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Spack: HDF 1.14.6 -> 2.1.0

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This commit is contained in:
Matthias Krack 2026-03-12 17:30:11 +01:00
parent 039bc03734
commit 212c5a64b9
14 changed files with 1189 additions and 3 deletions
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2
tools/spack/cp2k_deps_p.yaml
View file

@ -189,7 +189,7 @@ spack:
- "elpa@2025.06.001"
- "fftw@3.3.10"
- "greenx@2.2"
- "hdf5@1.14.6"
- "hdf5@2.1.0"
- "libfabric@2.4.0"
- "libint@2.13.1-cp2k-lmax-5"
- "libsmeagol@1.2"

2
tools/spack/cp2k_deps_s-static.yaml
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@ -100,7 +100,7 @@ spack:
- "dbcsr@2.9.1"
- "dftd4@3.7.0"
- "fftw@3.3.10"
# - "hdf5@1.14.6"
# - "hdf5@2.1.0"
- "libint@2.13.1-cp2k-lmax-5"
- "libvori@220621"
- "libxc@7.0.0"

2
tools/spack/cp2k_deps_s.yaml
View file

@ -115,7 +115,7 @@ spack:
- "dftd4@3.7.0"
- "fftw@3.3.10"
- "greenx@2.2"
- "hdf5@1.14.6"
- "hdf5@2.1.0"
- "libint@2.13.1-cp2k-lmax-5"
- "libvori@220621"
- "libxc@7.0.0"

12
tools/spack/spack_repo/cp2k_dev/packages/hdf5/find_package_zlib.patch Normal file
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@ -0,0 +1,12 @@
diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
index dbd68fd110..3d06b13d57 100644
--- a/CMakeFilters.cmake
+++ b/CMakeFilters.cmake
@@ -70,7 +70,6 @@ option (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
if (HDF5_ENABLE_Z_LIB_SUPPORT)
if (NOT H5_ZLIB_HEADER)
if (NOT ZLIB_USE_EXTERNAL)
- find_package (ZLIB NAMES ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
if (NOT ZLIB_FOUND)
find_package (ZLIB) # Legacy find
endif ()

24
tools/spack/spack_repo/cp2k_dev/packages/hdf5/fortran-kinds-2.patch Normal file
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@ -0,0 +1,24 @@
From 598df49b738fd99df9f2671e4e967fd9c33ae8a9 Mon Sep 17 00:00:00 2001
From: Seth R Johnson <johnsonsr@ornl.gov>
Date: Wed, 16 Feb 2022 20:38:03 -0500
Subject: [PATCH] Close file to work around GCC11.2/macOS12 bug
---
m4/aclocal_fc.f90 | 1 +
1 file changed, 1 insertion(+)
diff --git a/m4/aclocal_fc.f90 b/m4/aclocal_fc.f90
index e9a11c0ab5..bfda49aa40 100644
--- a/m4/aclocal_fc.f90
+++ b/m4/aclocal_fc.f90
@@ -151,6 +151,7 @@ PROGRAM FC_AVAIL_KINDS
WRITE(8,'(I0)') max_decimal_prec
WRITE(8,'(I0)') num_ikinds
WRITE(8,'(I0)') num_rkinds
+ CLOSE(8)
END PROGRAM FC_AVAIL_KINDS
!---- END ----- Determine the available KINDs for REALs and INTEGERs
--
2.32.0

20
tools/spack/spack_repo/cp2k_dev/packages/hdf5/fortran-kinds.patch Normal file
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@ -0,0 +1,20 @@
--- a/config/cmake/HDF5UseFortran.cmake
+++ a/config/cmake/HDF5UseFortran.cmake
@@ -181,6 +181,7 @@
WRITE(8,'(I0)') max_decimal_prec
WRITE(8,'(I0)') num_ikinds
WRITE(8,'(I0)') num_rkinds
+ CLOSE(8)
END PROGRAM FC_AVAIL_KINDS
"
)
--- a/m4/aclocal_fc.f90
+++ b/m4/aclocal_fc.f90
@@ -151,6 +151,7 @@
WRITE(8,'(I0)') max_decimal_prec
WRITE(8,'(I0)') num_ikinds
WRITE(8,'(I0)') num_rkinds
+ CLOSE(8)
END PROGRAM FC_AVAIL_KINDS
!---- END ----- Determine the available KINDs for REALs and INTEGERs

