcheck errors. if [[ "$BASH_SOURCE" == "$0" ]]; then
# shellcheck disable=all BUILD_LOCATION=${PWD}
INSTALL_LOCATION=/avfs/people/parl703
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0 LOG_LINES=200
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)" else
source ${BUILD_LOCATION}/build.env
fftw_ver="3.3.10" ROOT=${PWD}
fftw_sha256="56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467"
fftw_pkg="fftw-${fftw_ver}.tar.gz"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_fftw" ] && rm "${BUILDDIR}/setup_fftw"
FFTW_CFLAGS=''
FFTW_LDFLAGS=''
FFTW_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_fftw" in
__INSTALL__)
require_env MPI_LIBS
echo "==================== Installing FFTW ===================="
pkg_install_dir="${INSTALLDIR}/fftw/${fftw_ver}/omp"
[ "${MPI_MODE}" != "no" ] && pkg_install_dir="${INSTALLDIR}/fftw/${fftw_ver}/mpi"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "fftw-${fftw_ver} is already installed, skipping it."
else
if [ -f ${fftw_pkg} ]; then
echo "${fftw_pkg} is found"
else
download_pkg_from_cp2k_org "${fftw_sha256}" "${fftw_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d fftw-${fftw_ver} ] && rm -rf fftw-${fftw_ver}
tar -xzf ${fftw_pkg}
cd fftw-${fftw_ver}
FFTW_FLAGS="--enable-openmp --disable-shared --enable-static"
# fftw has mpi support but not compiled by default. so compile it if we build with mpi.
# it will create a second library to link with if needed
[ "${MPI_MODE}" != "no" ] && FFTW_FLAGS="--enable-mpi ${FFTW_FLAGS}"
if [ "${TARGET_CPU}" = "native" ]; then
if [ -f /proc/cpuinfo ]; then
grep '\bavx\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx"
grep '\bavx2\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx2"
grep '\bavx512f\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx512"
fi
fi
./configure --prefix=${pkg_install_dir} --libdir="${pkg_install_dir}/lib" ${FFTW_FLAGS} \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage3/$(basename ${SCRIPT_NAME})"
fi
FFTW_CFLAGS="-I'${pkg_install_dir}/include'"
FFTW_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding FFTW from system paths ===================="
check_lib -lfftw3 "FFTW"
check_lib -lfftw3_omp "FFTW"
[ "${MPI_MODE}" != "no" ] && check_lib -lfftw3_mpi "FFTW"
add_include_from_paths FFTW_CFLAGS "fftw3.h" FFTW_INC ${INCLUDE_PATHS}
add_lib_from_paths FFTW_LDFLAGS "libfftw3.*" ${LIB_PATHS}
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking FFTW to user paths ===================="
pkg_install_dir="$with_fftw"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
FFTW_CFLAGS="-I'${pkg_install_dir}/include'"
FFTW_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_fftw" != "__DONTUSE__" ]; then
[ "$MPI_MODE" != "no" ] && FFTW_LIBS="IF_MPI(-lfftw3_mpi|) "
FFTW_LIBS+="-lfftw3 -lfftw3_omp"
if [ "$with_fftw" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_fftw"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
# we may also want to cover FFT_SG
cat << EOF >> "${BUILDDIR}/setup_fftw"
export FFTW3_INCLUDES="${FFTW_CFLAGS}"
export FFTW3_LIBS="${FFTW_LIBS}"
export FFTW_CFLAGS="${FFTW_CFLAGS}"
export FFTW_LDFLAGS="${FFTW_LDFLAGS}"
export FFTW_LIBS="${FFTW_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__FFTW3 IF_COVERAGE(IF_MPI(|-U__FFTW3)|)"
export CP_CFLAGS="\${CP_CFLAGS} ${FFTW_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${FFTW_LDFLAGS}"
export CP_LIBS="${FFTW_LIBS} \${CP_LIBS}"
export FFTW_ROOT=${FFTW_ROOT:-${pkg_install_dir}}
export FFTW3_ROOT=${pkg_install_dir}
EOF
cat "${BUILDDIR}/setup_fftw" >> $SETUPFILE
fi fi
cd "${ROOTDIR}"
# ---------------------------------------------------------------------- TARGET_CPU=${TARGET_CPU:-"native"}
# Suppress reporting of known leaks
# ----------------------------------------------------------------------
cat << EOF >> ${INSTALLDIR}/valgrind.supp
{
<BuggyFFTW3>
Memcheck:Addr32
fun:cdot
...
fun:invoke_solver
fun:search0
}
EOF
load "${BUILDDIR}/setup_fftw" echo "==================== Installing FFTW ===================="
write_toolchain_env "${INSTALLDIR}" FFTW_VERSION=3.3.10
report_timing "fftw" FFTW_BUILD_DIR=${BUILD_LOCATION}/fftw
FFTW_INSTALL_DIR=${INSTALL_LOCATION}/fftw/${FFTW_VERSION}
mkdir -p ${FFTW_BUILD_DIR}
mkdir -p ${FFTW_INSTALL_DIR}
cd ${FFTW_BUILD_DIR}
if [ -f fftw-${FFTW_VERSION}.tar.gz ]; then
echo "fftw-${FFTW_VERSION}.tar.gz is found"
else
wget -c ftp://ftp.fftw.org/pub/fftw/fftw-${FFTW_VERSION}.tar.gz
fi
#[ -d fftw-${FFTW_VERSION}/build ] && rm -rf fftw-${FFTW_VERSION}/build
#tar -xf fftw-${FFTW_VERSION}.tar.gz
cd fftw-${FFTW_VERSION}
mkdir -p build && cd build
FFTW_FLAGS="--enable-shared"
if [ "${TARGET_CPU}" = "native" ]; then
if [ -f /proc/cpuinfo ]; then
grep '\bavx\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx"
grep '\bavx2\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx2"
grep '\bavx512f\b' /proc/cpuinfo 1> /dev/null && FFTW_FLAGS="${FFTW_FLAGS} --enable-avx512"
fi
fi
if [ "$BUILD_SINGLE" = true ]; then
FFTW_FLAGS="--enable-float ${FFTW_FLAGS}"
fi
if [ "$OPENMP_ENALBED" = true ]; then
FFTW_FLAGS="--enable-openmp ${FFTW_FLAGS}"
OTHER=openmp
else
FFTW_FLAGS="--enable-threads ${FFTW_FLAGS}"
OTHER=smp
fi
if [ "$MPI_ENABLED" = true ]; then
FFTW_FLAGS="--enable-mpi ${FFTW_FLAGS}"
FFTW_INSTALL_DIR=${FFTW_INSTALL_DIR}/${MPI_MODE}/${MPI_VERSION}
else
FFTW_INSTALL_DIR=${FFTW_INSTALL_DIR}/${OTHER}
fi
echo "Installing from scratch into ${FFTW_INSTALL_DIR}"
echo ${FFTW_FLAGS}
../configure --prefix=${FFTW_INSTALL_DIR} ${FFTW_FLAGS} > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j$(nproc) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
if [ -z "$SKIP_CHECK" ]; then
echo -n "Checking that everything is working properly ... "
make -j$(nproc) check > check.log 2>&1 || tail -n ${LOG_LINES} check.log
echo "Success!"
fi
#make -j$(nproc) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
if [[ "$BASH_SOURCE" != "$0" ]]; then
cd ${ROOT}
echo "Exiting ..."
fi

108
scripts/stage3/install_libgrpp.sh
View file

@ -1,108 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
libgrpp_ver="20231215"
libgrpp_sha="3b0f55795a0c2699b81f403b1c81c56e26332f780a87655410745a0ccb51ef2f"
libgrpp_pkg="libgrpp-main-${libgrpp_ver}.zip"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libgrpp" ] && rm "${BUILDDIR}/setup_libgrpp"
LIBGRPP_CFLAGS=""
LIBGRPP_LDFLAGS=""
LIBGRPP_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_libgrpp}" in
__INSTALL__)
echo "==================== Installing LIBGRPP ===================="
pkg_install_dir="${INSTALLDIR}/libgrpp/${libgrpp_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libgrpp-main-${libgrpp_ver} is already installed, skipping it."
else
if [ -f ${libgrpp_pkg} ]; then
echo "${libgrpp_pkg} is found"
else
download_pkg_from_cp2k_org "${libgrpp_sha}" "${libgrpp_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d libgrpp-main ] && rm -rf libgrpp-main
unzip -qq ${libgrpp_pkg}
cd libgrpp-main
mkdir build
cd build
CC=${CC} FC=${FC} cmake .. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make > make.log 2>&1 || tail -n ${LOG_LINES} make.log
cd ..
install -d "${pkg_install_dir}/lib" >> install.log 2>&1
install -d "${pkg_install_dir}/include" >> install.log 2>&1
install -m 644 build/libgrpp/liblibgrpp.a "${pkg_install_dir}/lib" >> install.log 2>&1
install -m 644 build/libgrpp.mod "${pkg_install_dir}/include" >> install.log 2>&1
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage3/$(basename ${SCRIPT_NAME})"
fi
LIBGRPP_CFLAGS="-I'${pkg_install_dir}/include'"
LIBGRPP_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding libgrpp from system paths ===================="
check_lib -llibgrpp "libgrpp"
add_include_from_paths -p LIBGRPP_CFLAGS "libgrpp" $INCLUDE_PATHS
add_lib_from_paths LIBGRPP_LDFLAGS "liblibgrpp.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking libgrpp to user paths ===================="
pkg_install_dir="$with_libgrpp"
check_dir "${pkg_install_dir}/include"
check_dir "${pkg_install_dir}/lib"
LIBGRPP_CFLAGS="-I'${pkg_install_dir}/include'"
LIBGRPP_LDFLAGS="-L'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_libgrpp" != "__DONTUSE__" ]; then
LIBGRPP_LIBS="-llibgrpp"
if [ "$with_libgrpp" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libgrpp"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
export LIBGRPP_ROOT="${pkg_install_dir}"
EOF
cat "${BUILDDIR}/setup_libgrpp" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_libgrpp"
export LIBGRPP_CFLAGS="${LIBGRPP_CFLAGS}"
export LIBGRPP_LDFLAGS="${LIBGRPP_LDFLAGS}"
export LIBGRPP_LIBS="${LIBGRPP_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBGRPP"
export CP_CFLAGS="\${CP_CFLAGS} ${LIBGRPP_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBGRPP_LDFLAGS}"
export CP_LIBS="${LIBGRPP_LIBS} \${CP_LIBS}"
EOF
fi
load "${BUILDDIR}/setup_libgrpp"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libgrpp"

145
scripts/stage3/install_libint.sh
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@ -1,145 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
libint_ver="2.6.0"
libint_pkg="libint-v${libint_ver}-cp2k-lmax-${LIBINT_LMAX}.tgz"
case "$LIBINT_LMAX" in
4)
libint_sha256="7c8d28bfb03920936231228b79686ba0fd87ea922c267199789bc131cf21ac08"
;;
5)
libint_sha256="1cd72206afddb232bcf2179c6229fbf6e42e4ba8440e701e6aa57ff1e871e9db"
;;
6)
libint_sha256="bea76a433cd32bde280879f73b5fc8228c78b62e3ea57ace4c6d74b65910b8af"
;;
7)
libint_sha256="3bcdcc55e1dbafe38a785d4af171df8e300bb8b7775894b57186cdf35807c334"
;;
*)
report_error "Unsupported value --libint-lmax=${LIBINT_LMAX}."
exit 1
;;
esac
[ -f "${BUILDDIR}/setup_libint" ] && rm "${BUILDDIR}/setup_libint"
LIBINT_CFLAGS=""
LIBINT_LDFLAGS=""
LIBINT_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_libint" in
__INSTALL__)
echo "==================== Installing LIBINT ===================="
pkg_install_dir="${INSTALLDIR}/libint/${libint_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libint-${libint_ver} is already installed, skipping it."
else
if [ -f ${libint_pkg} ]; then
echo "${libint_pkg} is found"
else
download_pkg_from_cp2k_org "${libint_sha256}" "${libint_pkg}"
fi
[ -d libint-v${libint_ver}-cp2k-lmax-${LIBINT_LMAX} ] && rm -rf libint-v${libint_ver}-cp2k-lmax-${LIBINT_LMAX}
tar -xzf ${libint_pkg}
echo "Installing from scratch into ${pkg_install_dir}"
cd libint-v${libint_ver}-cp2k-lmax-${LIBINT_LMAX}
# reduce debug information to level 1 since
# level 2 (default for -g flag) leads to very large binary size
LIBINT_CXXFLAGS="$CXXFLAGS -g1"
# cmake build broken with libint 2.6, uncomment for libint 2.7 and above
#cmake . -DCMAKE_INSTALL_PREFIX=${pkg_install_dir} \
# -DCMAKE_CXX_COMPILER="$CXX" \
# -DLIBINT2_INSTALL_LIBDIR="${pkg_install_dir}/lib" \
# -DENABLE_FORTRAN=ON \
# -DCXXFLAGS="$LIBINT_CXXFLAGS" > configure.log 2>&1
#cmake --build . > cmake.log 2>&1
#cmake --build . --target install > install.log 2>&1
./configure --prefix=${pkg_install_dir} \
--with-cxx="$CXX $LIBINT_CXXFLAGS" \
--with-cxx-optflags="$LIBINT_CXXFLAGS" \
--enable-fortran \
--with-pic \
--libdir="${pkg_install_dir}/lib" \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
if [ "${MPI_MODE}" = "intelmpi" ]; then
# Fix bug in makefile for Fortran module
sed -i -e "s/\$(CXX) \$(CXXFLAGS)/\$(FC) \$(FCFLAGS)/g" -e "s/\$(FCLIBS) -o/\$(FCLIBS) -lstdc++ -o/" fortran/Makefile
fi
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage3/$(basename ${SCRIPT_NAME})"
fi
LIBINT_CFLAGS="-I'${pkg_install_dir}/include'"
LIBINT_LDFLAGS="-L'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding LIBINT from system paths ===================="
check_lib -lint2 "libint"
add_include_from_paths -p LIBINT_CFLAGS "libint" $INCLUDE_PATHS
add_lib_from_paths LIBINT_LDFLAGS "libint2.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking LIBINT to user paths ===================="
pkg_install_dir="$with_libint"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
LIBINT_CFLAGS="-I'${pkg_install_dir}/include'"
LIBINT_LDFLAGS="-L'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_libint" != "__DONTUSE__" ]; then
LIBINT_LIBS="-lint2"
if [ "$with_libint" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libint"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
export LIBINT2_ROOT="${pkg_install_dir}"
EOF
cat "${BUILDDIR}/setup_libint" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_libint"
export LIBINT_CFLAGS="${LIBINT_CFLAGS}"
export LIBINT_LDFLAGS="${LIBINT_LDFLAGS}"
export LIBINT_LIBS="${LIBINT_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBINT"
export CP_CFLAGS="\${CP_CFLAGS} ${LIBINT_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBINT_LDFLAGS}"
export CP_LIBS="${LIBINT_LIBS} \${CP_LIBS}"
EOF
fi
load "${BUILDDIR}/setup_libint"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libint"

101
scripts/stage3/install_libxc.sh
View file

@ -1,101 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
libxc_ver="6.2.2"
libxc_sha256="a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libxc" ] && rm "${BUILDDIR}/setup_libxc"
LIBXC_CFLAGS=""
LIBXC_LDFLAGS=""
LIBXC_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_libxc" in
__INSTALL__)
echo "==================== Installing LIBXC ===================="
pkg_install_dir="${INSTALLDIR}/libxc/${libxc_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libxc-${libxc_ver} is already installed, skipping it."
else
if [ -f libxc-${libxc_ver}.tar.gz ]; then
echo "libxc-${libxc_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${libxc_sha256}" "libxc-${libxc_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d libxc-${libxc_ver} ] && rm -rf libxc-${libxc_ver}
tar -xzf libxc-${libxc_ver}.tar.gz
cd libxc-${libxc_ver}
# CP2K does not make use of fourth derivatives, so skip their compilation with --disable-lxc
./configure --prefix="${pkg_install_dir}" --libdir="${pkg_install_dir}/lib" --disable-lxc \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage3/$(basename ${SCRIPT_NAME})"
fi
LIBXC_CFLAGS="-I'${pkg_install_dir}/include'"
LIBXC_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding LIBXC from system paths ===================="
check_lib -lxcf03 "libxc"
check_lib -lxc "libxc"
add_include_from_paths LIBXC_CFLAGS "xc.h" $INCLUDE_PATHS
add_lib_from_paths LIBXC_LDFLAGS "libxc.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking LIBXC to user paths ===================="
pkg_install_dir="$with_libxc"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
LIBXC_CFLAGS="-I'${pkg_install_dir}/include'"
LIBXC_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_libxc" != "__DONTUSE__" ]; then
LIBXC_LIBS="-lxcf03 -lxc"
if [ "$with_libxc" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libxc"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_libxc" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_libxc"
export LIBXC_CFLAGS="${LIBXC_CFLAGS}"
export LIBXC_LDFLAGS="${LIBXC_LDFLAGS}"
export LIBXC_LIBS="${LIBXC_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBXC"
export CP_CFLAGS="\${CP_CFLAGS} ${LIBXC_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBXC_LDFLAGS}"
export CP_LIBS="${LIBXC_LIBS} \${CP_LIBS}"
export LIBXC_ROOT="$pkg_install_dir"
EOF
fi
load "${BUILDDIR}/setup_libxc"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libxc"

11
scripts/stage3/install_stage3.sh
View file

@ -1,11 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage3/install_fftw.sh
./scripts/stage3/install_libint.sh
./scripts/stage3/install_libxc.sh
./scripts/stage3/install_libgrpp.sh
#EOF

