From 8945a8922f18939e377a8fa16f291c1beea8605a Mon Sep 17 00:00:00 2001
From: Adam Parler <adamparler@aol.com>
Date: Tue, 2 Jan 2024 02:03:55 -0500
Subject: [PATCH] Added files to create SMB share and basic scientific
 computing environment

---
 make_cluster.sh  | 338 +++++++++++++++++++++++++++++++++++++++++++++++
 set_smb_share.sh |  81 ++++++++++++
 2 files changed, 419 insertions(+)
 create mode 100644 make_cluster.sh
 create mode 100644 set_smb_share.sh

diff --git a/make_cluster.sh b/make_cluster.sh
new file mode 100644
index 0000000..0778489
--- /dev/null
+++ b/make_cluster.sh
@@ -0,0 +1,338 @@
+#!/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: ${INSTALL_LOCATION}"
+else
+    echo "This script is not the top-level bash file being run."
+fi
+
+## INSTALL GCC FROM SOURCE
+GCC_BUILD_DIR=${BUILD_LOCATION}/gcc
+GCC_INSTALL_DIR=${INSTALL_LOCATION}/gcc
+mkdir -p ${GCC_INSTALL_DIR}
+
+GCC_VERSION=7.5.0
+cd ${GCC_BUILD_DIR}
+mkdir gcc-${GCC_VERSION}-build
+
+wget https://ftp.gnu.org/gnu/gcc/gcc-${GCC_VERSION}/gcc-${GCC_VERSION}.tar.gz
+tar -xf gcc-${GCC_VERSION}.tar.gz
+mv gcc-${GCC_VERSION} gcc-${GCC_VERSION}-source
+cd gcc-${GCC_VERSION}-source
+./contrib/download_prerequisites
+cd ../gcc-${GCC_VERSION}-build
+${GCC_BUILD_DIR}/gcc-${GCC_VERSION}-source/configure --prefix=${GCC_INSTALL_DIR}/${GCC_VERSION} --enable-languages=c,c++,fortran,go --disable-multilib --enable-bootstrap --enable-lto --enable-plugins
+make -j$(nproc)
+make install
+
+## INSTALL ENVIRONMENT MODULES FROM SOURCE
+MODULES_BUILD_DIR=${BUILD_LOCATION}
+MODULES_INSTALL_DIR=${INSTALL_LOCATION}/modules
+mkdir -p ${MODULES_INSTALL_DIR}
+
+cd ${MODULES_BUILD_DIR}
+MODULES_VERSION=5.3.1
+
+curl -LJO https://github.com/cea-hpc/modules/releases/download/v${MODULES_VERSION}/modules-${MODULES_VERSION}.tar.gz
+tar xfz modules-${MODULES_VERSION}.tar.gz
+cd modules-${MODULES_VERSION}
+
+mkdir build && cd build
+./configure --prefix=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION} --modulefilesdir=${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/modulefiles
+make -j$(nproc)
+make install
+ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.sh /etc/profile.d/modules.sh
+ln -s ${MODULES_INSTALL_DIR}/Modules/${MODULES_VERSION}/init/profile.csh /etc/profile.d/modules.csh
+
+## INSTALL OPENSSL FOR CMAKE
+SSL_BUILD_DIR=${BUILD_LOCATION}/openssl
+SSL_INSTALL_DIR=${INSTALL_LOCATION}/openssl
+mkdir -p ${SSL_BUILD_DIR}
+mkdir -p ${SSL_INSTALL_DIR}
+
+SSL_VERSION=1.1.1w
+
+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
+
+## INSTALL Qt FOR CMAKE-GUI
+QT_BUILD_DIR=${BUILD_LOCATION}/qt
+QT_INSTALL_DIR=${INSTALL_LOCATION}/qt
+mkdir -p ${QT_BUILD_DIR}
+mkdir -p ${QT_INSTALL_DIR}
+
+## SOME COMBINATION WILL INSTALL GL