16
tools/spack/spack_repo/cp2k_dev/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch Normal file
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@ -0,0 +1,16 @@
diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
index dd2b171..629418a 100644
--- a/fortran/src/H5f90global.F90
+++ b/fortran/src/H5f90global.F90
@@ -142,10 +142,7 @@ MODULE H5GLOBAL
INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
- EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
- EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
- EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
- EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
+ ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)

11
tools/spack/spack_repo/cp2k_dev/packages/hdf5/h5public-skip-mpicxx.patch Normal file
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@ -0,0 +1,11 @@
--- a/src/H5public.h 2019-08-28 18:51:39.393781356 -0400
+++ b/src/H5public.h 2019-08-28 20:59:50.315181711 -0400
@@ -57,6 +57,8 @@
# include <stddef.h>
#endif
#ifdef H5_HAVE_PARALLEL
+# define MPICH_SKIP_MPICXX 1
+# define OMPI_SKIP_MPICXX 1
# include <mpi.h>
#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
# include <mpio.h>

12
tools/spack/spack_repo/cp2k_dev/packages/hdf5/hdf5_1.8_gcc10.patch Normal file
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@ -0,0 +1,12 @@
diff -Naur hdf5.orig/fortran/test/tH5T_F03.f90 hdf5/fortran/test/tH5T_F03.f90
--- hdf5.orig/fortran/test/tH5T_F03.f90 2021-01-19 13:23:11.298000000 +0100
+++ hdf5/fortran/test/tH5T_F03.f90 2021-01-19 13:19:17.637000000 +0100
@@ -1541,7 +1541,7 @@
INTEGER :: A, B, C, D
INTEGER :: Aw, Bw, Cw, Dw
INTEGER :: i, j
- INTEGER, PARAMETER :: hex = Z'00000003'
+ INTEGER, PARAMETER :: hex = INT(Z'00000003')
TYPE(C_PTR) :: f_ptr
INTEGER :: error ! Error flag
!

13
tools/spack/spack_repo/cp2k_dev/packages/hdf5/hdf5_1_14_0_config_find_mpi.patch Normal file
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@ -0,0 +1,13 @@
diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
index 35cee4f..b336377 100644
--- a/config/cmake/hdf5-config.cmake.in
+++ b/config/cmake/hdf5-config.cmake.in
@@ -63,6 +63,8 @@ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
set (${HDF5_PACKAGE_NAME}_MPI_Fortran_INCLUDE_PATH "@MPI_Fortran_INCLUDE_DIRS@")
set (${HDF5_PACKAGE_NAME}_MPI_Fortran_LIBRARIES "@MPI_Fortran_LIBRARIES@")
endif ()
+
+ find_package(MPI QUIET REQUIRED)
endif ()
if (${HDF5_PACKAGE_NAME}_BUILD_JAVA)

203
tools/spack/spack_repo/cp2k_dev/packages/hdf5/hdf5_1_14_3_fpe.patch Normal file
View file