294
scripts/stage4/install_cosma.sh
View file

@ -1,294 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
cosma_ver="2.6.6"
cosma_sha256="1604be101e77192fbcc5551236bc87888d336e402f5409bbdd9dea900401cc37"
costa_ver="2.2.2"
costa_sha256="e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c"
tiled_mm_ver="2.2"
tiled_mm_sha256="6d0b49c9588ece744166822fd44a7bc5bec3dc666b836de8bf4bf1a7bb675aac"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_cosma" ] && rm "${BUILDDIR}/setup_cosma"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_cosma" in
__INSTALL__)
require_env OPENBLAS_ROOT
require_env SCALAPACK_ROOT
echo "==================== Installing COSMA ===================="
pkg_install_dir="${INSTALLDIR}/COSMA/${cosma_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "COSMA-${cosma_ver} is already installed, skipping it."
else
if [ -f COSMA-v${cosma_ver}.tar.gz ]; then
echo "COSMA-v${cosma_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${cosma_sha256}" "COSMA-v${cosma_ver}.tar.gz"
download_pkg_from_cp2k_org "${costa_sha256}" "COSTA-v${costa_ver}.tar.gz"
download_pkg_from_cp2k_org "${tiled_mm_sha256}" "Tiled-MM-v${tiled_mm_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d COSMA-${cosma_ver} ] && rm -rf COSMA-${cosma_ver}
tar -xzf COSMA-v${cosma_ver}.tar.gz
[ -d Tiled-MM-${tiled_mm_ver} ] && rm -rf Tiled-MM-${tiled_mm_ver}
tar -xzf Tiled-MM-v${tiled_mm_ver}.tar.gz
[ -d COSTA-${costa_ver} ] && rm -rf COSTA-${costa_ver}
tar -xzf COSTA-v${costa_ver}.tar.gz
case "$MATH_MODE" in
mkl)
cosma_blas="MKL"
cosma_sl="MKL"
;;
cray)
cosma_blas="CRAY_LIBSCI"
cosma_sl="CRAY_LIBSCI"
;;
*)
cosma_blas="OPENBLAS"
cosma_sl="CUSTOM"
;;
esac
cd "COSTA-${costa_ver}"
[ -d build-cpu ] && rm -Rf build-cpu
mkdir build-cpu && cd build-cpu
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSTA_SCALAPACK=${cosma_sl} \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
[ -d build-cuda ] && rm -Rf build-cuda
mkdir build-cuda && cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-cuda" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSTA_SCALAPACK=${cosma_sl} \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
if [ "$ENABLE_HIP" = "__TRUE__" ]; then
[ -d build-hip ] && rm -Rf build-hip
mkdir build-hip && cd build-hip
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-hip" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSTA_BLAS=${cosma_blas} \
-DCOSTA_SCALAPACK=${cosma_sl} \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
cd ..
cd Tiled-MM-${tiled_mm_ver}
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
mkdir build-cuda && cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-cuda" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DTILEDMM_GPU_BACKEND=CUDA \
-DTILEDMM_WITH_EXAMPLES=OFF \
-DTILEDMM_WITH_TESTS=OFF \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
if [ "$ENABLE_HIP" = "__TRUE__" ]; then
mkdir build-hip && cd build-hip
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-hip" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DTILEDMM_GPU_BACKEND=ROCM \
-DTILEDMM_WITH_EXAMPLES=OFF \
-DTILEDMM_WITH_TESTS=OFF \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
cd ..
cd COSMA-${cosma_ver} && mkdir build-cpu && cd build-cpu
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSMA_BLAS=${cosma_blas} \
-DCOSMA_SCALAPACK=${cosma_sl} \
-DCOSMA_WITH_TESTS=NO \
-DCOSMA_WITH_APPS=NO \
-DCOSMA_WITH_BENCHMARKS=NO .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
# Build CUDA version.
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-cuda" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSMA_BLAS=CUDA \
-DCOSMA_SCALAPACK=${cosma_sl} \
-DCOSMA_WITH_TESTS=NO \
-DCOSMA_WITH_APPS=NO \
-DCOSMA_WITH_BENCHMARKS=NO .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
# Build HIP version.
if [ "$ENABLE_HIP" = "__TRUE__" ] && $(check_lib -lrocblas "rocm" &> /dev/null); then
[ -d build-hip ] && rm -rf "build-hip"
mkdir build-hip
cd build-hip
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}-hip" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DBUILD_SHARED_LIBS=NO \
-DCOSMA_BLAS=ROCM \
-DCOSMA_SCALAPACK=${cosma_sl} \
-DCOSMA_WITH_TESTS=NO \
-DCOSMA_WITH_APPS=NO \
-DCOSMA_WITH_BENCHMARKS=NO .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
fi
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage4/$(basename ${SCRIPT_NAME})"
fi
COSMA_ROOT="${pkg_install_dir}"
COSMA_CFLAGS="-I'${pkg_install_dir}/include'"
# Check if COSMA is compiled with 64bits and set up COSMA_LIBDIR accordingly.
COSMA_LIBDIR="${pkg_install_dir}/lib"
COSMA_LDFLAGS="-L'${COSMA_LIBDIR}' -Wl,-rpath,'${COSMA_LIBDIR}'"
COSMA_CUDA_LIBDIR="${pkg_install_dir}-cuda/lib"
COSMA_CUDA_LDFLAGS="-L'${COSMA_CUDA_LIBDIR}' -Wl,-rpath,'${COSMA_CUDA_LIBDIR}'"
COSMA_HIP_LIBDIR="${pkg_install_dir}-hip/lib"
COSMA_HIP_LDFLAGS="-L'${COSMA_HIP_LIBDIR}' -Wl,-rpath,'${COSMA_HIP_LIBDIR}'"
;;
__SYSTEM__)
echo "==================== Finding COSMA from system paths ===================="
check_command pkg-config --modversion cosma
add_include_from_paths COSMA_CFLAGS "cosma.h" $INCLUDE_PATHS
add_lib_from_paths COSMA_LDFLAGS "libcosma.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking COSMA to user paths ===================="
pkg_install_dir="$with_cosma"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
COSMA_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && COSMA_LIBDIR="${pkg_install_dir}/lib64"
check_dir "$pkg_install_dir/lib"
check_dir "$pkg_install_dir/include"
COSMA_CFLAGS="-I'${pkg_install_dir}/include'"
COSMA_LDFLAGS="-L'${COSMA_LIBDIR}' -Wl,-rpath,'${COSMA_LIBDIR}'"
;;
esac
if [ "$with_cosma" != "__DONTUSE__" ]; then
COSMA_LIBS="-lcosma_prefixed_pxgemm -lcosma -lcosta IF_CUDA(-lTiled-MM|)"
if [ "$ENABLE_HIP" = "__TRUE__" ] && $(check_lib -lrocblas "rocm" &> /dev/null); then
COSMA_LIBS+=" IF_HIP(-lTiled-MM|)"
fi
if [ "$with_cosma" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_cosma"
prepend_path LD_LIBRARY_PATH "${COSMA_LIBDIR}"
prepend_path LD_RUN_PATH "${COSMA_LIBDIR}"
prepend_path LIBRARY_PATH "${COSMA_LIBDIR}"
prepend_path CPATH "$pkg_install_dir/include"
export COSMA_INCLUDE_DIR="$pkg_install_dir/include"
export COSMA_ROOT="${pkg_install_dir}"
export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:${COSMA_LIBDIR}/pkgconfig"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_cosma"
export COSMA_CFLAGS="${COSMA_CFLAGS}"
export COSMA_LDFLAGS="${COSMA_LDFLAGS}"
export COSMA_CUDA_LDFLAGS="${COSMA_CUDA_LDFLAGS}"
export COSMA_HIP_LDFLAGS="${COSMA_HIP_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__COSMA|)"
export CP_CFLAGS="\${CP_CFLAGS} ${COSMA_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_CUDA(${COSMA_CUDA_LDFLAGS}|IF_HIP(${COSMA_HIP_LDFLAGS}|${COSMA_LDFLAGS}))"
export COSMA_LIBS="${COSMA_LIBS}"
export COSMA_ROOT="$pkg_install_dir"
export COSMA_INCLUDE_DIR="$pkg_install_dir/include"
export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:${COSMA_LIBDIR}/pkgconfig"
export COSMA_VERSION=${cosma_ver}
export CP_LIBS="IF_MPI(${COSMA_LIBS}|) \${CP_LIBS}"
EOF
cat "${BUILDDIR}/setup_cosma" >> $SETUPFILE
cat << EOF >> ${INSTALLDIR}/lsan.supp
# leaks related to COSMA (probably, only the last one is actually needed)
leak:cosma::communicator::communicator
leak:cosma::cosma_context<double>::register_state
leak:cosma::pxgemm<double>
leak:cosma::cosma_context<std::complex<double> >::register_state
EOF
fi
load "${BUILDDIR}/setup_cosma"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "cosma"

126
scripts/stage4/install_libxsmm.sh
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@ -1,126 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
libxsmm_ver="1.17"
libxsmm_sha256="8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libxsmm" ] && rm "${BUILDDIR}/setup_libxsmm"
LIBXSMM_CFLAGS=''
LIBXSMM_LDFLAGS=''
LIBXSMM_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_libxsmm" in
__INSTALL__)
echo "==================== Installing Libxsmm ===================="
if [[ ("$OPENBLAS_ARCH" != "x86_64") && ("$OPENBLAS_ARCH" != "arm64") ]]; then
report_warning $LINENO "libxsmm is not supported on arch ${OPENBLAS_ARCH}"
cat << EOF > "${BUILDDIR}/setup_libxsmm"
with_libxsmm="__DONTUSE__"
EOF
exit 0
fi
pkg_install_dir="${INSTALLDIR}/libxsmm/${libxsmm_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libxsmm-${libxsmm_ver} is already installed, skipping it."
else
if [ -f libxsmm-${libxsmm_ver}.tar.gz ]; then
echo "libxsmm-${libxsmm_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${libxsmm_sha256}" "libxsmm-${libxsmm_ver}.tar.gz"
fi
[ -d libxsmm-${libxsmm_ver} ] && rm -rf libxsmm-${libxsmm_ver}
tar -xzf libxsmm-${libxsmm_ver}.tar.gz
echo "Installing from scratch into ${pkg_install_dir}"
# note that we do not have to set -L flags to ld for the
# linked math libraries for the libxsmm build, as for a
# library this is not required, you just have to provide
# the appropriate -L flags (LDFLAGS) during the linking
# stage of building an executable that uses the libxsmm
# library
cd libxsmm-${libxsmm_ver}
# Avoid an unintended (incompatible) setting of FORTRAN
unset FORTRAN
make -j $(get_nprocs) \
CXX=$CXX \
CC=$CC \
FC=$FC \
INTRINSICS=1 \
PREFIX=${pkg_install_dir} \
> make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) \
CXX=$CXX \
CC=$CC \
FC=$FC \
INTRINSICS=1 \
PREFIX=${pkg_install_dir} \
install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage4/$(basename ${SCRIPT_NAME})"
mkdir ${pkg_install_dir}/lib/pkgconfig
cp ${pkg_install_dir}/lib/*.pc ${pkg_install_dir}/lib/pkgconfig
fi
LIBXSMM_CFLAGS="-I'${pkg_install_dir}/include'"
LIBXSMM_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding Libxsmm from system paths ===================="
check_lib -lxsmm "libxsmm"
check_lib -lxsmmf "libxsmm"
add_include_from_paths LIBXSMM_CFLAGS "libxsmm.h" $INCLUDE_PATHS
add_lib_from_paths LIBXSMM_LDFLAGS "libxsmm.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking Libxsmm to user paths ===================="
pkg_install_dir="$with_libxsmm"
check_dir "${pkg_install_dir}/bin"
check_dir "${pkg_install_dir}/include"
check_dir "${pkg_install_dir}/lib"
LIBXSMM_CFLAGS="-I'${pkg_install_dir}/include'"
LIBXSMM_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_libxsmm" != "__DONTUSE__" ]; then
LIBXSMM_LIBS="-lxsmmf -lxsmm -ldl -lpthread"
if [ "$with_libxsmm" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libxsmm"
prepend_path PATH "${pkg_install_dir}/bin"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
EOF
cat "${BUILDDIR}/setup_libxsmm" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_libxsmm"
export LIBXSMM_CFLAGS="${LIBXSMM_CFLAGS}"
export LIBXSMM_LDFLAGS="${LIBXSMM_LDFLAGS}"
export LIBXSMM_LIBS="${LIBXSMM_LIBS}"
export CP_DFLAGS="-D__LIBXSMM \${CP_DFLAGS}"
export CP_CFLAGS="\${CP_CFLAGS} ${LIBXSMM_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBXSMM_LDFLAGS}"
export CP_LIBS="\${LIBXSMM_LIBS} \${CP_LIBS}"
EOF
fi
cd "${ROOTDIR}"
load "${BUILDDIR}/setup_libxsmm"
write_toolchain_env "${INSTALLDIR}"
report_timing "libxsmm"

117
scripts/stage4/install_scalapack.sh
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@ -1,117 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
scalapack_ver="2.2.1"
scalapack_sha256="4aede775fdb28fa44b331875730bcd5bab130caaec225fadeccf424c8fcb55aa"
scalapack_pkg="scalapack-${scalapack_ver}.tgz"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_scalapack" ] && rm "${BUILDDIR}/setup_scalapack"
SCALAPACK_CFLAGS=''
SCALAPACK_LDFLAGS=''
SCALAPACK_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_scalapack" in
__INSTALL__)
echo "==================== Installing ScaLAPACK ===================="
pkg_install_dir="${INSTALLDIR}/scalapack/${scalapack_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "scalapack-${scalapack_ver} is already installed, skipping it."
else
require_env MATH_LIBS
if [ -f ${scalapack_pkg} ]; then
echo "${scalapack_pkg} is found"
else
download_pkg_from_cp2k_org "${scalapack_sha256}" "${scalapack_pkg}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d scalapack-${scalapack_ver} ] && rm -rf scalapack-${scalapack_ver}
tar -xzf ${scalapack_pkg}
mkdir -p "scalapack-${scalapack_ver}/build"
pushd "scalapack-${scalapack_ver}/build" > /dev/null
flags=""
if ("${FC}" --version | grep -q 'GNU'); then
flags=$(allowed_gfortran_flags "-fallow-argument-mismatch")
fi
FFLAGS=$flags cmake -DCMAKE_FIND_ROOT_PATH="$ROOTDIR" \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR="lib" \
-DBUILD_SHARED_LIBS=NO \
-DCMAKE_BUILD_TYPE=Release .. \
-DBUILD_TESTING=NO \
-DSCALAPACK_BUILD_TESTS=NO \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install >> make.log 2>&1 || tail -n ${LOG_LINES} make.log
popd > /dev/null
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage4/$(basename ${SCRIPT_NAME})"
fi
SCALAPACK_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding ScaLAPACK from system paths ===================="
check_lib -lscalapack "ScaLAPACK"
add_lib_from_paths SCALAPACK_LDFLAGS "libscalapack.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking ScaLAPACK to user paths ===================="
pkg_install_dir="$with_scalapack"
check_dir "${pkg_install_dir}/lib"
SCALAPACK_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_scalapack" != "__DONTUSE__" ]; then
SCALAPACK_LIBS="-lscalapack"
if [ "$with_scalapack" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_scalapack"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
export SCALAPACK_ROOT="${pkg_install_dir}"
EOF
cat "${BUILDDIR}/setup_scalapack" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_scalapack"
export SCALAPACK_LDFLAGS="${SCALAPACK_LDFLAGS}"
export SCALAPACK_LIBS="${SCALAPACK_LIBS}"
export SCALAPACK_ROOT="${pkg_install_dir}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__SCALAPACK|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${SCALAPACK_LDFLAGS}|)"
export CP_LIBS="IF_MPI(-lscalapack|) \${CP_LIBS}"
EOF
fi
cd "${ROOTDIR}"
# ----------------------------------------------------------------------
# Suppress reporting of known leaks
# ----------------------------------------------------------------------
cat << EOF >> ${INSTALLDIR}/lsan.supp
# leaks related to SCALAPACK
leak:pdpotrf_
EOF
load "${BUILDDIR}/setup_scalapack"
write_toolchain_env "${INSTALLDIR}"
report_timing "scalapack"

10
scripts/stage4/install_stage4.sh
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@ -1,10 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage4/install_libxsmm.sh
./scripts/stage4/install_scalapack.sh
./scripts/stage4/install_cosma.sh
#EOF