+install build-essential libgl1-mesa-dev libglu1-mesa-dev libglut-dev libgl2-mesa-dev libdrm-dev
+
+QT_VERSION=5.15.12
+QT_MAJOR_VERSION=$(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
+
+## INSTALL CMAKE FROM SOURCE
+CMAKE_BUILD_DIR=${BUILD_LOCATION}/cmake
+CMAKE_INSTALL_DIR=${INSTALL_LOCATION}/cmake
+mkdir -p ${CMAKE_BUILD_DIR}
+mkdir -p ${CMAKE_INSTALL_DIR}
+
+VERSIONS=(3.5.2
+3.12.4
+3.17.5
+3.21.3
+3.24.4
+3.28.1)
+
+OPENSSL_ROOT_DIR=${SSL_INSTALL_DIR}/${SSL_VERSION}
+for CMAKE_VERSION in "${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
+
+../configure --prefix=${CMAKE_INSTALL_DIR}/${CMAKE_VERSION} --parallel=$(nproc)
+make -j$(nproc)
+make install
+done
+
+## 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}
+
+cd ${GIT_BUILD_DIR}
+GIT_VERSION=2.11.3
+wget -c https://mirrors.edge.kernel.org/pub/software/scm/git/git-${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$(nproc)
+make test
+make install
+
+## INSTALL LLVM FROM SOURCE
+LLVM_BUILD_DIR=${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
+
+module load gcc/${GCC_VERSION} cmake/${CMAKE_VERSION}
+
+## INSTALL OPENMPI FROM SOURCE
+
+if [ $(command -v srun) ]; then
+    echo "Slurm installation found. OpenMPI will be configured with --with-pmi."
+    EXTRA_CONFIGURE_FLAGS="--with-pmi"
+else
+    EXTRA_CONFIGURE_FLAGS=""
+fi
+
+./configure CFLAGS="${CFLAGS}" \
+        --prefix=${pkg_install_dir} \
+        --libdir="${pkg_install_dir}/lib" \
+        --enable-mpi1-compatibility \
+        ${EXTRA_CONFIGURE_FLAGS}
+
+## INSTALL MPICH FROM SOURCE
+
+
+./configure \
+        --prefix="${pkg_install_dir}" \
+        MPICC="" \
+        FFLAGS="${FCFLAGS} ${compat_flag}" \
+        FCFLAGS="${FCFLAGS} ${compat_flag}" \
+        --without-x \
+        --enable-gl=no \
+        --with-device=${MPICH_DEVICE} \
+
+make -j$(nproc)
+make install
+
+
+MPIRUN="${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 ${OPENBLAS_BUILD_DIR}
+wget -c openblas
+tar -xf openblas-${OPENBLAS_VERSION}.tar.gz
+cd openblas-${OPENBLAS_VERSION}
+make -j$(nproc)
+make install PREFIX=${OPENBLAS_INSTALL_DIR}/${OPENBLAS_VERSION}
+
+## INSTALL LAPACK FROM SOURCE
+LAPACK_BUILD_DIR=${BUILD_LOCATION}/lapack
+LAPACK_INSTALL_DIR=${INSTALL_LOCATION}/lapack
+mkdir -p ${LAPACK_BUILD_DIR}
+mkdir -p ${LAPACK_INSTALL_DIR}
+
+LAPACK_VERSION=3.10.0
+
+## INSTALL HDF5 FROM SOURCE
+module load gcc/8.1.0 openmpi/4.1.4 cmake/3.21.3
+
+# Check if MPI is enabled
+if [ -n "$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 .
+
+
+
+
+
+
+
+
+
+
diff --git a/set_smb_share.sh b/set_smb_share.sh
new file mode 100644
index 0000000..d9fbb2c
--- /dev/null
+++ b/set_smb_share.sh
@@ -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
\ No newline at end of file