@ -0,0 +1,203 @@
diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
index 328f8d3cec..079f08d96c 100644
--- a/config/linux-gnulibc1
+++ b/config/linux-gnulibc1
@@ -173,10 +173,7 @@ case $FC_BASENAME in
nagfor)
F9XSUFFIXFLAG=""
- # NOTE: The default is -ieee=stop, which will cause problems
- # when the H5T module performs floating-point type
- # introspection
- AM_FCFLAGS="$AM_FCFLAGS -ieee=full"
+ AM_FCFLAGS="$AM_FCFLAGS"
FSEARCH_DIRS=""
# Production
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 200576332b..0aa139761d 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -246,6 +246,27 @@ Support for new platforms, languages and compilers
-
+Patches applied since the HDF5-1.14.3 release
+=============================================
+ Library
+ -------
+ - Suppressed floating-point exceptions in H5T init code
+
+ The floating-point datatype initialization code in H5Tinit_float.c
+ could raise FE_INVALID exceptions while munging bits and performing
+ comparisons that might involve NaN. This was not a problem when the
+ initialization code was executed in H5detect at compile time (prior
+ to 1.14.3), but now that the code is executed at library startup
+ (1.14.3+), these exceptions can be caught by user code, as is the
+ default in the NAG Fortran compiler.
+
+ Starting in 1.14.4, we now suppress floating-point exceptions while
+ initializing the floating-point types and clear FE_INVALID before
+ restoring the original environment.
+
+ Fixes GitHub #3831
+
+
Bug Fixes since HDF5-1.14.2 release
===================================
Library
@@ -619,12 +640,6 @@ Known Problems
this release with link errors. As a result, Windows binaries for this release
will not include Fortran. The problem will be addressed in HDF5 1.14.4.
- IEEE standard arithmetic enables software to raise exceptions such as overflow,
- division by zero, and other illegal operations without interrupting or halting
- the program flow. The HDF5 C library intentionally performs these exceptions.
- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program
- to avoid stopping on an exception.
-
CMake files do not behave correctly with paths containing spaces.
Do not use spaces in paths because the required escaping for handling spaces
results in very complex and fragile build files.
diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c
index 3b9e127fe4..02bb3bad77 100644
--- a/src/H5Tinit_float.c
+++ b/src/H5Tinit_float.c
@@ -51,19 +51,23 @@
* Function: DETECT_F
*
* Purpose: This macro takes a floating point type like `double' and
- * a base name like `natd' and detects byte order, mantissa
- * location, exponent location, sign bit location, presence or
- * absence of implicit mantissa bit, and exponent bias and
- * initializes a detected_t structure with those properties.
+ * detects byte order, mantissa location, exponent location,
+ * sign bit location, presence or absence of implicit mantissa
+ * bit, and exponent bias and initializes a detected_t structure
+ * with those properties.
+ *
+ * Note that these operations can raise floating-point
+ * exceptions and building with some compiler options
+ * (especially Fortran) can cause problems.
*-------------------------------------------------------------------------
*/
-#define DETECT_F(TYPE, VAR, INFO) \
+#define DETECT_F(TYPE, INFO) \
do { \
- TYPE _v1, _v2, _v3; \
- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \
- unsigned char _pad_mask[sizeof(TYPE)]; \
- unsigned char _byte_mask; \
- int _i, _j, _last = (-1); \
+ TYPE _v1, _v2, _v3; \
+ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \
+ uint8_t _pad_mask[sizeof(TYPE)]; \
+ uint8_t _byte_mask; \
+ int _i, _j, _last = -1; \
\
memset(&INFO, 0, sizeof(INFO)); \
INFO.size = sizeof(TYPE); \
@@ -81,7 +85,7 @@
_v1 = (TYPE)4.0L; \
H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \
for (_i = 0; _i < (int)sizeof(TYPE); _i++) \
- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \
+ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \
_buf1[_i] ^= _byte_mask; \
H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \
H5_GCC_CLANG_DIAG_OFF("float-equal") \
@@ -118,7 +122,7 @@
_v1 = (TYPE)1.0L; \
_v2 = (TYPE)-1.0L; \
if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \
\
/* Mantissa */ \
INFO.mpos = 0; \
@@ -126,12 +130,11 @@
_v1 = (TYPE)1.0L; \
_v2 = (TYPE)1.5L; \
if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \
INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \
\
/* Exponent */ \
- INFO.epos = INFO.mpos + INFO.msize; \
- \
+ INFO.epos = INFO.mpos + INFO.msize; \
INFO.esize = INFO.sign - INFO.epos; \
\
_v1 = (TYPE)1.0L; \
@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d)
herr_t H5_NO_UBSAN
H5T__init_native_float_types(void)
{
+ fenv_t saved_fenv;
H5T_fpoint_det_t det;
H5T_t *dt = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
+ /* Turn off floating-point exceptions while initializing to avoid
+ * tripping over signaling NaNs while looking at "don't care" bits.
+ */
+ if (feholdexcept(&saved_fenv) != 0)
+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment");
+
/* H5T_NATIVE_FLOAT */
/* Get the type's characteristics */
memset(&det, 0, sizeof(H5T_fpoint_det_t));
- DETECT_F(float, FLOAT, det);
+ DETECT_F(float, det);
/* Allocate and fill type structure */
if (NULL == (dt = H5T__alloc()))
@@ -497,7 +507,7 @@ H5T__init_native_float_types(void)
/* Get the type's characteristics */
memset(&det, 0, sizeof(H5T_fpoint_det_t));
- DETECT_F(double, DOUBLE, det);
+ DETECT_F(double, det);
/* Allocate and fill type structure */
if (NULL == (dt = H5T__alloc()))
@@ -528,7 +538,7 @@ H5T__init_native_float_types(void)
/* Get the type's characteristics */
memset(&det, 0, sizeof(H5T_fpoint_det_t));
- DETECT_F(long double, LDOUBLE, det);
+ DETECT_F(long double, det);
/* Allocate and fill type structure */
if (NULL == (dt = H5T__alloc()))
@@ -561,6 +571,14 @@ H5T__init_native_float_types(void)
H5T_native_order_g = det.order;
done:
+ /* Clear any FE_INVALID exceptions from NaN handling */
+ if (feclearexcept(FE_INVALID) != 0)
+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions");
+
+ /* Restore the original environment */
+ if (feupdateenv(&saved_fenv) != 0)
+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment");
+
if (ret_value < 0) {
if (dt != NULL) {
dt->shared = H5FL_FREE(H5T_shared_t, dt->shared);
diff --git a/src/H5private.h b/src/H5private.h
index 14a0ac3225..3aaa0d5245 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -26,6 +26,7 @@
#include <ctype.h>
#include <errno.h>
#include <fcntl.h>
+#include <fenv.h>
#include <float.h>
#include <math.h>
#include <setjmp.h>