203
scripts/stage5/install_elpa.sh
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@ -1,203 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
# From https://elpa.mpcdf.mpg.de/software/tarball-archive/ELPA_TARBALL_ARCHIVE.html
elpa_ver="2023.05.001"
elpa_sha256="ec64be5d6522810d601a3b8e6a31720e3c3eb4af33a434d8a64570d76e6462b6"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_elpa" ] && rm "${BUILDDIR}/setup_elpa"
ELPA_CFLAGS=''
ELPA_LDFLAGS=''
ELPA_LIBS=''
elpa_dir_openmp="_openmp"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
# elpa only works with MPI switched on
if [ $MPI_MODE = no ]; then
report_warning $LINENO "MPI is disabled, skipping elpa installation"
cat << EOF > "${BUILDDIR}/setup_elpa"
with_elpa="__FALSE__"
EOF
exit 0
fi
case "$with_elpa" in
__INSTALL__)
echo "==================== Installing ELPA ===================="
pkg_install_dir="${INSTALLDIR}/elpa/${elpa_ver}"
install_lock_file="$pkg_install_dir/install_successful"
enable_openmp="yes"
# specific settings needed on CRAY Linux Environment
if [ "$ENABLE_CRAY" = "__TRUE__" ]; then
if [ ${CRAY_PRGENVCRAY} ]; then
# extra LDFLAGS needed
cray_ldflags="-dynamic"
fi
enable_openmp="no"
fi
if verify_checksums "${install_lock_file}"; then
echo "elpa-${elpa_ver} is already installed, skipping it."
else
require_env MATH_LIBS
if [ -f elpa-${elpa_ver}.tar.gz ]; then
echo "elpa-${elpa_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${elpa_sha256}" "elpa-${elpa_ver}.tar.gz"
fi
[ -d elpa-${elpa_ver} ] && rm -rf elpa-${elpa_ver}
tar -xzf elpa-${elpa_ver}.tar.gz
# elpa expect FC to be an mpi fortran compiler that is happy
# with long lines, and that a bunch of libs can be found
cd elpa-${elpa_ver}
# ELPA-2017xxxx enables AVX2 by default, switch off if machine doesn't support it.
AVX_flag=""
AVX512_flags=""
FMA_flag=""
SSE4_flag=""
config_flags="--disable-avx --disable-avx2 --disable-avx512 --disable-sse --disable-sse-assembly"
if [ "${TARGET_CPU}" = "native" ]; then
if [ -f /proc/cpuinfo ] && [ "${OPENBLAS_ARCH}" = "x86_64" ]; then
has_AVX=$(grep '\bavx\b' /proc/cpuinfo 1> /dev/null && echo 'yes' || echo 'no')
[ "${has_AVX}" = "yes" ] && AVX_flag="-mavx" || AVX_flag=""
has_AVX2=$(grep '\bavx2\b' /proc/cpuinfo 1> /dev/null && echo 'yes' || echo 'no')
[ "${has_AVX2}" = "yes" ] && AVX_flag="-mavx2"
has_AVX512=$(grep '\bavx512f\b' /proc/cpuinfo 1> /dev/null && echo 'yes' || echo 'no')
[ "${has_AVX512}" = "yes" ] && AVX512_flags="-mavx512f"
FMA_flag=$(grep '\bfma\b' /proc/cpuinfo 1> /dev/null && echo '-mfma' || echo '-mno-fma')
SSE4_flag=$(grep '\bsse4_1\b' /proc/cpuinfo 1> /dev/null && echo '-msse4' || echo '-mno-sse4')
grep '\bavx512dq\b' /proc/cpuinfo 1> /dev/null && AVX512_flags+=" -mavx512dq"
grep '\bavx512cd\b' /proc/cpuinfo 1> /dev/null && AVX512_flags+=" -mavx512cd"
grep '\bavx512bw\b' /proc/cpuinfo 1> /dev/null && AVX512_flags+=" -mavx512bw"
grep '\bavx512vl\b' /proc/cpuinfo 1> /dev/null && AVX512_flags+=" -mavx512vl"
config_flags="--enable-avx=${has_AVX} --enable-avx2=${has_AVX2} --enable-avx512=${has_AVX512}"
fi
fi
for TARGET in "cpu" "nvidia"; do
[ "$TARGET" = "nvidia" ] && [ "$ENABLE_CUDA" != "__TRUE__" ] && continue
echo "Installing from scratch into ${pkg_install_dir}/${TARGET}"
mkdir -p "build_${TARGET}"
cd "build_${TARGET}"
../configure --prefix="${pkg_install_dir}/${TARGET}/" \
--libdir="${pkg_install_dir}/${TARGET}/lib" \
--enable-openmp=${enable_openmp} \
--enable-shared=no \
--enable-static=yes \
--disable-c-tests \
--disable-cpp-tests \
${config_flags} \
--enable-nvidia-gpu=$([ "$TARGET" = "nvidia" ] && echo "yes" || echo "no") \
--with-cuda-path=${CUDA_PATH:-${CUDA_HOME:-/CUDA_HOME-notset}} \
--with-NVIDIA-GPU-compute-capability=$([ "$TARGET" = "nvidia" ] && echo "sm_$ARCH_NUM" || echo "sm_35") \
CUDA_CFLAGS="-std=c++14 -allow-unsupported-compiler" \
OMPI_MCA_plm_rsh_agent=/bin/false \
FC=${MPIFC} \
CC=${MPICC} \
CXX=${MPICXX} \
CPP="cpp -E" \
FCFLAGS="${FCFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} -ffree-line-length-none ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
CFLAGS="${CFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
CXXFLAGS="${CXXFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
LDFLAGS="-Wl,--allow-multiple-definition -Wl,--enable-new-dtags ${MATH_LDFLAGS} ${SCALAPACK_LDFLAGS} ${cray_ldflags}" \
LIBS="${SCALAPACK_LIBS} $(resolve_string "${MATH_LIBS}" "MPI")" \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
done
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage5/$(basename ${SCRIPT_NAME})"
fi
[ "$enable_openmp" != "yes" ] && elpa_dir_openmp=""
ELPA_CFLAGS="-I'${pkg_install_dir}/IF_CUDA(nvidia|cpu)/include/elpa${elpa_dir_openmp}-${elpa_ver}/modules' -I'${pkg_install_dir}/IF_CUDA(nvidia|cpu)/include/elpa${elpa_dir_openmp}-${elpa_ver}/elpa'"
ELPA_LDFLAGS="-L'${pkg_install_dir}/IF_CUDA(nvidia|cpu)/lib' -Wl,-rpath,'${pkg_install_dir}/IF_CUDA(nvidia|cpu)/lib'"
;;
__SYSTEM__)
echo "==================== Finding ELPA from system paths ===================="
check_lib -lelpa_openmp "ELPA"
# get the include paths
elpa_include="$(find_in_paths "elpa_openmp-*" $INCLUDE_PATHS)"
if [ "$elpa_include" != "__FALSE__" ]; then
echo "ELPA include directory threaded version is found to be $elpa_include"
ELPA_CFLAGS="-I'$elpa_include/modules' -I'$elpa_include/elpa'"
else
echo "Cannot find elpa_openmp-${elpa_ver} from paths $INCLUDE_PATHS"
exit 1
fi
# get the lib paths
add_lib_from_paths ELPA_LDFLAGS "libelpa.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking ELPA to user paths ===================="
pkg_install_dir="$with_elpa"
check_dir "${pkg_install_dir}/include"
check_dir "${pkg_install_dir}/lib"
user_include_path="$pkg_install_dir/include"
elpa_include="$(find_in_paths "elpa_openmp-*" user_include_path)"
if [ "$elpa_include" != "__FALSE__" ]; then
echo "ELPA include directory threaded version is found to be $elpa_include/modules"
check_dir "$elpa_include/modules"
ELPA_CFLAGS="-I'$elpa_include/modules' -I'$elpa_include/elpa'"
else
echo "Cannot find elpa_openmp-* from path $user_include_path"
exit 1
fi
ELPA_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_elpa" != "__DONTUSE__" ]; then
ELPA_LIBS="-lelpa${elpa_dir_openmp}"
cat << EOF > "${BUILDDIR}/setup_elpa"
prepend_path CPATH "$elpa_include"
EOF
if [ "$with_elpa" != "__SYSTEM__" ]; then
cat << EOF >> "${BUILDDIR}/setup_elpa"
prepend_path PATH "$pkg_install_dir/bin"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
export ELPA_ROOT="$pkg_install_dir"
EOF
fi
cat "${BUILDDIR}/setup_elpa" >> $SETUPFILE
cat << EOF >> "${BUILDDIR}/setup_elpa"
export ELPA_CFLAGS="${ELPA_CFLAGS}"
export ELPA_LDFLAGS="${ELPA_LDFLAGS}"
export ELPA_LIBS="${ELPA_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__ELPA IF_CUDA(-D__ELPA_NVIDIA_GPU|)|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${ELPA_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${ELPA_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${ELPA_LIBS}|) \${CP_LIBS}"
export ELPA_ROOT="$pkg_install_dir"
export ELPA_VERSION="${elpa_ver}"
EOF
fi
load "${BUILDDIR}/setup_elpa"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "elpa"

151
scripts/stage5/install_pexsi.sh
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@ -1,151 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
pexsi_ver="1.2.0"
pexsi_sha256="8bfad6ec6866c6a29e1cc87fb1c17a39809795e79ede98373c8ba9a3aaf820dd"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_pexsi" ] && rm "${BUILDDIR}/setup_pexsi"
PEXSI_CFLAGS=''
PEXSI_LDFLAGS=''
PEXSI_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_pexsi" in
__INSTALL__)
echo "==================== Installing PEXSI ===================="
require_env SUPERLU_LDFLAGS
require_env SUPERLU_LIBS
require_env MATH_LIBS
require_env MPI_LDFLAGS
require_env MPI_LIBS
pkg_install_dir="${INSTALLDIR}/pexsi/${pexsi_ver}"
mkdir -p "${pkg_install_dir}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "pexsi_dist-${pexsi_ver} is already installed, skipping it."
else
if [ -f pexsi_v${pexsi_ver}.tar.gz ]; then
echo "pexsi_v${pexsi_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${pexsi_sha256}" "pexsi_v${pexsi_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d pexsi_v${pexsi_ver} ] && rm -rf pexsi_v${pexsi_ver}
tar -xzf pexsi_v${pexsi_ver}.tar.gz
cd pexsi_v${pexsi_ver}
cat config/make.inc.linux.gnu |
sed -e "s|\(CC *=\).*|\1 ${MPICC}|g" \
-e "s|\(CXX *=\).*|\1 ${MPICXX}|g" \
-e "s|\(FC *=\).*|\1 ${MPIFC}|g" \
-e "s|\(LOADER *=\).*|\1 ${MPICXX}|g" \
-e "s|\(USE_SYMPACK *=\).*|\1 0|g" \
-e "s|\(PEXSI_DIR *=\).*|\1 ${PWD}|g" \
-e "s|\(PEXSI_BUILD_DIR *=\).*|\1 ${pkg_install_dir}|g" \
-e "s|\(CPP_LIB *=\).*|\1 -lstdc++ ${MPI_LDFLAGS} ${MPI_LIBS} |g" \
-e "s|\(LAPACK_LIB *=\).*|\1 ${MATH_LDFLAGS} $(resolve_string "${MATH_LIBS}" "MPI")|g" \
-e "s|\(BLAS_LIB *=\).*|\1|g" \
-e "s|\(\bMETIS_LIB *=\).*|\1 ${METIS_LDFLAGS} ${METIS_LIBS}|g" \
-e "s|\(PARMETIS_LIB *=\).*|\1 |g" \
-e "s|\(DSUPERLU_LIB *=\).*|\1 ${SUPERLU_LDFLAGS} -lsuperlu_dist|g" \
-e "s|\(SCOTCH_LIB *=\).*|\1 ${SCOTCH_LDFLAGS} -lscotchmetis -lscotch -lscotcherr|g" \
-e "s|\(PTSCOTCH_LIB *=\).*|\1 ${SCOTCH_LDFLAGS} -lptscotchparmetis -lptscotch -lptscotcherr -lscotch|g" \
-e "s|\(DSUPERLU_INCLUDE *=\).*|\1 ${SUPERLU_CFLAGS}|g" \
-e "s|\(INCLUDES *=\).*|\1 ${MATH_CFLAGS} \${DSUPERLU_INCLUDE} \${PEXSI_INCLUDE}|g" \
-e "s|\(COMPILE_FLAG *=\).*|\1 ${CFLAGS}|g" \
-e "s|\(SUFFIX *=\).*|\1 ${OPENBLAS_ARCH}|g" \
-e "s|\(DSUPERLU_DIR *=\).*|\1|g" \
-e "s|\(METIS_DIR *=\).*|\1|g" \
-e "s|\(PARMETIS_DIR *=\).*|\1|g" \
-e "s|\(PTSCOTCH_DIR *=\).*|\1|g" \
-e "s|\(LAPACK_DIR *=\).*|\1|g" \
-e "s|\(BLAS_DIR *=\).*|\1|g" \
-e "s|-DCOREDUMPER||g" \
-e "s|\(COREDUMPER_LIB *=\).*||g" \
-e "s|\(GFORTRAN_LIB *=\).*|\1 -lgfortran|g" > make.inc
# Seemingly this should've been moved together with the other fortran files.
mv ./src/f_interface.f90 ./fortran/
# Patch to include <limits> explicitly as required by gcc >= 11.
sed -i '/^#include <numeric>/a #include <limits>' ./include/pexsi/utility_impl.hpp
# Still issues with parallel make (fortran_examples target)
make finstall > make.log 2>&1 || tail -n ${LOG_LINES} make.log
ln -sf "${pkg_install_dir}/lib/libpexsi_${OPENBLAS_ARCH}.a" \
"${pkg_install_dir}/lib/libpexsi.a"
cp -r ./include/* ${pkg_install_dir}/include/ # bug: make install neglects most header files
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage5/$(basename ${SCRIPT_NAME})"
fi
PEXSI_CFLAGS="-I'${pkg_install_dir}/include'"
PEXSI_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding Pexsi_DIST from system paths ===================="
check_lib -lpexsi "PEXSI"
# add_include_from_paths PEXSI_CFLAGS "pexsi*" $INCLUDE_PATHS
add_lib_from_paths PEXSI_LDFLAGS "libpexsi.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking Pexsi_Dist to user paths ===================="
pkg_install_dir="$with_pexsi"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
;;
esac
if [ "$with_pexsi" != "__DONTUSE__" ]; then
PEXSI_LIBS="-lpexsi"
if [ "$with_pexsi" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_pexsi"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_pexsi" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_pexsi"
export PEXSI_CFLAGS="${PEXSI_CFLAGS}"
export PEXSI_LDFLAGS="${PEXSI_LDFLAGS}"
export PEXSI_LIBS="${PEXSI_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__LIBPEXSI|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${PEXSI_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${PEXSI_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${PEXSI_LIBS}|) \${CP_LIBS}"
EOF
cat << EOF >> ${INSTALLDIR}/lsan.supp
# leaks related to PEXSI
leak:PPEXSIDFTDriver
# leaks in MPICH triggered by PEXSI
leak:MPIR_Dataloop_alloc_and_copy
leak:MPIR_Type_contiguous_impl
leak:MPIR_Typerep_init
# leaks in SuperLU triggered by PEXSI
leak:symbfact_distributeMatrix
EOF
fi
load "${BUILDDIR}/setup_pexsi"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "pexsi"

117
scripts/stage5/install_ptscotch.sh
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@ -1,117 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
scotch_ver="6.0.0"
scotch_sha256="e57e16c965bab68c1b03389005ecd8a03745ba20fd9c23081c0bb2336972d879"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_ptscotch" ] && rm "${BUILDDIR}/setup_ptscotch"
SCOTCH_CFLAGS=""
SCOTCH_LDFLAGS=""
SCOTCH_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_ptscotch}" in
__INSTALL__)
echo "==================== Installing PT-Scotch ===================="
pkg_install_dir="${INSTALLDIR}/scotch/${scotch_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "scotch-${scotch_ver} is already installed, skipping it."
else
if [ -f scotch_${scotch_ver}.tar.gz ]; then
echo "scotch_${scotch_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${scotch_sha256}" "scotch_${scotch_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d scotch_${scotch_ver} ] && rm -rf scotch_${scotch_ver}
tar -xzf scotch_${scotch_ver}.tar.gz
cd scotch_${scotch_ver}/src
cat Make.inc/Makefile.inc.x86-64_pc_linux2 |
sed -e "s|\(^CCS\).*|\1 = ${MPICC}|g" \
-e "s|\(^CCP\).*|\1 = ${MPICC}|g" \
-e "s|\(^CCD\).*|\1 = ${MPICC}|g" \
-e "s|\(^CFLAGS\).*|\1 = ${CFLAGS} -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -DIDXSIZE64 ${MPI_CFLAGS}|g" \
> Makefile.inc
make scotch -j $(get_nprocs) > make-scotch.log 2>&1 || tail -n ${LOG_LINES} make-scotch.log
make ptscotch -j $(get_nprocs) > make-ptscotch.log 2>&1 || tail -n ${LOG_LINES} make-ptscotch.log
# PT-scotch make install is buggy in that it cannot create
# intermediate directories
! [ -d "${pkg_install_dir}" ] && mkdir -p "${pkg_install_dir}"
make install prefix=${pkg_install_dir} > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
# PEXSI also needs parmetis.h
cp ./include/parmetis.h "${pkg_install_dir}/include/"
sed -i "s|SCOTCH_Num|int|g" "${pkg_install_dir}/include/parmetis.h"
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage5/$(basename ${SCRIPT_NAME})"
fi
SCOTCH_CFLAGS="-I'${pkg_install_dir}/include'"
SCOTCH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding PT-Scotch from system paths ===================="
check_lib -lptscotchparmetis "PT-Scotch"
check_lib -lptscotch "PT-Scotch"
check_lib -lptscotcherr "PT-Scotch"
check_lib -lscotchmetis "PT-Scotch"
check_lib -lscotch "PT-Scotch"
check_lib -lscotcherr "PT-Scotch"
check_lib -lptscotchparmetis "PT-Scotch"
add_include_from_paths SCOTCH_CFLAGS "ptscotch.h" $INCLUDE_PATHS
add_lib_from_paths SCOTCH_LDFLAGS "libptscotch.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking PT-Scotch to user paths ===================="
pkg_install_dir="$with_ptscotch"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
SCOTCH_CFLAGS="-I'${pkg_install_dir}/include'"
SCOTCH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_ptscotch" != "__DONTUSE__" ]; then
SCOTCH_LIBS="-lptscotchparmetis -lptscotch -lptscotcherr -lscotchmetis -lscotch -lscotcherr"
if [ "$with_ptscotch" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_ptscotch"
prepend_path PATH "$pkg_install_dir/bin"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_ptscotch" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_ptscotch"
export SCOTCH_CFLAGS="${SCOTCH_CFLAGS}"
export SCOTCH_LDFLAGS="${SCOTCH_LDFLAGS}"
export SCOTCH_LIBS="${SCOTCH_LIBS}"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${SCOTCH_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${SCOTCH_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${SCOTCH_LIBS}|) \${CP_LIBS}"
export PTSCOTCH_ROOT="$pkg_install_dir"
EOF
fi
load "${BUILDDIR}/setup_ptscotch"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "ptscotch"

11
scripts/stage5/install_stage5.sh
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@ -1,11 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage5/install_elpa.sh
./scripts/stage5/install_ptscotch.sh
./scripts/stage5/install_superlu.sh
./scripts/stage5/install_pexsi.sh
#EOF

107
scripts/stage5/install_superlu.sh
View file

@ -1,107 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
superlu_ver="6.1.0" # Newer versions don't work with PEXSI 1.2.0.
superlu_sha256="92c6d1424dd830ee2d1e7396a418a5f6645160aea8472e558c4e4bfe006593c4"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_superlu" ] && rm "${BUILDDIR}/setup_superlu"
SUPERLU_CFLAGS=''
SUPERLU_LDFLAGS=''
SUPERLU_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_superlu" in
__INSTALL__)
echo "==================== Installing SuperLU_DIST ===================="
require_env MATH_LIBS
pkg_install_dir="${INSTALLDIR}/superlu_dist/${superlu_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "superlu_dist-${superlu_ver} is already installed, skipping it."
else
if [ -f superlu_dist_${superlu_ver}.tar.gz ]; then
echo "superlu_dist_${superlu_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${superlu_sha256}" "superlu_dist_${superlu_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d superlu_dist-${superlu_ver} ] && rm -rf superlu_dist-${superlu_ver}
tar -xzf superlu_dist_${superlu_ver}.tar.gz
cd superlu_dist-${superlu_ver}
cd build
# Explicitly set LIBDIR to "lib", otherwise it sometimes defaults to "lib64".
cmake -DTPL_ENABLE_PARMETISLIB=FALSE \
-DCMAKE_INSTALL_PREFIX=${pkg_install_dir} \
-DCMAKE_INSTALL_LIBDIR=${pkg_install_dir}/lib \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
# PEXSI needs some more headers.
cp SRC/*.h "${pkg_install_dir}/include"
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage5/$(basename ${SCRIPT_NAME})"
fi
SUPERLU_CFLAGS="-I'${pkg_install_dir}/include'"
SUPERLU_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding SuperLU_DIST from system paths ===================="
check_lib -lsuperlu_dist "SuperLU_DIST"
add_include_from_paths SUPERLU_CFLAGS "superlu*" $INCLUDE_PATHS
add_lib_from_paths SUPERLU_LDFLAGS "libsuperlu*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking Superlu_Dist to user paths ===================="
pkg_install_dir="$with_superlu"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
SUPERLU_CFLAGS="-I'${pkg_install_dir}/include'"
SUPERLU_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_superlu" != "__DONTUSE__" ]; then
SUPERLU_LIBS="-lsuperlu_dist"
if [ "$with_superlu" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_superlu"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_superlu" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_superlu"
export SUPERLU_CFLAGS="${SUPERLU_CFLAGS}"
export SUPERLU_LDFLAGS="${SUPERLU_LDFLAGS}"
export SUPERLU_LIBS="${SUPERLU_LIBS}"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${SUPERLU_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${SUPERLU_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${SUPERLU_LIBS}|) \${CP_LIBS}"
export SUPERLU_ROOT="${pkg_install_dir}"
EOF
fi
load "${BUILDDIR}/setup_superlu"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "superlu"

112
scripts/stage6/install_gsl.sh
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@ -1,112 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
gsl_ver="2.7"
gls_sha256="efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_gsl" ] && rm "${BUILDDIR}/setup_gsl"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_gsl" in
__INSTALL__)
echo "==================== Installing gsl ===================="
pkg_install_dir="${INSTALLDIR}/gsl/${gsl_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "gsl-${gsl_ver} is already installed, skipping it."
else
if [ -f gsl-${gsl_ver}.tar.gz ]; then
echo "gsl-${gsl_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${gls_sha256}" "gsl-${gsl_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d gsl-${gsl_ver} ] && rm -rf gsl-${gsl_ver}
tar -xzf gsl-${gsl_ver}.tar.gz
cd gsl-${gsl_ver}
./configure --prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
--disable-shared \
--enable-static \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage6/$(basename ${SCRIPT_NAME})"
fi
GSL_CFLAGS="-I'${pkg_install_dir}/include'"
GSL_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding gsl from system paths ===================="
check_command pkg-config --modversion gsl
add_include_from_paths GSL_CFLAGS "gsl.h" $INCLUDE_PATHS
add_lib_from_paths GSL_LDFLAGS "libgsl.*" $LIB_PATHS
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking gsl to user paths ===================="
pkg_install_dir="$with_gsl"
check_dir "$pkg_install_dir/lib"
check_dir "$pkg_install_dir/include"
GSL_CFLAGS="-I'${pkg_install_dir}/include'"
GSL_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_gsl" != "__DONTUSE__" ]; then
GSL_LIBS="-lgsl"
if [ "$with_gsl" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_gsl"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
export GSL_INCLUDE_DIR="$pkg_install_dir/include"
export GSL_LIBRARY="-lgsl"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_gsl"
export GSL_CFLAGS="${GSL_CFLAGS}"
export GSL_LDFLAGS="${GSL_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__GSL|)"
export CP_CFLAGS="\${CP_CFLAGS} ${GSL_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${GSL_LDFLAGS}"
export GSL_LIBRARY="-lgsl"
export GSL_ROOT="$pkg_install_dir"
export GSL_INCLUDE_DIR="$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib64/pkgconfig"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
##########################################################
#
# I only include the library when SIRIUS is activated
# which depends explicitly on MPI
#
##########################################################
export CP_LIBS="IF_MPI(${GSL_LIBS}|) \${CP_LIBS}"
EOF
cat "${BUILDDIR}/setup_gsl" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_gsl"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "gsl"

125
scripts/stage6/install_plumed.sh
View file

@ -1,125 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
plumed_ver="2.9.0"
plumed_pkg="plumed-src-${plumed_ver}.tgz"
plumed_sha256="16e3fc77f2f4bc024bd279209e4dd49bfd8ed555325a0c868fe9c6b8fae19862"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_plumed" ] && rm "${BUILDDIR}/setup_plumed"
PLUMED_LDFLAGS=''
PLUMED_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_plumed" in
__INSTALL__)
echo "==================== Installing PLUMED ===================="
pkg_install_dir="${INSTALLDIR}/plumed/${plumed_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "plumed-${plumed_ver} is already installed, skipping it."
else
if [ -f ${plumed_pkg} ]; then
echo "${plumed_pkg} is found"
else
download_pkg_from_cp2k_org "${plumed_sha256}" "${plumed_pkg}"
fi
[ -d plumed-${plumed_ver} ] && rm -rf plumed-${plumed_ver}
tar -xzf ${plumed_pkg}
echo "Installing from scratch into ${pkg_install_dir}"
cd plumed-${plumed_ver}
# disable generating debugging infos for now to work around an issue in gcc-10.2:
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=96354
# note: some MPI wrappers carry a -g forward, thus stripping is not enough
case "$(uname -s)" in
Darwin)
libs="-lgomp"
;;
*)
libs=""
;;
esac
[ -n "${MKL_LIBS}" ] && libs+="$(resolve_string "${MKL_LIBS}" "MPI")"
# Patch to include <limits> explicitly as required by gcc >= 11.
sed -i'' -e '/^#include <algorithm>/a\'$'\n''#include <limits>' ./src/lepton/Operation.h
./configure \
CXX="${MPICXX}" \
CXXFLAGS="${CXXFLAGS//-g/-g0} ${GSL_CFLAGS}" \
LDFLAGS="${LDFLAGS} ${GSL_LDFLAGS}" \
LIBS="${libs}" \
--prefix=${pkg_install_dir} \
--libdir="${pkg_install_dir}/lib" \
--enable-modules=all \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make VERBOSE=1 -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage6/$(basename ${SCRIPT_NAME})"
fi
PLUMED_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding PLUMED from system paths ===================="
check_lib -lplumed "PLUMED"
add_lib_from_paths PLUMED_LDFLAGS "libplumed*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking PLUMED to user paths ===================="
pkg_install_dir="$with_plumed"
check_dir "${pkg_install_dir}/lib"
PLUMED_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_plumed" != "__DONTUSE__" ]; then
# Prefer static library if available
if [ -f "${pkg_install_dir}/lib/libplumed.a" ]; then
PLUMED_LIBS="-l:libplumed.a -ldl -lstdc++ -lz -ldl"
else
PLUMED_LIBS="-lplumed -ldl -lstdc++ -lz -ldl"
fi
if [ "$with_plumed" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_plumed"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_plumed" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_plumed"
export PLUMED_LDFLAGS="${PLUMED_LDFLAGS}"
export PLUMED_LIBS="${PLUMED_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__PLUMED2|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${PLUMED_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${PLUMED_LIBS}|) \${CP_LIBS}"
export PLUMED_ROOT=${pkg_install_dir}
EOF
fi
load "${BUILDDIR}/setup_plumed"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "plumed"

192
scripts/stage6/install_quip.sh
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@ -1,192 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
# Installing QUIP without GAP because its ASL licence is not GPL-compatible.
# See also https://github.com/libAtoms/QUIP/issues/481
quip_ver="0.9.10"
quip_sha256="c03505779634459ea0ba3f7ddc120ac17f0546d44dc9b5096f008f1c3c6620ef"
fox_ver="b5b69ef9a46837bd944ba5c9bc1cf9d00a6198a7"
fox_sha256="a87dd7faf80612a0df94dc272474f37689c6213c6ac4705fb637644409c5cd4e"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_quip" ] && rm "${BUILDDIR}/setup_quip"
if [ "${ENABLE_TSAN}" = "__TRUE__" ]; then
report_warning "QUIP is not compatible with the thread sanitizer. The QUIP package will not be installed."
cat << EOF > ${BUILDDIR}/setup_quip
with_quip="__DONTUSE__"
EOF
exit 0
fi
if [ "${with_quip}" != "__DONTUSE__" ] && [ "${with_intel}" != "__DONTUSE__" ]; then
report_warning "A QUIP installation using the Intel compiler is currently not supported. The QUIP package will not be installed."
exit 0
fi
QUIP_CFLAGS=""
QUIP_LDFLAGS=""
QUIP_LIBS=""
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_quip}" in
__INSTALL__)
echo "==================== Installing QUIP ===================="
require_env MATH_LIBS
pkg_install_dir="${INSTALLDIR}/quip/${quip_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "quip_dist-${quip_ver} is already installed, skipping it."
else
if [ -f QUIP-${quip_ver}.tar.gz ]; then
echo "QUIP-${quip_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${quip_sha256}" "QUIP-${quip_ver}.tar.gz"
fi
if [ -f fox-${fox_ver}.tar.gz ]; then
echo "fox-${fox_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${fox_sha256}" "fox-${fox_ver}.tar.gz"
fi
[ -d QUIP-${quip_ver} ] && rm -rf QUIP-${quip_ver}
[ -d fox-${fox_ver} ] && rm -rf fox-${fox_ver}
echo "Installing from scratch into ${pkg_install_dir}"
tar -xzf QUIP-${quip_ver}.tar.gz
tar -xzf fox-${fox_ver}.tar.gz
cd QUIP-${quip_ver}
rmdir ./src/fox
ln -s ../../fox-${fox_ver} ./src/fox
# translate OPENBLAS_ARCH
case $OPENBLAS_ARCH in
x86_64)
quip_arch="x86_64"
;;
i386)
quip_arch="x86_32"
;;
arm*)
quip_arch="x86_64"
;;
*)
report_error ${LINENO} "arch $OPENBLAS_ARCH is currently not supported."
exit 1
;;
esac
# The ARCHER cd has a very annoying habit of printing out
# dir names to stdout for any target directories that are
# more than one level deep, and one cannot seem to disable
# it. This unfortunately messes up the installation script
# for QUIP. So this hack will help to resolve the issue
if [ "${ENABLE_CRAY}" = "__TRUE__" ]; then
sed -i \
-e "s|\(cd build/.*\)|\1 >&- 2>&-|g" \
bin/find_sizeof_fortran_t
fi
sed -i \
-e "s|\(F77 *=\).*|\1 ${FC}|g" \
-e "s|\(F90 *=\).*|\1 ${FC}|g" \
-e "s|\(F95 *=\).*|\1 ${FC}|g" \
-e "s|\(CC *=\).*|\1 ${CC}|g" \
-e "s|\(CPLUSPLUS *=\).*|\1 ${CXX}|g" \
-e "s|\(LINKER *=\).*|\1 ${FC}|g" \
-e "s|\(FPP *=\).*|\1 ${FC} -E -x f95-cpp-input|g" \
-e "s|\(QUIPPY_FCOMPILER *=\).*|\1 ${FC}|g" \
-e "s|\(QUIPPY_CPP *=\).*|\1 ${FC} -E -x f95-cpp-input|g" \
arch/Makefile.linux_${quip_arch}_gfortran
# workaround for compilation with GCC-10, until properly fixed:
# https://github.com/libAtoms/QUIP/issues/209
if ("${FC}" --version | grep -q 'GNU'); then
compat_flag=$(allowed_gfortran_flags "-fallow-argument-mismatch")
fi
# enable debug symbols
echo "F95FLAGS += -g ${compat_flag}" >> arch/Makefile.linux_${quip_arch}_gfortran
echo "F77FLAGS += -g ${compat_flag}" >> arch/Makefile.linux_${quip_arch}_gfortran
echo "CFLAGS += -g" >> arch/Makefile.linux_${quip_arch}_gfortran
echo "CPLUSPLUSFLAGS += -g" >> arch/Makefile.linux_${quip_arch}_gfortran
# Makefile.linux_${quip_arch}_gfortran_openmp includes Makefile.linux_${quip_arch}_gfortran
export QUIP_ARCH=linux_${quip_arch}_gfortran_openmp
# hit enter a few times to accept defaults
echo -e "${MATH_LDFLAGS} $(resolve_string "${MATH_LIBS}") \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" | make config > configure.log
# make -j does not work :-(
make > make.log 2>&1 || tail -n ${LOG_LINES} make.log
! [ -d "${pkg_install_dir}/include" ] && mkdir -p "${pkg_install_dir}/include"
! [ -d "${pkg_install_dir}/lib" ] && mkdir -p "${pkg_install_dir}/lib"
cp build/${QUIP_ARCH}/quip_unified_wrapper_module.mod \
"${pkg_install_dir}/include/"
cp build/${QUIP_ARCH}/*.a \
"${pkg_install_dir}/lib/"
cp src/fox/objs.${QUIP_ARCH}/lib/*.a \
"${pkg_install_dir}/lib/"
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage6/$(basename ${SCRIPT_NAME})"
fi
QUIP_CFLAGS="-I'${pkg_install_dir}/include'"
QUIP_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding Quip_DIST from system paths ===================="
check_lib -lquip_core "QUIP"
check_lib -latoms "QUIP"
check_lib -lFoX_sax "QUIP"
check_lib -lFoX_common "QUIP"
check_lib -lFoX_utils "QUIP"
check_lib -lFoX_fsys "QUIP"
add_include_from_paths QUIP_CFLAGS "quip*" $INCLUDE_PATHS
add_lib_from_paths QUIP_LDFLAGS "libquip_core*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking Quip_Dist to user paths ===================="
pkg_install_dir="$with_quip"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
QUIP_CFLAGS="-I'${pkg_install_dir}/include'"
QUIP_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_quip}" != "__DONTUSE__" ]; then
QUIP_LIBS="-lquip_core -latoms -lFoX_sax -lFoX_common -lFoX_utils -lFoX_fsys"
if [ "${with_quip}" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_quip"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_quip"
export QUIP_CFLAGS="${QUIP_CFLAGS}"
export QUIP_LDFLAGS="${QUIP_LDFLAGS}"
export QUIP_LIBS="${QUIP_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__QUIP"
export CP_CFLAGS="\${CP_CFLAGS} ${QUIP_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${QUIP_LDFLAGS}"
export CP_LIBS="${QUIP_LIBS} \${CP_LIBS}"
export QUIP_ROOT="${pkg_install_dir}"
EOF
cat "${BUILDDIR}/setup_quip" >> ${SETUPFILE}
fi
load "${BUILDDIR}/setup_quip"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "quip"

10
scripts/stage6/install_stage6.sh
View file

@ -1,10 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage6/install_quip.sh
./scripts/stage6/install_gsl.sh
./scripts/stage6/install_plumed.sh
#EOF

110
scripts/stage7/install_hdf5.sh
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@ -1,110 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
hdf5_ver="1.14.2"
hdf5_sha256="ea3c5e257ef322af5e77fc1e52ead3ad6bf3bb4ac06480dd17ee3900d7a24cfb"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_hdf5" ] && rm "${BUILDDIR}/setup_hdf5"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_hdf5" in
__INSTALL__)
echo "==================== Installing hdf5 ===================="
pkg_install_dir="${INSTALLDIR}/hdf5/${hdf5_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "hdf5-${hdf5_ver} is already installed, skipping it."
else
if [ -f hdf5-${hdf5_ver}.tar.bz2 ]; then
echo "hdf5-${hdf5_ver}.tar.bz2 is found"
else
download_pkg_from_cp2k_org "${hdf5_sha256}" "hdf5-${hdf5_ver}.tar.bz2"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d hdf5-${hdf5_ver} ] && rm -rf hdf5-${hdf5_ver}
tar xf hdf5-${hdf5_ver}.tar.bz2
cd hdf5-${hdf5_ver}
./configure \
--prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
--enable-fortran \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename ${SCRIPT_NAME})"
fi
HDF5_CFLAGS="-I${pkg_install_dir}/include"
HDF5_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding hdf5 from system paths ===================="
check_command pkg-config --modversion hdf5
pkg_install_dir=$(h5cc -show | tr " " "\n" | grep "\-L" | cut -c3-)
HDF5_CFLAGS="-I${pkg_install_dir}/include"
HDF5_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking hdf5 to user paths ===================="
pkg_install_dir="${with_hdf5}"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/include"
HDF5_CFLAGS="-I'${pkg_install_dir}/include'"
HDF5_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "${with_hdf5}" != "__DONTUSE__" ]; then
# Prefer static libraries if available
if [ -f "${pkg_install_dir}/lib/libhdf5.a" ]; then
HDF5_LIBS="-l:libhdf5_fortran.a -l:libhdf5_hl.a -l:libhdf5.a -lz"
else
HDF5_LIBS="-lhdf5_fortran -lhdf5_hl -lhdf5 -lz"
fi
if [ "${with_hdf5}" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_hdf5"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path CPATH "${pkg_install_dir}/include"
prepend_path PKG_CONFIG_PATH "${pkg_install_dir}/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "${pkg_install_dir}"
EOF
else
HDF5_LIBS="${HDF5_LIBS} -lsz"
fi
cat << EOF >> "${BUILDDIR}/setup_hdf5"
export HDF5_CFLAGS="${HDF5_CFLAGS}"
export HDF5_LDFLAGS="${HDF5_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__HDF5"
export CP_CFLAGS="\${CP_CFLAGS} ${HDF5_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${HDF5_LDFLAGS}"
export CP_LIBS="${HDF5_LIBS} \${CP_LIBS}"
export HDF5_ROOT="${pkg_install_dir}"
export HDF5_LIBRARIES="${HDF5_LIBS}"
export HDF5_HL_LIBRARIES="${HDF5_LIBS}"
export HDF5_INCLUDE_DIRS="${pkg_install_dir}/include"
EOF
cat "${BUILDDIR}/setup_hdf5" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_hdf5"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "hdf5"