832
tools/spack/spack_repo/cp2k_dev/packages/hdf5/package.py Normal file
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@ -0,0 +1,832 @@
# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import re
import shutil
import sys
from spack_repo.builtin.build_systems.cmake import CMakePackage
from spack.package import *
class Hdf5(CMakePackage):
"""HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data.
"""
homepage = "https://support.hdfgroup.org"
url = "https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz"
git = "https://github.com/HDFGroup/hdf5.git"
maintainers("lrknox", "brtnfld", "byrnHDF", "gheber", "hyoklee", "lkurz")
tags = ["e4s", "windows"]
executables = ["^h5cc$", "^h5pcc$"]
test_requires_compiler = True
license("custom")
# The 'develop' version is renamed so that we could uninstall (or patch) it
# without affecting other develop version.
version("develop-2.0", branch="develop")
version("develop-1.14", branch="hdf5_1_14")
version("develop-1.12", branch="hdf5_1_12")
version("develop-1.10", branch="hdf5_1_10")
version("develop-1.8", branch="hdf5_1_8")
version(
"2.1.0",
sha256="ce7f5515a95d588b8606c3fb50643f8b88ac52ffbbde9c63bb1edca6a256e964",
url="https://support.hdfgroup.org/releases/hdf5/2.1.0/downloads/hdf5-2.1.0.tar.gz",
)
# Odd versions are considered experimental releases
# Even versions are maintenance versions
version(
"1.14.6",
sha256="e4defbac30f50d64e1556374aa49e574417c9e72c6b1de7a4ff88c4b1bea6e9b",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/downloads/hdf5-1.14.6.tar.gz",
preferred=True,
)
version(
"1.14.5",
sha256="ec2e13c52e60f9a01491bb3158cb3778c985697131fc6a342262d32a26e58e44",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz",
)
version(
"1.14.4-3",
sha256="019ac451d9e1cf89c0482ba2a06f07a46166caf23f60fea5ef3c37724a318e03",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/downloads/hdf5-1.14.4-3.tar.gz",
)
version(
"1.14.3",
sha256="09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_3/downloads/hdf5-1.14.3.tar.gz",
)
version(
"1.14.2",
sha256="1c342e634008284a8c2794c8e7608e2eaf26d01d445fb3dfd7f33cb2fb51ac53",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_2/downloads/hdf5-1.14.2.tar.gz",
)
version(
"1.14.1-2",
sha256="cbe93f275d5231df28ced9549253793e40cd2b555e3d288df09d7b89a9967b07",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_1/downloads/hdf5-1.14.1-2.tar.gz",
)
version(
"1.14.0",
sha256="a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_0/downloads/hdf5-1.14.0.tar.gz",
)
version("1.12.3", sha256="c15adf34647918dd48150ea1bd9dffd3b32a3aec5298991d56048cc3d39b4f6f")
version("1.12.2", sha256="2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14")
version("1.12.1", sha256="79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca")
version("1.12.0", sha256="a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a")
version("1.10.11", sha256="341684c5c0976b8c7e6951735a400275a90693604464cac73e9f323c696fc79c")
version("1.10.10", sha256="a6877ab7bd5d769d2d68618fdb54beb50263dcc2a8c157fe7e2186925cdb02db")
version("1.10.9", sha256="f5b77f59b705a755a5a223372d0222c7bc408fe8db6fa8d9d7ecf8bce291b8dd")
version("1.10.8", sha256="d341b80d380dd763753a0ebe22915e11e87aac4e44a084a850646ff934d19c80")
version("1.10.7", sha256="7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15")
version("1.10.6", sha256="5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa")
version("1.10.5", sha256="6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8")
version("1.10.4", sha256="8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2")
version("1.10.3", sha256="b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39")
version("1.10.2", sha256="bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866")
version("1.10.1", sha256="048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172")
version(
"1.10.0-patch1", sha256="6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0"
)
version("1.10.0", sha256="81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a")
version("1.8.23", sha256="37fa4eb6cd0e181eb49a10d54611cb00700e9537f805d03e6853503afe5abc27")
version("1.8.22", sha256="8406d96d9355ef8961d2739fb8fd5474ad4cdf52f3cfac657733defd9709bfaa")
version("1.8.21", sha256="87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37")
version("1.8.19", sha256="a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38")