113
scripts/stage7/install_libtorch.sh
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@ -1,113 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
# From https://pytorch.org/get-started/locally/
libtorch_ver="1.12.1"
libtorch_sha256="82c7be80860f2aa7963f8700004a40af8205e1d721298f2e09b700e766a9d283"
# shellcheck source=/dev/null
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libtorch" ] && rm "${BUILDDIR}/setup_libtorch"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_libtorch}" in
__INSTALL__)
echo "==================== Installing libtorch ===================="
pkg_install_dir="${INSTALLDIR}/libtorch/${libtorch_ver}"
mkdir -p /avfs/projects/ops/libtorch/1.12.1
install_lock_file="${pkg_install_dir}/install_successful"
archive_file="libtorch-cxx11-abi-shared-with-deps-${libtorch_ver}+cpu.zip"
if verify_checksums "${install_lock_file}"; then
echo "libtorch-${libtorch_ver} is already installed, skipping it."
else
if [ -f ${archive_file} ]; then
echo "${archive_file} is found"
else
download_pkg_from_cp2k_org "${libtorch_sha256}" "${archive_file}"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d libtorch ] && rm -rf libtorch
[ -d ${pkg_install_dir} ] && rm -rf ${pkg_install_dir}
unzip -q ${archive_file}
mv libtorch ${pkg_install_dir}
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename "${SCRIPT_NAME}")"
fi
LIBTORCH_CXXFLAGS="-I${pkg_install_dir}/include"
LIBTORCH_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath='${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding libtorch from system paths ===================="
check_lib -ltorch "libtorch"
add_include_from_paths LIBTORCH_CXXFLAGS "libtorch.h" $INCLUDE_PATHS
add_lib_from_paths LIBTORCH_LDFLAGS "libtorch.*" "$LIB_PATHS"
;;
__DONTUSE__) ;;
*)
echo "==================== Linking libtorch to user paths ===================="
pkg_install_dir="${with_libtorch}"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
LIBTORCH_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && LIBTORCH_LIBDIR="${pkg_install_dir}/lib64"
check_dir "${LIBTORCH_LIBDIR}"
LIBTORCH_CXXFLAGS="-I${pkg_install_dir}/include"
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
LIBTORCH_LDFLAGS="-Wl,--no-as-needed,-L'${LIBTORCH_LIBDIR}' -Wl,--no-as-needed,-rpath='${LIBTORCH_LIBDIR}'"
else
LIBTORCH_LDFLAGS="-L'${LIBTORCH_LIBDIR}' -Wl,-rpath='${LIBTORCH_LIBDIR}'"
fi
;;
esac
if [ "$with_libtorch" != "__DONTUSE__" ]; then
if [ "$with_libtorch" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libtorch"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
cat << EOF >> "${BUILDDIR}/setup_libtorch"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBTORCH"
export CXXFLAGS="\${CXXFLAGS} ${LIBTORCH_CXXFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBTORCH_LDFLAGS}"
export CP_LIBS="\${CP_LIBS} -lc10 -lc10_cuda -ltorch_cpu -ltorch_cuda -ltorch"
EOF
cat "${BUILDDIR}/setup_libtorch" >> "${SETUPFILE}"
else
cat << EOF >> "${BUILDDIR}/setup_libtorch"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBTORCH"
export CXXFLAGS="\${CXXFLAGS} ${LIBTORCH_CXXFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBTORCH_LDFLAGS}"
export CP_LIBS="\${CP_LIBS} -lc10 -ltorch_cpu -ltorch"
EOF
cat "${BUILDDIR}/setup_libtorch" >> "${SETUPFILE}"
fi
fi
load "${BUILDDIR}/setup_libtorch"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libtorch"

126
scripts/stage7/install_libvdwxc.sh
View file

@ -1,126 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
libvdwxc_ver="0.4.0"
libvdwxc_sha256="3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libvdwxc" ] && rm "${BUILDDIR}/setup_libvdwxc"
if [ "$MPI_MODE" = "no" ] && [ $with_sirius = "__FALSE__" ]; then
report_warning $LINENO "MPI and SIRIUS are disabled, skipping libvdwxc installation"
exit 0
fi
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_libvdwxc" in
__INSTALL__)
require_env FFTW3_INCLUDES
require_env FFTW3_LIBS
echo "==================== Installing libvdwxc ===================="
pkg_install_dir="${INSTALLDIR}/libvdwxc/${libvdwxc_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libvdwxc-${libvdwxc_ver} is already installed, skipping it."
else
if [ -f libvdwxc-${libvdwxc_ver}.tar.gz ]; then
echo "libvdwxc-${libvdwxc_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${libvdwxc_sha256}" "libvdwxc-${libvdwxc_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d libvdwxc-${libvdwxc_ver} ] && rm -rf libvdwxc-${libvdwxc_ver}
tar -xzf libvdwxc-${libvdwxc_ver}.tar.gz
cd libvdwxc-${libvdwxc_ver}
if [ "${MPI_MODE}" = "no" ]; then
# compile libvdwxc without mpi support since fftw (or mkl) do not have mpi support activated
./configure \
CC="${CC}" \
FC="${FC}" \
FFTW3_INCLUDES="${FFTW3_INCLUDES}" \
FFTW3_LIBS="$(resolve_string "${FFTW3_LIBS}" "MPI")" \
--prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
--disable-shared \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
else
./configure \
CC="${MPICC}" \
FC="${MPIFC}" \
FFTW3_INCLUDES="${FFTW3_INCLUDES}" \
FFTW3_LIBS="$(resolve_string "${FFTW3_LIBS}" "MPI")" \
--prefix="${pkg_install_dir}" \
--libdir="${pkg_install_dir}/lib" \
--disable-shared \
> configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
fi
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename ${SCRIPT_NAME})"
fi
LIBVDWXC_CFLAGS="-I${pkg_install_dir}/include"
LIBVDWXC_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding libvdwxc from system paths ===================="
check_command pkg-config --modversion libvdwxc
add_include_from_paths LIBVDWXC_CFLAGS "vdwxc.h" $INCLUDE_PATHS
add_lib_from_paths LIBVDWXC_LDFLAGS "libvdwxc*" $LIB_PATHS
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking libvdwxc to user paths ===================="
pkg_install_dir="$with_libvdwxc"
check_dir "$pkg_install_dir/lib"
check_dir "$pkg_install_dir/include"
LIBVDWXC_CFLAGS="-I'${pkg_install_dir}/include'"
LIBVDWXC_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_libvdwxc" != "__DONTUSE__" ]; then
LIBVDWXC_LIBS="-lvdwxc"
if [ "$with_libvdwxc" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libvdwxc"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_libvdwxc"
export LIBVDWXC_CFLAGS="-I$pkg_install_dir/include ${LIBVDWXC_CFLAGS}"
export LIBVDWXC_LDFLAGS="${LIBVDWXC_LDFLAGS}"
export LIBVDWXC_LIBS="${LIBVDWXC_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__LIBVDWXC|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI(${LIBVDWXC_CFLAGS}|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(${LIBVDWXC_LDFLAGS}|)"
export CP_LIBS="IF_MPI(${LIBVDWXC_LIBS}|) \${CP_LIBS}"
export PKG_CONFIG_PATH="$pkg_install_dir/lib/pkgconfig:$PKG_CONFIG_PATH"
export VDWXC_ROOT="$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_libvdwxc" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_libvdwxc"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libvdwxc"

109
scripts/stage7/install_libvori.sh
View file

@ -1,109 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
libvori_ver="220621"
libvori_sha256="1cfa98c564814bddacf1c0e7f11582137d758668f6307e6eb392c72317984c14"
# shellcheck source=/dev/null
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_libvori" ] && rm "${BUILDDIR}/setup_libvori"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_libvori:=__INSTALL__}" in
__INSTALL__)
echo "==================== Installing libvori ===================="
pkg_install_dir="${INSTALLDIR}/libvori/${libvori_ver}"
install_lock_file="${pkg_install_dir}/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "libvori-${libvori_ver} is already installed, skipping it."
else
if [ -f libvori-${libvori_ver}.tar.gz ]; then
echo "libvori-${libvori_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${libvori_sha256}" "libvori-${libvori_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d libvori-${libvori_ver} ] && rm -rf libvori-${libvori_ver}
tar -xzf libvori-${libvori_ver}.tar.gz
mkdir "libvori-${libvori_ver}/build"
cd "libvori-${libvori_ver}/build"
cmake \
-DCMAKE_BUILD_TYPE=RelWithDebInfo \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON \
-DCMAKE_VERBOSE_MAKEFILE=ON \
.. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
CMAKE_BUILD_PARALLEL_LEVEL="$(get_nprocs)" cmake --build . > build.log 2>&1 || tail -n ${LOG_LINES} build.log
CMAKE_BUILD_PARALLEL_LEVEL="$(get_nprocs)" cmake --build . --target test > test.log 2>&1 || tail -n ${LOG_LINES} test.log
CMAKE_BUILD_PARALLEL_LEVEL="$(get_nprocs)" cmake --build . --target install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename "${SCRIPT_NAME}")"
fi
LIBVORI_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
__SYSTEM__)
echo "==================== Finding libvori from system paths ===================="
check_lib -lvori "libvori"
add_lib_from_paths LIBVORI_LDFLAGS "libvori.*" "$LIB_PATHS"
;;
__DONTUSE__) ;;
*)
echo "==================== Linking libvori to user paths ===================="
pkg_install_dir="${with_libvori}"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
LIBVORI_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && LIBVORI_LIBDIR="${pkg_install_dir}/lib64"
check_dir "${LIBVORI_LIBDIR}"
LIBVORI_LDFLAGS="-L'${LIBVORI_LIBDIR}' -Wl,-rpath,'${LIBVORI_LIBDIR}'"
;;
esac
if [ "$with_libvori" != "__DONTUSE__" ]; then
LIBVORI_LIBS="-lvori -lstdc++"
if [ "$with_libvori" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_libvori"
prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
export LIBVORI_LIBS="${LIBVORI_LIBS}"
export LIBVORI_ROOT="${pkg_install_dir}"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_libvori"
export LIBVORI_ROOT="${pkg_install_dir}"
export LIBVORI_VERSION=${libvori_ver}
export LIBVORI_LDFLAGS="${LIBVORI_LDFLAGS}"
export LIBVORI_LIBRARY="-lvori"
export CP_DFLAGS="\${CP_DFLAGS} -D__LIBVORI"
export CP_LDFLAGS="\${CP_LDFLAGS} ${LIBVORI_LDFLAGS}"
export CP_LIBS="\${CP_LIBS} ${LIBVORI_LIBS}"
EOF
cat "${BUILDDIR}/setup_libvori" >> "${SETUPFILE}"
fi
load "${BUILDDIR}/setup_libvori"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "libvori"

109
scripts/stage7/install_spglib.sh
View file

@ -1,109 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
spglib_ver="1.16.2"
spglib_sha256="5723789bee7371ebba91d78c729d2a608f198fad5e1c95eebe18fda9f2914ec8"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_spglib" ] && rm "${BUILDDIR}/setup_spglib"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_spglib" in
__INSTALL__)
echo "==================== Installing spglib ===================="
pkg_install_dir="${INSTALLDIR}/spglib/${spglib_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "spglib-${spglib_ver} is already installed, skipping it."
else
if [ -f spglib-${spglib_ver}.tar.gz ]; then
echo "spglib-${spglib_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${spglib_sha256}" "spglib-${spglib_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
rm -rf spglib-${spglib_ver} "${pkg_install_dir}"
tar -xzf spglib-${spglib_ver}.tar.gz
cd spglib-${spglib_ver}
mkdir build
cd build
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS=NO \
-DCMAKE_VERBOSE_MAKEFILE=ON \
.. > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
make -j $(get_nprocs) symspg > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make install >> install.log 2>&1 || tail -n ${LOG_LINES} install.log
# Despite -DBUILD_SHARED_LIBS=NO the shared library gets build and installed.
rm -f "${pkg_install_dir}"/lib*/*.so*
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename ${SCRIPT_NAME})"
fi
SPGLIB_CFLAGS="-I${pkg_install_dir}/include"
SPGLIB_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
if [ -d "${pkg_install_dir}/lib64" ]; then
ln -sf lib64 ${pkg_install_dir}/lib
cd ${pkg_install_dir}
fi
;;
__SYSTEM__)
echo "==================== Finding spglib from system paths ===================="
check_command pkg-config --modversion spglib
add_include_from_paths SPGLIB_CFLAGS "spglib.h" $INCLUDE_PATHS
add_lib_from_paths SPGLIB_LDFLAGS "libspglib.*" $LIB_PATHS
;;
__DONTUSE__) ;;
*)
echo "==================== Linking spglib to user paths ===================="
pkg_install_dir="$with_spglib"
check_dir "$pkg_install_dir/lib"
check_dir "$pkg_install_dir/include"
SPGLIB_CFLAGS="-I'${pkg_install_dir}/include'"
SPGLIB_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
;;
esac
if [ "$with_spglib" != "__DONTUSE__" ]; then
SPGLIB_LIBS="-lsymspg"
if [ "$with_spglib" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_spglib"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_spglib"
export SPGLIB_CFLAGS="-I$pkg_install_dir/include ${SPGLIB_CFLAGS}"
export SPGLIB_LDFLAGS="${SPGLIB_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} -D__SPGLIB"
export CP_CFLAGS="\${CP_CFLAGS} ${SPGLIB_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${SPGLIB_LDFLAGS}"
export CP_LIBS="${SPGLIB_LIBS} \${CP_LIBS}"
export LIBSPG_ROOT="$pkg_install_dir"
export LIBSPG_INCLUDE_DIR="$pkg_install_dir/include"
EOF
cat "${BUILDDIR}/setup_spglib" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_spglib"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "spglib"

12
scripts/stage7/install_stage7.sh
View file

@ -1,12 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage7/install_hdf5.sh
./scripts/stage7/install_libvdwxc.sh
./scripts/stage7/install_spglib.sh
./scripts/stage7/install_libvori.sh
./scripts/stage7/install_libtorch.sh
#EOF

305
scripts/stage8/install_sirius.sh
View file

@ -1,305 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
sirius_ver="7.4.3"
sirius_sha256="015679a60a39fa750c5d1bd8fb1ce73945524bef561270d8a171ea2fd4687fec"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
if [ "$MPI_MODE" = "no" ]; then
report_warning $LINENO "MPI is disabled, skipping sirius installation"
echo 'with_sirius="__FALSE__"' >> ${BUILDDIR}/setup_sirius
exit 0
fi
[ -f "${BUILDDIR}/setup_sirius" ] && rm "${BUILDDIR}/setup_sirius"
SIRIUS_CFLAGS=''
SIRIUS_LDFLAGS=''
SIRIUS_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_sirius" in
__DONTUSE__) ;;
__INSTALL__)
echo "==================== Installing SIRIUS ===================="
require_env FFTW_LDFLAGS
require_env FFTW_LIBS
require_env FFTW_CFLAGS
require_env ELPA_ROOT
require_env ELPA_LDFLAGS
require_env ELPA_LIBS
require_env ELPA_CFLAGS
require_env GSL_ROOT
require_env GSL_LDFLAGS
require_env GSL_CFLAGS
require_env GSL_LIBS
require_env GSL_INCLUDE_DIR
require_env GSL_LIBRARY
require_env MATH_LIBS
require_env MPI_LDFLAGS
require_env MPI_LIBS
require_env SCALAPACK_ROOT
require_env SCALAPACK_LDFLAGS
require_env SCALAPACK_CFLAGS
require_env SCALAPACK_LIBS
require_env LIBXC_LIBS
require_env LIBXC_CFLAGS
require_env LIBXC_LDFLAGS
require_env SPGLIB_LIBS
require_env SPGLIB_CFLAGS
require_env SPGLIB_LDFLAGS
require_env HDF5_LIBS
require_env HDF5_CFLAGS
require_env HDF5_LDFLAGS
require_env LIBVDWXC_CFLAGS
require_env LIBVDWXC_LIBS
require_env LIBVDWXC_LDFLAGS
require_env SPFFT_ROOT
require_env SPFFT_CFLAGS
require_env SPFFT_LDFLAGS
require_env SPFFT_LIBS
require_env SPLA_ROOT
require_env SPLA_CFLAGS
require_env SPLA_LDFLAGS
require_env SPLA_LIBS
require_env COSMA_ROOT
ARCH=$(uname -m)
SIRIUS_OPT="-O3 -DNDEBUG -mtune=native -ftree-loop-vectorize ${MATH_CFLAGS}"
if [ "$ARCH" = "ppc64le" ]; then
SIRIUS_OPT="-O3 -DNDEBUG -mcpu=power8 -mtune=power8 -funroll-loops -ftree-vectorize -mvsx -maltivec -mpopcntd -mveclibabi=mass -fvect-cost-model -fpeel-loops -mcmodel=medium ${MATH_CFLAGS}"
SIRIUS_DBG="-O2 -g -mcpu=power8 -mtune=power8 -funroll-loops -ftree-vectorize -mvsx -maltivec -mpopcntd -mveclibabi=mass -fvect-cost-model -fpeel-loops -mcmodel=medium ${MATH_CFLAGS}"
fi
if [ "$ARCH" = "x86_64" ]; then
if [ "${with_intel}" != "__DONTUSE__" ]; then
SIRIUS_OPT="-DNDEBUG -O2 -g ${MATH_CFLAGS}"
SIRIUS_DBG="-O1 -g ${MATH_CFLAGS}"
# SIRIUS_DBG and SIRIUS_OPT are not really considered by CMake and rather the CMAKE_BUILD_TYPE matters.
# The CMAKE_BUILD_TYPEs "Release" and "RelWithDebInfo" employ -O3/-O2, but already -O2 makes the SIRIUS
# build quite memory and time intensive. The CMAKE_BUILD_TYPE "Debug" allows for fast compilation, but it
# generates very slow code.
# EXTRA_CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS= ${EXTRA_CMAKE_FLAGS}"
EXTRA_CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_CXX_FLAGS= ${EXTRA_CMAKE_FLAGS}"
else
SIRIUS_OPT="-O3 -DNDEBUG -mtune=native -ftree-loop-vectorize ${MATH_CFLAGS}"
SIRIUS_DBG="-O2 -g -mtune=native -ftree-loop-vectorize ${MATH_CFLAGS}"
fi
fi
pkg_install_dir="${INSTALLDIR}/sirius/${sirius_ver}"
install_lock_file="${pkg_install_dir}/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "sirius_dist-${sirius_ver} is already installed, skipping it."
else
if [ -f SIRIUS-${sirius_ver}.tar.gz ]; then
echo "sirius_${sirius_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${sirius_sha256}" "SIRIUS-${sirius_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d sirius-${sirius_ver} ] && rm -rf sirius-${sirius_ver}
tar -xzf SIRIUS-${sirius_ver}.tar.gz
cd SIRIUS-${sirius_ver}
# GCC 13 stopped including some common headers.
# https://github.com/electronic-structure/SIRIUS/issues/854
sed -i'' -e '1s/.*/#include <cstdint>\n&/' src/*.hpp
rm -Rf build
mkdir build
cd build
# if [ -n "$ELPA_LIBS" ] ; then
# if [ -s "$ELPA_ROOT" ] ; then
# export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$ELPA_ROOT/lib/pkgconfig:$ELPA_ROOT/lib64/pkgconfig
# fi
# EXTRA_CMAKE_FLAGS="-DUSE_ELPA=ON -DELPA_INCLUDE_DIR=${ELPA_ROOT}/include/elpa-${ELPA_VERSION} ${EXTRA_CMAKE_FLAGS}"
# fi
if [ -n "${SCALAPACK_LIBS}" ]; then
export SCALAPACK_LIB="${SCALAPACK_LIBS}"
if [ -s "${SCALAPACK_ROOT}" ]; then
EXTRA_CMAKE_FLAGS="-DUSE_SCALAPACK=ON -DSCALAPACK_INCLUDE_DIR=${SCALAPACK_ROOT}/include ${EXTRA_CMAKE_FLAGS}"
else
EXTRA_CMAKE_FLAGS="-DUSE_SCALAPACK=ON ${EXTRA_CMAKE_FLAGS}"
fi
fi
if [ -n "${HDF5_LIBS}" ]; then
CMAKE_PREFIX_PATH="${HDF5_ROOT} ${CMAKE_PREFIX_PATH}"
fi
if [ -n "${LIBVDWXC_LIBS}" ]; then
CMAKE_PREFIX_PATH="${LIBVDWXC_ROOT} ${CMAKE_PREFIX_PATH}"
EXTRA_CMAKE_FLAGS="-DUSE_VDWXC=ON ${EXTRA_CMAKE_FLAGS}"
else
EXTRA_CMAKE_FLAGS="-DUSE_VDWXC=OFF ${EXTRA_CMAKE_FLAGS}"
fi
if [ -n "${MKL_LIBS}" ]; then
EXTRA_CMAKE_FLAGS="-DUSE_MKL=ON -DMKL_DEF_LIBRARY=${MKLROOT}/lib/intel64 -DUSE_SCALAPACK=ON ${EXTRA_CMAKE_FLAGS}"
fi
SpFFT_DIR="${SpFFT_ROOT}/lib/cmake/SpFFT"
SpLA_DIR="${SpLA_ROOT}/lib/cmake/SPLA"
COSTA_DIR="${COSMA_ROOT}/lib/cmake/costa"
CMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH}:${GSL_ROOT}:${SPGLIB_ROOT}:${LIBXC_ROOT}:${SpFFT_DIR}:${SpLA_DIR}:${COSTA_DIR}" cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_CXX_FLAGS_RELEASE="${SIRIUS_OPT}" \
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO="${SIRIUS_DBG}" \
-DCMAKE_CXX_COMPILER="${MPICXX}" \
-DCMAKE_C_COMPILER="${MPICC}" \
-DCMAKE_Fortran_COMPILER="${MPIFC}" \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DBUILD_SHARED_LIBS=OFF \
-DUSE_MEMORY_POOL=OFF \
-DUSE_ELPA=OFF \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) -C src >> make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d "${pkg_install_dir}/include" >> install.log 2>&1
install -d "${pkg_install_dir}/lib" >> install.log 2>&1
cp -R ../src/* "${pkg_install_dir}/include" >> install.log 2>&1
install -m 644 src/*.a "${pkg_install_dir}/lib" >> install.log 2>&1
install -m 644 src/mod_files/*.mod "${pkg_install_dir}/include" >> install.log 2>&1
cd ..
# now do we have cuda as well
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
CMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH}:${GSL_ROOT}:${SPGLIB_ROOT}:${LIBXC_ROOT}:${SpFFT_DIR}:${SpLA_DIR}:${COSTA_DIR}" cmake \
-DCMAKE_INSTALL_PREFIX=${pkg_install_dir} \
-DCMAKE_CXX_FLAGS_RELEASE="${SIRIUS_OPT}" \
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO="${SIRIUS_DBG}" \
-DCMAKE_CUDA_FLAGS="-std=c++14 -allow-unsupported-compiler" \
-DUSE_CUDA=ON \
-DUSE_ELPA=OFF \
-DGPU_MODEL=P100 \
-DUSE_MEMORY_POOL=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_CXX_COMPILER="${MPICXX}" \
-DCMAKE_C_COMPILER="${MPICC}" \
-DCMAKE_Fortran_COMPILER="${MPIFC}" \
${EXTRA_CMAKE_FLAGS} .. \
>> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) -C src >> make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/cuda
install -d ${pkg_install_dir}/include/cuda
install -m 644 src/*.a ${pkg_install_dir}/lib/cuda >> install.log 2>&1
install -m 644 src/mod_files/*.mod ${pkg_install_dir}/include/cuda >> install.log 2>&1
SIRIUS_CUDA_LDFLAGS="-L'${pkg_install_dir}/lib/cuda' -Wl,-rpath,'${pkg_install_dir}/lib/cuda'"
cd ..
fi
SIRIUS_CFLAGS="-I'${pkg_install_dir}/include/cuda'"
SIRIUS_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage8/$(basename ${SCRIPT_NAME})"
fi
;;
__SYSTEM__)
require_env FFTW_LDFLAGS
require_env FFTW_LIBS
require_env FFTW_CFLAGS
require_env ELPA_ROOT
require_env ELPA_LDFLAGS
require_env ELPA_LIBS
require_env ELPA_CFLAGS
require_env GSL_LDFLAGS
require_env GSL_CFLAGS
require_env GSL_LIBS
require_env MATH_LIBS
require_env MPI_LDFLAGS
require_env MPI_LIBS
require_env SCALAPACK_ROOT
require_env SCALAPACK_LDFLAGS
require_env SCALAPACK_CFLAGS
require_env SCALAPACK_LIBS
require_env LIBXC_LIBS
require_env LIBXC_CFLAGS
require_env LIBXC_LDFLAGS
require_env SPGLIB_LIBS
require_env SPGLIB_CFLAGS
require_env SPGLIB_LDFLAGS
require_env HDF5_LIBS
require_env HDF5_CFLAGS
require_env HDF5_LDFLAGS
require_env LIBVDWXC_CFLAGS
require_env LIBVDWXC_LDFLAGS
require_env LIBVDWXC_LIBS
require_env SPFFT_ROOT
require_env SPFFT_CFLAGS
require_env SPFFT_LDFLAGS
require_env SPFFT_LIBS
require_env SPLA_ROOT
require_env SPLA_CFLAGS
require_env SPLA_LDFLAGS
require_env SPLA_LIBS
check_lib -lsirius "sirius"
add_include_from_paths SIRIUS_CFLAGS "sirius*" $INCLUDE_PATHS
add_lib_from_paths SIRIUS_LDFLAGS "libsirius.*" $LIB_PATHS
;;
*)
echo "==================== Linking SIRIUS_Dist to user paths ===================="
pkg_install_dir="$with_sirius"
check_dir "${pkg_install_dir}/lib"
check_dir "${pkg_install_dir}/lib64"
check_dir "${pkg_install_dir}/include"
;;
esac
if [ "$with_sirius" != "__DONTUSE__" ]; then
SIRIUS_LIBS="-lsirius IF_CUDA(-lcusolver|)"
SIRIUS_CUDA_LDFLAGS="-L'${pkg_install_dir}/lib/cuda' -Wl,-rpath,'${pkg_install_dir}/lib/cuda'"
SIRIUS_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
SIRIUS_CFLAGS="-I'${pkg_install_dir}/include'"
if [ "$with_sirius" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_sirius"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib/cuda"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib/cuda"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib/cuda"
prepend_path CPATH "$pkg_install_dir/include"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
cat "${BUILDDIR}/setup_sirius" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_sirius"
export SIRIUS_CFLAGS="IF_CUDA(-I${pkg_install_dir}/include/cuda|-I${pkg_install_dir}/include)"
export SIRIUS_FFLAGS="IF_CUDA(-I${pkg_install_dir}/include/cuda|-I${pkg_install_dir}/include)"
export SIRIUS_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
export SIRIUS_CUDA_LDFLAGS="-L'${pkg_install_dir}/lib/cuda' -Wl,-rpath,'${pkg_install_dir}/lib/cuda'"
export SIRIUS_LIBS="${SIRIUS_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI("-D__SIRIUS"|)"
export CP_CFLAGS="\${CP_CFLAGS} IF_MPI("\${SIRIUS_CFLAGS}"|)"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_MPI(IF_CUDA("\${SIRIUS_CUDA_LDFLAGS}"|"\${SIRIUS_LDFLAGS}")|)"
export CP_LIBS="IF_MPI("\${SIRIUS_LIBS}"|) \${CP_LIBS}"
EOF
cat << EOF >> ${INSTALLDIR}/lsan.supp
# leaks related to SIRIUS
leak:cublasXtDeviceSelect
leak:sirius::sirius_free_object_handler
leak:sirius::sddk::memory_pool::free
leak:sirius::sddk::memory_block_descriptor::free_subblock
EOF
fi
load "${BUILDDIR}/setup_sirius"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "sirius"

205
scripts/stage8/install_spfft.sh
View file

@ -1,205 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
spfft_ver="1.0.6"
spfft_sha256="d179ccdce65890587d0cbf72dc2e5ec0b200ffc56e723ed01a2f5063de6a8630"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_SpFFT" ] && rm "${BUILDDIR}/setup_SpFFT"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_spfft}" in
__INSTALL__)
echo "==================== Installing spfft ===================="
pkg_install_dir="${INSTALLDIR}/SpFFT/${spfft_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "SpFFT-${spfft_ver} is already installed, skipping it."
else
if [ -f SpFFT-${spfft_ver}.tar.gz ]; then
echo "SpFFT-${spfft_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${spfft_sha256}" "SpFFT-${spfft_ver}.tar.gz"
fi
if [ "${MATH_MODE}" = "mkl" ]; then
EXTRA_CMAKE_FLAGS="-DSPFFT_MKL=ON -DSPFFT_FFTW_LIB=MKL"
else
EXTRA_CMAKE_FLAGS=""
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d SpFFT-${spfft_ver} ] && rm -rf SpFFT-${spfft_ver}
tar -xzf SpFFT-${spfft_ver}.tar.gz
cd SpFFT-${spfft_ver}
mkdir build-cpu
cd build-cpu
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_CXX_COMPILER="${MPICXX}" \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPFFT_OMP=ON \
-DSPFFT_MPI=ON \
-DSPFFT_STATIC=ON \
-DSPFFT_FORTRAN=ON \
-DSPFFT_INSTALL=ON \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_CXX_COMPILER="${MPICXX}" \
-DCMAKE_CUDA_FLAGS="-std=c++14 -allow-unsupported-compiler" \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPFFT_OMP=ON \
-DSPFFT_MPI=ON \
-DSPFFT_STATIC=ON \
-DSPFFT_FORTRAN=ON \
-DSPFFT_INSTALL=ON \
-DSPFFT_GPU_BACKEND=CUDA \
${EXTRA_CMAKE_FLAGS} .. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/cuda
[ -f src/libspfft.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/cuda >> install.log 2>&1
[ -f src/libspfft.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/cuda >> install.log 2>&1
fi
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage8/$(basename ${SCRIPT_NAME})"
if [ "$ENABLE_HIP" = "__TRUE__" ]; then
case "${GPUVER}" in
K20X | K40 | K80 | P100 | V100 | A100)
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_CXX_COMPILER="${MPICXX}" \
-DCMAKE_CUDA_FLAGS="-std=c++14 -allow-unsupported-compiler" \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPFFT_OMP=ON \
-DSPFFT_MPI=ON \
-DSPFFT_STATIC=ON \
-DSPFFT_FORTRAN=ON \
-DSPFFT_INSTALL=ON \
-DSPFFT_GPU_BACKEND=CUDA \
${EXTRA_CMAKE_FLAGS} .. > cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/cuda
[ -f src/libspfft.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/cuda >> install.log 2>&1
[ -f src/libspfft.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/cuda >> install.log 2>&1
;;
Mi50 | Mi100 | Mi200 | Mi250)
[ -d build-hip ] && rm -rf "build-hip"
mkdir build-hip
cd build-hip
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPLA_OMP=ON \
-DSPLA_FORTRAN=ON \
-DSPLA_INSTALL=ON \
-DSPLA_STATIC=ON \
-DSPLA_GPU_BACKEND=ROCM \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/rocm
[ -f src/libspla.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/rocm >> install.log 2>&1
[ -f src/libspla.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/rocm >> install.log 2>&1
;;
*) ;;
esac
fi
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage8/$(basename ${SCRIPT_NAME})"
fi
SPFFT_ROOT="${pkg_install_dir}"
SPFFT_CFLAGS="-I'${pkg_install_dir}/include'"
SPFFT_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
SPFFT_CUDA_LDFLAGS="-L'${pkg_install_dir}/lib/cuda' -Wl,-rpath,'${pkg_install_dir}/lib/cuda'"
;;
__SYSTEM__)
echo "==================== Finding spfft from system paths ===================="
check_command pkg-config --modversion spfft
add_include_from_paths SPFFT_CFLAGS "spfft.h" $INCLUDE_PATHS
add_lib_from_paths SPFFT_LDFLAGS "libspfft.*" $LIB_PATHS
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking spfft to user paths ===================="
pkg_install_dir="$with_spfft"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
SPFFT_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && SPFFT_LIBDIR="${pkg_install_dir}/lib64"
check_dir "${SPFFT_LIBDIR}"
check_dir "${pkg_install_dir}/include"
SPFFT_CFLAGS="-I'${pkg_install_dir}/include'"
SPFFT_LDFLAGS="-L'${SPFFT_LIBDIR}' -Wl,-rpath,'${SPFFT_LIBDIR}'"
;;
esac
if [ "$with_spfft" != "__DONTUSE__" ]; then
SPFFT_LIBS="-lspfft"
if [ "$with_spfft" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_spfft"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include"
export SPFFT_INCLUDE_DIR="$pkg_install_dir/include"
export SPFFT_LIBS="-lspfft"
export SPFFT_ROOT="${pkg_install_dir}"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_spfft"
export SPFFT_CFLAGS="${SPFFT_CFLAGS}"
export SPFFT_LDFLAGS="${SPFFT_LDFLAGS}"
export SPFFT_CUDA_LDFLAGS="${SPFFT_CUDA_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_MPI(-D__SPFFT|)"
export CP_CFLAGS="\${CP_CFLAGS} ${SPFFT_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_CUDA(${SPFFT_CUDA_LDFLAGS}|${SPFFT_LDFLAGS})"
export SPFFT_LIBRARY="-lspfft"
export SPFFT_ROOT="$pkg_install_dir"
export SPFFT_INCLUDE_DIR="$pkg_install_dir/include"
export SPFFT_VERSION=${spfft-ver}
export CP_LIBS="IF_MPI(${SPFFT_LIBS}|) \${CP_LIBS}"
EOF
cat "${BUILDDIR}/setup_spfft" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_spfft"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "spfft"