version("1.8.18", sha256="cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063")
version("1.8.17", sha256="d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263")
version("1.8.16", sha256="ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771")
version("1.8.15", sha256="4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275")
version("1.8.14", sha256="1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639")
version("1.8.13", sha256="82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1")
version("1.8.12", sha256="b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb")
version("1.8.10", sha256="4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a")
variant("shared", default=True, description="Builds a shared version of the library")
variant("hl", default=False, description="Enable the high-level library")
variant("cxx", default=False, description="Enable C++ support")
variant("map", when="@1.14:", default=False, description="Enable MAP API support")
variant(
"subfiling", when="@1.14: +mpi", default=False, description="Enable Subfiling VFD support"
)
variant("fortran", default=False, description="Enable Fortran support")
variant("java", when="@1.10:", default=False, description="Enable Java support")
variant("threadsafe", default=False, description="Enable thread-safe capabilities")
variant("tools", default=True, description="Enable building tools")
variant("mpi", default=True, description="Enable MPI support")
variant("szip", default=False, description="Enable szip support")
# Build HDF5 with API compatibility.
variant(
"api",
default="default",
description="Choose api compatibility for earlier version",
values=("default", "v200", "v114", "v112", "v110", "v18", "v16"),
multi=False,
)
depends_on("c", type="build")
depends_on("cxx", type="build", when="+cxx")
depends_on("fortran", type="build", when="+fortran")
depends_on("cmake@3.12:", type="build")
depends_on("cmake@3.18:", type="build", when="@1.14:")
depends_on("cmake@3.26:", type="build", when="@2.0:")
with when("+mpi"):
depends_on("mpi")
depends_on("mpich+fortran", when="+fortran ^[virtuals=mpi] mpich")
depends_on("java", type=("build", "run"), when="+java")
depends_on("szip", when="+szip")
depends_on("zlib-api")
# See https://github.com/HDFGroup/hdf5/pull/4147
depends_on(
"zlib-ng~new_strategies",
when="@:1.14.3,develop-1.8:develop-1.12 ^[virtuals=zlib-api] zlib-ng",
)
# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
# Skip this on Windows since pkgconfig is autotools
for plat in ["darwin", "linux"]:
depends_on("pkgconfig", when=f"platform={plat}", type="run")
conflicts("+mpi", "^mpich@4.0:4.0.3")
conflicts("api=v200", when="@1.6:1.14", msg="v200 is not compatible with this release")
conflicts(
"api=v200",
when="@develop-1.8:develop-1.14",
msg="v200 is not compatible with this release",
)
conflicts("api=v114", when="@1.6:1.12", msg="v114 is not compatible with this release")
conflicts(
"api=v114",
when="@develop-1.8:develop-1.12",
msg="v114 is not compatible with this release",
)
conflicts("api=v112", when="@1.6:1.10", msg="v112 is not compatible with this release")
conflicts(
"api=v112",
when="@develop-1.8:develop-1.10",
msg="v112 is not compatible with this release",
)
conflicts("api=v110", when="@1.6:1.8", msg="v110 is not compatible with this release")
conflicts("api=v110", when="@develop-1.8", msg="v110 is not compatible with this release")
conflicts("api=v18", when="@1.6", msg="v18 is not compatible with this release")
# The Java wrappers cannot be built without shared libs.
conflicts("+java", when="~shared")
# Fortran fails built with shared for old HDF5 versions
conflicts("+fortran", when="+shared@:1.8.15")
# See https://github.com/spack/spack/issues/31085
conflicts("+fortran+mpi", when="@1.8.22")
# See https://github.com/HDFGroup/hdf5/issues/2906#issue-1697749645
conflicts(
"+fortran", when="@1.13.3:^cmake@:3.22", msg="cmake_minimum_required is not set correctly."
)
# https://github.com/HDFGroup/hdf5/pull/6267
patch(
"https://github.com/HDFGroup/hdf5/commit/84e5adf753cdd97a807df2da6338bb0e0cdf9862.patch",
sha256="f52187754844009d4fbde07a3f885e8ad9bf33abc255edb08b1a659efd03d5ba",
when="@2.1.0",
)