217
scripts/stage8/install_spla.sh
View file

@ -1,217 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
spla_ver="1.5.5"
spla_sha256="bc0c366e228344b1b2df55b9ce750d73c1165380e512da5a04d471db126d66ce"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_SpLA" ] && rm "${BUILDDIR}/setup_SpLA"
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "${with_spla}" in
__INSTALL__)
echo "==================== Installing spla ===================="
pkg_install_dir="${INSTALLDIR}/SpLA/${spla_ver}"
install_lock_file="$pkg_install_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "SpLA-${spla_ver} is already installed, skipping it."
else
if [ -f SpLA-${spla_ver}.tar.gz ]; then
echo "SpLA-${spla_ver}.tar.gz is found"
else
download_pkg_from_cp2k_org "${spla_sha256}" "SpLA-${spla_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d SpLA-${spla_ver} ] && rm -rf SpLA-${spla_ver}
tar -xzf SpLA-${spla_ver}.tar.gz
cd spla-${spla_ver}
mkdir -p build-cpu
cd build-cpu
case "${MATH_MODE}" in
cray)
EXTRA_CMAKE_FLAGS="-DSPLA_HOST_BLAS=CRAY_LIBSCI"
;;
mkl)
EXTRA_CMAKE_FLAGS="-DSPLA_HOST_BLAS=MKL"
;;
*)
EXTRA_CMAKE_FLAGS="-DSPLA_HOST_BLAS=AUTO"
;;
esac
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPLA_OMP=OFF \
-DSPLA_FORTRAN=ON \
-DSPLA_INSTALL=ON \
-DSPLA_STATIC=ON \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
make -j $(get_nprocs) install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
cd ..
if [ "$ENABLE_CUDA" = "__TRUE__" ]; then
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPLA_OMP=OFF \
-DSPLA_FORTRAN=ON \
-DSPLA_INSTALL=ON \
-DSPLA_STATIC=ON \
-DSPLA_GPU_BACKEND=CUDA \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/cuda
[ -f src/libspla.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/cuda >> install.log 2>&1
[ -f src/libspla.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/cuda >> install.log 2>&1
fi
if [ "$ENABLE_HIP" = "__TRUE__" ]; then
case "${GPUVER}" in
K20X | K40 | K80 | P100 | V100 | A100)
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
cd build-cuda
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPLA_OMP=OFF \
-DSPLA_FORTRAN=ON \
-DSPLA_INSTALL=ON \
-DSPLA_STATIC=ON \
-DSPLA_GPU_BACKEND=CUDA \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/hip
[ -f src/libspla.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/hip >> install.log 2>&1
[ -f src/libspla.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/hip >> install.log 2>&1
;;
Mi50 | Mi100 | Mi200 | Mi250)
[ -d build-hip ] && rm -rf "build-hip"
mkdir build-hip
cd build-hip
cmake \
-DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-DCMAKE_INSTALL_LIBDIR=lib \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_BUILD_TYPE="RelWithDebInfo" \
-DSPLA_OMP=OFF \
-DSPLA_FORTRAN=ON \
-DSPLA_INSTALL=ON \
-DSPLA_STATIC=ON \
-DSPLA_GPU_BACKEND=ROCM \
${EXTRA_CMAKE_FLAGS} .. \
> cmake.log 2>&1 || tail -n ${LOG_LINES} cmake.log
make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
install -d ${pkg_install_dir}/lib/hip
[ -f src/libspla.a ] && install -m 644 src/*.a ${pkg_install_dir}/lib/hip >> install.log 2>&1
[ -f src/libspla.so ] && install -m 644 src/*.so ${pkg_install_dir}/lib/hip >> install.log 2>&1
;;
*) ;;
esac
fi
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage8/$(basename ${SCRIPT_NAME})"
fi
SPLA_ROOT="${pkg_install_dir}"
SPLA_CFLAGS="-I'${pkg_install_dir}/include/spla'"
SPLA_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
SPLA_CUDA_LDFLAGS="-L'${pkg_install_dir}/lib/cuda' -Wl,-rpath,'${pkg_install_dir}/lib/cuda'"
SPLA_HIP_LDFLAGS="-L'${pkg_install_dir}/lib/hip' -Wl,-rpath,'${pkg_install_dir}/lib/hip'"
;;
__SYSTEM__)
echo "==================== Finding spla from system paths ===================="
check_command pkg-config --modversion spla
add_include_from_paths SPLA_CFLAGS "spla.h" $INCLUDE_PATHS
add_lib_from_paths SPLA_LDFLAGS "libspla.*" $LIB_PATHS
;;
__DONTUSE__)
# Nothing to do
;;
*)
echo "==================== Linking spla to user paths ===================="
pkg_install_dir="$with_spla"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
SPLA_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && SPLA_LIBDIR="${pkg_install_dir}/lib64"
check_dir "${SPLA_LIBDIR}"
check_dir "${pkg_install_dir}/include/spla"
SPLA_CFLAGS="-I'${pkg_install_dir}/include/spla'"
SPLA_LDFLAGS="-L'${SPLA_LIBDIR}' -Wl,-rpath,'${SPLA_LIBDIR}'"
;;
esac
if [ "$with_spla" != "__DONTUSE__" ]; then
SPLA_LIBS="-lspla"
if [ "$with_spla" != "__SYSTEM__" ]; then
cat << EOF > "${BUILDDIR}/setup_spla"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
prepend_path CPATH "$pkg_install_dir/include/spla"
export SPLA_INCLUDE_DIR="$pkg_install_dir/include/spla"
export SPLA_LIBS="-lspla"
export SPLA_ROOT="${pkg_install_dir}"
prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
EOF
fi
cat << EOF >> "${BUILDDIR}/setup_spla"
export SPLA_CFLAGS="${SPLA_CFLAGS}"
export SPLA_LDFLAGS="${SPLA_LDFLAGS}"
export SPLA_CUDA_LDFLAGS="${SPLA_CUDA_LDFLAGS}"
export SPLA_HIP_LDFLAGS="${SPLA_HIP_LDFLAGS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_HIP(-D__OFFLOAD_GEMM|) IF_CUDA(-D__OFFLOAD_GEMM|) ${OFFLOAD_DFLAGS} IF_MPI(-D__SPLA|)"
export CP_CFLAGS="\${CP_CFLAGS} ${SPLA_CFLAGS}"
export SPLA_LIBRARY="-lspla"
export SPLA_ROOT="$pkg_install_dir"
export SPLA_INCLUDE_DIR="$pkg_install_dir/include/spla"
export SPLA_VERSION=${spla-ver}
export CP_LIBS="IF_MPI(${SPLA_LIBS}|) \${CP_LIBS}"
EOF
if [ "$ENABLE_HIP" = "__TRUE__" ]; then
cat << EOF >> "${BUILDDIR}/setup_spla"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_HIP(${SPLA_HIP_LDFLAGS}|${SPLA_LDFLAGS})"
EOF
elif [ "$ENABLE_CUDA" = "__TRUE__" ]; then
cat << EOF >> "${BUILDDIR}/setup_spla"
export CP_LDFLAGS="\${CP_LDFLAGS} IF_CUDA(${SPLA_CUDA_LDFLAGS}|${SPLA_LDFLAGS})"
EOF
else
cat << EOF >> "${BUILDDIR}/setup_spla"
export CP_LDFLAGS="\${CP_LDFLAGS} ${SPLA_LDFLAGS}"
EOF
fi
cat "${BUILDDIR}/setup_spla" >> $SETUPFILE
fi
load "${BUILDDIR}/setup_spla"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "spla"

9
scripts/stage8/install_stage8.sh
View file

@ -1,9 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
./scripts/stage8/install_spfft.sh
./scripts/stage8/install_spla.sh
./scripts/stage8/install_sirius.sh
#EOF

13
scripts/stage8/sirius-7.3.0-cudatoolkit.patch
View file

@ -1,13 +0,0 @@
diff --git a/cmake/cudalibs_target.cmake b/cmake/cudalibs_target.cmake
index 29802dd3..3d4d761b 100644
--- a/cmake/cudalibs_target.cmake
+++ b/cmake/cudalibs_target.cmake
@@ -1,6 +1,5 @@
+find_package(CUDAToolkit REQUIRED)
if (NOT TARGET sirius::cudalibs)
add_library(sirius::cudalibs INTERFACE IMPORTED)
- set_target_properties(sirius::cudalibs PROPERTIES
- INTERFACE_INCLUDE_DIRECTORIES "${CUDA_INCLUDE_DIRS}"
- INTERFACE_LINK_LIBRARIES "${CUDA_LIBRARIES};${CUDA_CUBLAS_LIBRARIES};${CUDA_CUFFT_LIBRARIES};${CUDA_cusolver_LIBRARY}")
+ target_link_libraries(sirius::cudalibs INTERFACE CUDA::cudart CUDA::cublas CUDA::cufft CUDA::cusolver)
endif()

149
scripts/stage9/install_dbcsr.sh
View file

@ -1,149 +0,0 @@
#!/bin/bash -e
# TODO: Review and if possible fix shellcheck errors.
# shellcheck disable=all
[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"
DBCSR_ver="2.5.0"
DBCSR_sha256="e5c545ec16688027537f7865976b905c0783d038ec289e65635e63e961330601"
source "${SCRIPT_DIR}"/common_vars.sh
source "${SCRIPT_DIR}"/tool_kit.sh
source "${SCRIPT_DIR}"/signal_trap.sh
source "${INSTALLDIR}"/toolchain.conf
source "${INSTALLDIR}"/toolchain.env
[ -f "${BUILDDIR}/setup_dbcsr" ] && rm "${BUILDDIR}/setup_dbcsr"
DBCSR_CFLAGS=''
DBCSR_LDFLAGS=''
DBCSR_LIBS=''
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
cd "${BUILDDIR}"
case "$with_dbcsr" in
__INSTALL__)
echo "==================== Installing DBCSR ===================="
#
# to be restored to the right value when this script is included in the toolchain
pkg_install_dir="${INSTALLDIR}/DBCSR/${DBCSR_ver}"
install_lock_file="$pkg_install_dirnstall_dir/install_successful"
if verify_checksums "${install_lock_file}"; then
echo "DBCSR-${DBCSR_ver} is already install_dbcsr.sh installed, skipping it."
else
if [ -f dbcsr-${DBCSR_ver}.tar.gz ]; then
echo "dbcsr-${DBCSR_ver}.tar.gz is found"
else
wget "https://github.com/cp2k/dbcsr/archive/refs/tags/v${DBCSR_ver}.tar.gz" -O "dbcsr-${DBCSR_ver}.tar.gz"
fi
echo "Installing from scratch into ${pkg_install_dir}"
[ -d dbcsr-${DBCSR_ver} ] && rm -rf dbcsr-${DBCSR_ver}
tar xzf dbcsr-${DBCSR_ver}.tar.gz
cd dbcsr-${DBCSR_ver}
COMPILATION_OPTIONS="-DUSE_OPENMP=ON -DBUILD_TESTING=NO -DWITH_EXAMPLES=NO"
[ -d build-cpu ] && rm -rf "build-cpu"
mkdir build-cpu
cd build-cpu
# build compilation option list
if [ "$MPI_MODE" == "no" ]; then
COMPILATION_OPTIONS="${COMPILATION_OPTIONS} -DUSE_MPI=no"
fi
cmake $COMPILATION_OPTIONS -DCMAKE_INSTALL_PREFIX=${pkg_install_dir} ..
make -j $(get_nprocs) > make.log 2>&1
make install > install.log 2>&1
cd ..
if [ "$ENABLE_CUDA" == "__TRUE__" ]; then
[ -d build-cuda ] && rm -rf "build-cuda"
mkdir build-cuda
COMPILATION_OPTIONS="${COMPILATION_OPTIONS} -DCMAKE_INSTALL_PREFIX=${pkg_install_dir}-cuda -DUSE_ACCEL=cuda -DWITH_GPU=P100"
cmake $COMPILATION_OPTIONS ..
make -j $(get_nprocs) > make.log 2>&1
make install > install.log 2>&1
cd ..
fi
if [ "$ENABLE_HIP" == "__TRUE__" ]; then
[ -d build-hip ] && rm -rf "build-hip"
mkdir build-hip
COMPILATION_OPTIONS="${COMPILATION_OPTIONS} -DCMAKE_INSTALL_PREFIX=${pkg_install_dir}-hip -DUSE_ACCEL=hip -DWITH_GPU=Mi250"
cmake $COMPILATION_OPTIONS ..
make -j $(get_nprocs) > make.log 2>&1
make install > install.log 2>&1
cd ..
fi
write_checksums "${install_lock_file}" "${SCRIPT_DIR}/$(basename ${SCRIPT_NAME})"
DBCSR_CFLAGS="-I'${pkg_install_dir}/include'"
DBCSR_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath='${pkg_install_dir}/lib'"
DBCSR_CUDA_CFLAGS="-I'${pkg_install_dir}-cuda/include'"
DBCSR_CUDA_LDFLAGS="-L'${pkg_install_dir}-cuda/lib' -Wl,-rpath='${pkg_install_dir}-cuda/lib'"
DBCSR_HIP_CFLAGS="-I'${pkg_install_dir}-hip/include'"
DBCSR_HIP_LDFLAGS="-L'${pkg_install_dir}-hip/lib' -Wl,-rpath='${pkg_install_dir}-hip/lib'"
fi
;;
__SYSTEM__)
echo "==================== Finding DBCSR from system paths ===================="
check_lib -ldbcsr "dbcsr"
add_include_from_paths DBCSR_CFLAGS "dbcsr.h" $INCLUDE_PATHS
add_lib_from_paths DBCSR_LDFLAGS "dbcsr.*" $LIB_PATHS
;;
__DONTUSE__)
report_error ${LINENO} "It is not possible to compile cp2k without dbcsr"
;;
*)
echo "==================== Linking spfft to user paths ===================="
pkg_install_dir="$with_dbcsr"
# use the lib64 directory if present (multi-abi distros may link lib/ to lib32/ instead)
DBCSR_LIBDIR="${pkg_install_dir}/lib"
[ -d "${pkg_install_dir}/lib64" ] && DBCSR_LIBDIR="${pkg_install_dir}/lib64"
check_dir "${DBCSR_LIBDIR}"
check_dir "${pkg_install_dir}/include"
DBCSR_CFLAGS="-I'${pkg_install_dir}/include'"
DBCSR_LDFLAGS="-L'${DBCSR_LIBDIR}' -Wl,-rpath,'${DBCSR_LIBDIR}'"
;;
esac
if [ "$with_dbcsr" != "__DONTUSE__" ]; then
DBCSR_LIBS="-ldbcsr"
if [ "$with_dbcsr" != "__SYSTEM__" ]; then
if [ "$ENABLE_CUDA" == "__TRUE__" ]; then
pkg_install_dir1="${pkg-install-dir}-cuda"
else
if [ "$ENABLE_HIP" == "__TRUE__" ]; then
pkg_install_dir1="${pkg-install-dir}-hip"
else
pkg_install_dir1="${pkg-install-dir}"
fi
fi
fi
cat << EOF > "${BUILDDIR}/setup_dbcsr"
prepend_path LD_LIBRARY_PATH "$pkg_install_dir1/lib"
prepend_path LD_RUN_PATH "$pkg_install_dir1/lib"
prepend_path LIBRARY_PATH "$pkg_install_dir1/lib"
prepend_path CPATH "$pkg_install_dir1/include"
prepend_path CMAKE_INSTALL_PREFIX "${pkg_install_dir1}"
export DBCSR_ROOT="${pkg_install_dir}"
export DBCSR_HIP_ROOT="${pkg_install_dir}-hip"
export DBCSR_CUDA_ROOT="${pkg_install_dir}-cuda"
EOF
cat "${BUILDDIR}/setup_dbcsr" >> $SETUPFILE
fi
cat << EOF >> "${BUILDDIR}/setup_dbcsr"
export DBCSR_CFLAGS="${DBCSR_CFLAGS}"
export DBCSR_LDFLAGS="IF_CUDA(${DBCSR_CUDA_LDFLAGS}|IF_HIP(${DBCSR_HIP_LDFLAGS}|${DBCSR_LDFLAGS}))"
export DBCSR_LIBS="${DBCSR_LIBS}"
export CP_DFLAGS="\${CP_DFLAGS} IF_CUDA(-D__DBCSR_ACC -D__DBCSR|IF_HIP(-D__DBCSR_ACC -D__DBCSR|-D__DBCSR))"
export CP_CFLAGS="\${CP_CFLAGS} ${DBCSR_CFLAGS}"
export CP_LDFLAGS="\${CP_LDFLAGS} ${DBCSR_LDFLAGS}"
export CP_LIBS="${DBCSR_LIBS} \${CP_LIBS}"
EOF
cat "${BUILDDIR}/setup_dbcsr" >> $SETUPFILE
load "${BUILDDIR}/setup_dbcsr"
write_toolchain_env "${INSTALLDIR}"
cd "${ROOTDIR}"
report_timing "DBCSR"

14
scripts/stage9/install_octave.sh Normal file
View file

@ -0,0 +1,14 @@
#!/bin/bash
OCTAVE_VERSION=8.4.0
wget -c https://mirrors.kernel.org/gnu/octave/octave-${OCTAVE_VERSION}.tar.gz
# wget -c ftp://ftp.gnu.org/gnu/octave/octave-3.6.3.tar.bz2
tar -xvf octave-${OCTAVE_VERSION}.tar.gz
cd octave-${OCTAVE_VERSION}
mkdir build && cd build
# ../configure --help
../configure --prefix=/opt/octave/${OCTAVE_VERSION} --enable-64 --enable-readline --with-blas --with-lapack --with-fftw3 --with-qt --with-magick
make
make check
make install

644
scripts/tool_kit.sh
View file

@ -1,607 +1,37 @@
# A set of tools used in the toolchain installer, intended to be used find_mpi() {
# for MPI, we try to detect system MPI variant
# TODO: Review and if possible fix shellcheck errors. if (command -v mpiexec > /dev/null 2>&1); then
# shellcheck disable=all export MPI_ENABLED = true
# shellcheck shell=bash # check if we are dealing with openmpi, mpich or intelmpi
if (mpiexec --version 2>&1 | grep -s -q "HYDRA"); then
# by sourcing this file inside other scripts. echo "MPI is detected and it appears to be MPICH"
export MPI_MODE="mpich"
SYS_INCLUDE_PATH=${SYS_INCLUDE_PATH:-"/usr/local/include:/usr/include"} # check openmpi version as reported by mpiexec
SYS_LIB_PATH=${SYS_LIB_PATH:-"/usr/local/lib64:/usr/local/lib:/usr/lib64:/usr/lib:/lib64:/lib"} export MPI_VERSION=$(mpiexec --version | grep "Version:" | awk '{print $2}')
INCLUDE_PATHS=${INCLUDE_PATHS:-"CPATH SYS_INCLUDE_PATH"} with_mpich="__SYSTEM__"
LIB_PATHS=${LIB_PATHS:-"LIBRARY_PATH LD_LIBRARY_PATH LD_RUN_PATH SYS_LIB_PATH"} elif (mpiexec --version 2>&1 | grep -s -q "OpenRTE"); then
time_start=$(date +%s) echo "MPI is detected and it appears to be OpenMPI"
export MPI_MODE="openmpi"
# report timing # check openmpi version as reported by mpiexec
report_timing() { export MPI_VERSION=$(mpiexec --version 2>&1 | grep "(Open MPI)" | awk '{print $4}')
time_stop=$(date +%s) with_openmpi="__SYSTEM__"
printf "Step %s took %0.2f seconds.\n" $1 $((time_stop - time_start)) elif (mpiexec --version 2>&1 | grep -s -q "Intel"); then
} echo "MPI is detected and it appears to be Intel MPI"
export MPI_MODE="intelmpi"
# report a warning message with script name and line number # check intelmpi version as reported by mpiicc
report_warning() { export MPI_VERSION=$(mpiexec --version | grep "Version" | awk '{print $8"."$10}')
if [ $# -gt 1 ]; then with_intelmpi="__SYSTEM__"
local __lineno=", line $1" else # default to mpich
local __message="$2" echo "MPI is detected and defaults to MPICH"
else export MPI_MODE="mpich"
local __lineno='' with_mpich="__SYSTEM__"
local __message="$1"
fi
echo "WARNING: (${SCRIPT_NAME}${__lineno}) $__message" >&2
}
# report an error message with script name and line number
report_error() {
if [ $# -gt 1 ]; then
local __lineno=", line $1"
local __message="$2"
else
local __lineno=''
local __message="$1"
fi
echo "ERROR: (${SCRIPT_NAME}${__lineno}) $__message" >&2
}
# error handler for line trap from set -e
error_handler() {
local __lineno="$1"
report_error $1 "Non-zero exit code detected."
exit 1
}
# source a file if it exists, otherwise do nothing
load() {
if [ -f "$1" ]; then
source "$1"
fi
}
# A more portable command that will give the full path, removing
# symlinks, of a given path. This is more portable than readlink -f
# which does not work on Mac OS X
realpath() {
local __path="$1"
if [ "x$__path" = x ]; then
return 0
fi
local __basename=$(basename "$__path")
if [ -e "$__path" ]; then
echo $(
cd "$(dirname "$__path")"
pwd -P
)/"$__basename"
return 0
else
return 1
fi
}
# given a list, outputs a list with duplicated items filtered out
unique() (
# given a list, outputs a list with duplicated items filtered out.
# If -d <delimiter> option exists, then output the list delimited
# by <delimiter>; note that this option does not effect the input.
local __result=''
local __delimiter=' '
local __item=''
if [ "$1" = "-d" ]; then
shift
__delimiter="$1"
shift
fi
# It is essential that we quote $@, which makes it equivalent to
# "$1" "$2" ... So this works if any of the arguments contains
# space. And we use \n to separate the fields in the
# __result for now, so that fields that contain spaces are
# correctly grepped.
for __item in "$@"; do
if [ x"$__result" = x ]; then
__result="${__item}"
# Note that quoting $__result after echo is essential to
# retain the \n in the variable from the output of echo. Also
# remember grep only works on a line by line basis, so if
# items are delimited by newlines, then for grep search it
# should be delimited by ^ and $ (beginning and end of line)
elif ! (echo "$__result" |
grep -s -q -e "^$__item\$"); then
__result="${__result}
${__item}"
fi fi
done
__result="$(echo "$__result" | paste -s -d "$__delimiter" -)"
# quoting $__result below is again essential for correct
# behaviour if IFS is set to be the same $__delimiter in the
# parent shell calling this macro
echo "$__result"
)
# reverse a list
reverse() (
# given a list, output a list with reversed order. If -d
# <delimiter> option exists, then output the list delimited by
# <delimiter>; note that this option does not effect the input.
local __result=''
local __delimiter=' '
local __item=''
if [ "$1" = "-d" ]; then
shift
__delimiter="$1"
shift
fi
for __item in "$@"; do
if [ x"$__result" = x ]; then
__result="$__item"
else
__result="${__item}${__delimiter}${__result}"
fi
done
echo "$__result"
)
# get the number of processes available for compilation
get_nprocs() {
if [ -n "${NPROCS_OVERWRITE}" ]; then
echo ${NPROCS_OVERWRITE} | sed 's/^0*//'
elif $(command -v nproc > /dev/null 2>&1); then
echo $(nproc --all)
elif $(command -v sysctl > /dev/null 2>&1); then
echo $(sysctl -n hw.ncpu)
else else
echo 1 report_warning $LINENO "No MPI installation detected (ignore this message in Cray Linux Environment or when MPI installation was requested)."
export MPI_MODE=""
fi fi
} }
# convert a list of paths to -L<dir> ... used by ld
paths_to_ld() {
# need to define the POSIX default IFS values here, cannot just do
# __ifs=$IFS first, because IFS can be unset, and if so __ifs will
# becomes an empty string (null) and NOT unset, so later when IFS
# is set to __ifs it becomes null rather than unset, and thus
# causing wrong behaviour. So if IFS is unset, __ifs should be
# the POSIX default value. Further more, due to shell
# automatically remove the tailing "\n" in a string during
# variable assignment, we need to add x after \n and then remove
# it.
local __paths=$@
local __name=''
local __raw_path=''
local __dir=''
local __lib_dirs=''
# set default IFS first
local __ifs=$(printf " \t\nx")
__ifs="${__ifs%x}"
[ "$IFS" ] && __ifs="$IFS"
for __name in $__paths; do
eval __raw_path=\$"$__name"
# change internal field separator to :
IFS=':'
# loop over all dirs in path, and filter out duplications
for __dir in $__raw_path; do
if ! [ x"$__dir" = x ]; then
if ! [[ "$__lib_dirs" =~ (^|[[:space:]])"-L'$__dir'"($|[[:space:]]) ]]; then
__lib_dirs="$__lib_dirs -L'$__dir'"
fi
fi
done
IFS="$__ifs"
done
echo $__lib_dirs
}
# Find a file from directories given in a list of paths, each has the
# same format as env variable PATH. If the file is found, then echoes
# the full path of the file. If the file is not found, then echoes
# __FALSE__. The file name can also contain wildcards that are
# acceptable for bash, and in that case the full path of the first
# matching file will be echoed.
find_in_paths() {
local __target=$1
shift
local __paths=$@
local __name=''
local __raw_path=''
local __dir=''
local __file=''
local __files=''
# use the IFS variable to take care of possible spaces in file/dir names
local __ifs="$(printf " \t\nx")"
__ifs="${__ifs%x}"
[ "$IFS" ] && __ifs="$IFS"
for __name in $__paths; do
eval __raw_path=\$"$__name"
# fields in paths are separated by :
IFS=':'
for __dir in $__raw_path; do
# files in possible glob expansion are to be delimited by "\n\b"
IFS="$(printf "\nx")"
IFS="${IFS%x}"
for __file in $__dir/$__target; do
if [ -e "$__file" ]; then
echo $(realpath "$__file")
# must remember to change IFS back when exiting
IFS="$__ifs"
return 0
fi
done
IFS=':'
done
IFS=$__ifs
done
echo "__FALSE__"
}
# search through a list of given paths, try to find the required file
# or directory, and if found then add full path of dirname file, or
# directory, to the -I include list for CFLAGS and append to a user
# specified variable (__cflags_name). If not found, then nothing is
# done. If the option -p is present, then if the search target is a
# directory, then the parent directory of the directory is used for -I
# instead. The search target accepts bash wildcards, and in this case
# the first match will be used.
add_include_from_paths() {
local __parent_dir_only=false
if [ $1 = "-p" ]; then
__parent_dir_only=true
shift
fi
local __cflags_name=$1
shift
local __search_target=$1
shift
local __paths=$@
local __found_target=""
local __cflags=""
__found_target="$(find_in_paths "$__search_target" \
$__paths)"
if [ "$__found_target" != "__FALSE__" ]; then
if [ -f "$__found_target" ] || $__parent_dir_only; then
__found_target="$(dirname "$__found_target")"
fi
echo "Found include directory $__found_target"
eval __cflags=\$"${__cflags_name}"
__cflags="${__cflags} -I'${__found_target}'"
# remove possible duplicates
__cflags="$(unique $__cflags)"
# must escape all quotes again before the last eval, as
# otherwise all quotes gets interpreted by the shell when
# assigning to variable because eval will reduce one escape
# level
__cflags="${__cflags//'/\\'/}"
eval $__cflags_name=\"$__cflags\"
fi
}
# search through a list of given paths, try to find the required file
# or directory, and if found then add full path of dirname file, or
# directory, to the -L library list (including -Wl,-rpath) for LDFLAGS
# and append to a user specified variable (__ldflags_name). If not
# found, then nothing is done. If the option -p is present, then if
# the search target is a directory, then the parent directory of the
# directory is used for -L instead. The search target accepts bash
# wildcards, and in this case the first match will be used.
add_lib_from_paths() {
local __parent_dir_only=false
if [ $1 = "-p" ]; then
__parent_dir_only=true
shift
fi
local __ldflags_name=$1
shift
local __search_target=$1
shift
local __paths=$@
local __found_target=""
local __ldflags=""
__found_target="$(find_in_paths "$__search_target" \
$__paths)"
if [ "$__found_target" != "__FALSE__" ]; then
if [ -f "$__found_target" ] || $__parent_dir_only; then
__found_target="$(dirname "$__found_target")"
fi
echo "Found lib directory $__found_target"
eval __ldflags=\$"${__ldflags_name}"
__ldflags="${__ldflags} -L'${__found_target}' -Wl,-rpath,'${__found_target}'"
# remove possible duplicates
__ldflags="$(unique $__ldflags)"
# must escape all quotes again before the last eval, as
# otherwise all quotes gets interpreted by the shell when
# assigning to variable because eval will reduce one escape
# level
__ldflags="${__ldflags//'/\\'/}"
eval $__ldflags_name=\"$__ldflags\"
fi
}
# check if environment variable is assigned and non-empty
# https://serverfault.com/questions/7503/how-to-determine-if-a-bash-variable-is-empty
require_env() {
local __env_var_name=$1
local __env_var="$(eval echo \"\$$__env_var_name\")"
if [ -z "${__env_var+set}" ]; then
report_error "requires environment variable $__env_var_name to work"
return 1
fi
}
resolve_string() {
local __to_resolve=$1
shift
local __flags=$@
echo $("${SCRIPTDIR}/parse_if.py" $__flags <<< "${__to_resolve}")
}
# check if a command is available
check_command() {
local __command=${1}
if [ $# -eq 1 ]; then
local __package=${1}
elif [ $# -gt 1 ]; then
local __package=${2}
fi
if $(command -v ${__command} > /dev/null 2>&1); then
echo "path to ${__command} is $(realpath $(command -v ${__command}))"
else
report_error "Cannot find ${__command}, please check if the package ${__package} is installed or in system search path"
return 1
fi
}
# check if directory exists
check_dir() {
local __dir=$1
if [ -d "$__dir" ]; then
echo "Found directory $__dir"
else
report_error "Cannot find $__dir"
return 1
fi
}
# check if a command has been installed correctly
check_install() {
local __command=${1}
if [ $# -eq 1 ]; then
local __package=${1}
elif [ $# -gt 1 ]; then
local __package=${2}
fi
if $(command -v ${__command} > /dev/null 2>&1); then
echo "$(basename ${__command}) is installed as $(command -v ${__command})"
else
report_error "cannot find ${__command}, please check if the package ${__package} has been installed correctly"
return 1
fi
}
# check if a library can be found by ld, library names should in the
# format -lname, which would then referred to libname.a or libname.so
# by ld
check_lib() {
local __libname="${1#-l}"
if [ $# -eq 1 ]; then
local __package=lib"$__libname"
elif [ $# -gt 1 ]; then
local __package=$2
fi
# Note that LD_LIBRARY_PATH is NOT used by ld during linking
# stage, and is only used for searching to the shared libraries
# required by the executable AFTER it has already been compiled, to
# override its internal search paths built into the binary when it
# was compiled. Here, we explicitly include the commonly defined
# library search paths---including LD_LIBRARY_PATH---in the -L
# search paths of ld. This is the only way ld can include
# non-standard directories in its search path. If we use gcc
# instead of ld for linker then we can use LIBRARY_PATH, which IS
# used during link stage. However, I think using ld is more
# general, as in most systems LIBRARY_PATH is rarely defined, and
# we would have to rely on gcc.
local __search_engine="ld -o /dev/null"
local __search_paths="$LIB_PATHS"
# convert a list of paths to -L<dir> list used by ld
__search_engine="$__search_engine $(paths_to_ld $__search_paths)"
# needed the eval to interpret the quoted directories correctly (somehow)
if (eval $__search_engine -l$__libname 2>&1 | grep -q -s "\-l$__libname"); then
# if library not found, ld will return error message
# containing the library name
report_error \
"ld cannot find -l$__libname, please check if $__package is installed or in system search path"
return 1
else
# if library is found, then ld will return error message about
# not able to find _start or _main symbol
echo "lib$__libname is found in ld search path"
fi
}
# check if a module is available for the current version of gfortran,
# returns 0 if available and 1 if not
check_gfortran_module() {
local __module_name=$1
local __FC=${FC:-gfortran}
cat << EOF | $__FC -c -o /dev/null -xf95 -ffree-form - > /dev/null 2>&1
PROGRAM check_gfortran_module
USE ${__module_name}
IMPLICIT NONE
PRINT *, "PASS"
END PROGRAM check_gfortran_module
EOF
}
# check if a flag is allowed for the current version of
# gfortran. returns 0 if allowed and 1 if not
check_gfortran_flag() {
local __flag=$1
local __FC=${FC:-gfortran}
# no need to do a full compilation, just -E -cpp would do for
# checking flags
cat << EOF | $__FC -E -cpp $__flag -xf95 -ffree-form - > /dev/null 2>&1
PROGRAM test_code
IMPLICIT NONE
PRINT *, "PASS"
END PROGRAM test_code
EOF
}
# check if a flag is allowed for the current version of
# gcc. returns 0 if allowed and 1 if not
check_gcc_flag() {
local __flag=$1
local __CC=${CC:-gcc}
# no need to do a full compilation, just -E -cpp would do for
# checking flags
cat << EOF | $__CC -E -cpp $__flag -xc - > /dev/null 2>&1
#include <stdio.h>
int main() {
printf("PASS\n");
}
EOF
}
# check if a flag is allowed for the current version of
# g++. returns 0 if allowed and 1 if not
check_gxx_flag() {
local __flag=$1
local __CXX=${CXX:-g++}
# no need to do a full compilation, just -E -cpp would do for
# checking flags
cat << EOF | $__CXX -E -cpp $__flag -xc - > /dev/null 2>&1
#include <stdio.h>
int main() {
printf("PASS\n");
}
EOF
}
# given a list of flags, only print out what is allowed by the current
# version of gfortran
allowed_gfortran_flags() {
local __flags=$@
local __flag=''
local __result=''
for __flag in $__flags; do
if (check_gfortran_flag $__flag); then
[ -z "$__result" ] && __result="$__flag" || __result="$__result $__flag"
fi
done
echo $__result
}
# given a list of flags, only print out what is allowed by the current
# version of gcc
allowed_gcc_flags() {
local __flags=$@
local __flag=''
local __result=''
for __flag in $__flags; do
if (check_gcc_flag $__flag); then
[ -z "$__result" ] && __result="$__flag" || __result="$__result $__flag"
fi
done
echo $__result
}
# given a list of flags, only print out what is allowed by the current
# version of g++
allowed_gxx_flags() {
local __flags=$@
local __flag=''
local __result=''
for __flag in $__flags; do
if (check_gxx_flag $__flag); then
[ -z "$__result" ] && __result="$__flag" || __result="$__result $__flag"
fi
done
echo $__result
}
# remove a directory to a given path
remove_path() {
local __path_name=$1
local __directory=$2
local __path="$(eval echo \$$__path_name)"
# must remove all the middle ones first before treating two ends,
# otherwise there can be cases where not all __directory are
# removed.
__path=${__path//:$__directory:/:}
__path=${__path#$__directory:}
__path=${__path%:$__directory}
__path=$(echo "$__path" | sed "s:^$__directory\$::g")
eval $__path_name=\"$__path\"
export $__path_name
}
# prepend a directory to a given path
prepend_path() {
# prepend directory to $path_name and then export path_name. If
# the directory already exists in path, bring the directory to the
# front of the list.
# $1 is path name
# $2 is directory
remove_path "$1" "$2"
eval $1=\"$2\${$1:+\":\$$1\"}\"
eval export $1
}
# append a directory to a given path
append_path() {
# append directory to $path_name and then export path_name. If
# the directory already exists in path, bring the directory to the
# back of the list.
# $1 is path name
# $2 is directory
remove_path "$1" "$2"
eval $1=\"\${$1:+\"\$$1:\"}$2\"
eval export $1
}
# helper routine for reading --enable=* input options
read_enable() {
local __input_var="${1#*=}"
case $__input_var in
"$1")
# if there is no "=" then treat as "yes"
echo "__TRUE__"
;;
yes)
echo "__TRUE__"
;;
no)
echo "__FALSE__"
;;
*)
echo "__INVALID__"
;;
esac
}
# helper routine for reading --with=* input options
read_with() {
local __input_var="${1#--with*=}"
case $__input_var in
"${1}")
# if there is no "=" then treat as "install"
if [ ${#} -gt 1 ]; then
echo "${2}"
else
echo "__INSTALL__"
fi
;;
install)
echo "__INSTALL__"
;;
system)
echo "__SYSTEM__"
;;
no)
echo "__DONTUSE__"
;;
*)
echo "${__input_var//\~/$HOME}"
;;
esac
}
# helper routine to check integrity of downloaded files # helper routine to check integrity of downloaded files
checksum() { checksum() {
local __filename=$1 local __filename=$1
@ -620,22 +50,6 @@ checksum() {
fi fi
} }
# downloader for the package tars, includes checksum
download_pkg_from_cp2k_org() {
# usage: download_pkg_from_cp2k_org sha256 filename
local __sha256="$1"
local __filename="$2"
local __url="https://www.cp2k.org/static/downloads/$__filename"
# download
echo "wget ${DOWNLOADER_FLAGS} --quiet $__url"
if ! wget ${DOWNLOADER_FLAGS} --quiet $__url; then
report_error "failed to download $__url"
return 1
fi
# checksum
checksum "$__filename" "$__sha256"
}
# verify the checksums inside the given checksum file # verify the checksums inside the given checksum file
verify_checksums() { verify_checksums() {
local __checksum_file=$1 local __checksum_file=$1

81
set_smb_share.sh Normal file
View file

@ -0,0 +1,81 @@
SHARE_DIR=/data/share
## DEBIAN
sudo apt-get install samba smbclient cifs-utils
## CENTOS
sudo yum install samba samba-common samba-client
## Create a directory to share
sudo mkdir -p ${SHARE_DIR}
sudo chmod -R 2770 ${SHARE_DIR}
sudo chown -R nobody:nogroup ${SHARE_DIR}
sudo chcon -t samba_share_t ${SHARE_DIR}
cat << EOF >> /etc/samba/smb.conf.bkp
[global]
interfaces = 10.0.0.0/24 eth0
# hosts allow = 127.0.0.1/8 192.168.1.0/24
workgroup = WORKGROUP
server string = Samba Server %v
netbios name = MYSHARES
# security = user
unix password sync = Yes
passwd program = /usr/bin/passwd %u
map to guest = bad user
dns proxy = no
[share]
path = ${SHARE_DIR}
available = yes
valid users = ${USER}
read only = no
browsable = yes
public = no
writable = yes
[Public]
comment = Public Folder
path = ${SHARE_DIR}/public
writable = yes
guest ok = yes
guest only = yes
force create mode = 770
force directory mode = 770
[Private]
comment = Private Folder
path = ${SHARE_DIR}
writable = yes
guest ok = no
valid users = @smbshare
# force create mode = 660
# force directory mode = 770
inherit permissions = yes
EOF
sudo testparm /etc/samba/smb.conf.bkp
## IF EXECUTION WORKS, THEN MOVE THE FILE TO THE ORIGINAL PATH
sudo mv /etc/samba/smb.conf.bkp /etc/samba/smb.conf
sudo useradd -M -s /sbin/nologin sambauser
sudo usermod -aG smbshare sambauser
sudo smbpasswd -a sambauser
sudo smbpasswd -e sambauser
## DEBIAN
sudo systemctl restart nmbd
sudo systemctl restart smbd
sudo ufw allow from 192.168.205.0/24 to any app Samba
## CENTOS
sudo firewall-cmd --add-service=samba --zone=public --permanent
sudo firewall-cmd --reload
sudo systemctl start smb
sudo systemctl enable smb
sudo systemctl status smb
sudo systemctl start nmb
sudo systemctl enable nmb
sudo systemctl status nmb