# HDF5 searches for zlib CMake config files before it falls back to
# FindZLIB.cmake. We don't build zlib with CMake by default, so have to
# delete the first search, otherwise it may find a system zlib. See
# https://github.com/HDFGroup/hdf5/issues/4904
patch("find_package_zlib.patch", when="@1.8.16:1.14.4")
# There are several officially unsupported combinations of the features:
# 1. Thread safety is not guaranteed via high-level C-API but in some cases
# it works.
# conflicts('+threadsafe+hl')
# 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's
# possible for a dependency tree to contain a package that uses Fortran
# (CXX) API in a single thread and another one that uses low-level C-API
# in multiple threads. To allow for such scenarios, we don't specify the
# following conflicts.
# conflicts('+threadsafe+cxx')
# conflicts('+threadsafe+fortran')
# 3. Parallel features are not supported via CXX API, but for the reasons
# described in #2 we allow for such combination.
# conflicts('+mpi+cxx')
# Patch needed for HDF5 1.14.3 to fix signaling FPE checks from triggering
# at dynamic type system initialization. The type system's builtin types
# were refactored in 1.14.3 and switched from compile-time to run-time
# initialization. This patch suppresses floating point exception checks
# that would otherwise be triggered by this code. Later HDF5 versions
# will include the patch code changes.
# See https://github.com/HDFGroup/hdf5/pull/3837
patch("hdf5_1_14_3_fpe.patch", when="@1.14.3")
# There are known build failures with intel@18.0.1. This issue is
# discussed and patch is provided at
# https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
patch("h5f90global-mult-obj-same-equivalence-same-common-block.patch", when="@1.10.1%intel@18")
# Turn line comments into block comments to conform with pre-C99 language
# standards. Versions of hdf5 after 1.8.10 don't require this patch,
# either because they conform to pre-C99 or neglect to ask for pre-C99
# language standards from their compiler. The hdf5 build system adds
# the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
# of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
# system does not provide an option to disable -ansi, but since the
# pre-C99 code is restricted to just five lines of line comments in
# three src files, this patch accomplishes the simple task of patching the
# three src files and leaves the hdf5 build system alone.
patch("pre-c99-comments.patch", when="@1.8.10")
# There are build errors with GCC 8, see
# https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
patch(
"https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch",
sha256="57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523",
when="@1.10.2%gcc@8:",
)
# Disable MPI C++ interface when C++ is disabled, otherwise downstream
# libraries fail to link; see https://github.com/spack/spack/issues/12586
patch(
"h5public-skip-mpicxx.patch",
when="@1.8.10:1.8.21,1.10.0:1.10.5+mpi~cxx",
sha256="b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c",
)
# Fixes BOZ literal constant error when compiled with GCC 10.
# The issue is described here: https://github.com/spack/spack/issues/18625
patch(
"hdf5_1.8_gcc10.patch",
when="@:1.8.21",
sha256="0e20187cda3980a4fdff410da92358b63de7ebef2df1d7a425371af78e50f666",
)
patch("fortran-kinds.patch", when="@1.10.7")
# This patch may only be needed with GCC 11.2 on macOS, but it's valid for
# any of the head HDF5 versions as of 12/2021. Since it's impossible to
# tell what Fortran version is part of a mixed apple-clang toolchain on
# macOS (which is the norm), and this might be an issue for other compilers
# as well, we just apply it to all platforms.
# See https://github.com/HDFGroup/hdf5/issues/1157
patch("fortran-kinds-2.patch", when="@1.10.8,1.12.1")
# Patch needed for HDF5 1.14.0 where dependency on MPI::MPI_C was declared
# PUBLIC. Dependent packages using the default hdf5 package but not
# expecting to use MPI then failed to configure because they did not call
# find_package(MPI). This patch does that for them. Later HDF5 versions
# will include the patch code changes.
patch("hdf5_1_14_0_config_find_mpi.patch", when="@1.14.0")
# The argument 'buf_size' of the C function 'h5fget_file_image_c' is
# declared as intent(in) though it is modified by the invocation. As a
# result, aggressive compilers such as Fujitsu's may do a wrong
# optimization to cause an error.
def patch(self):
filter_file(
"INTEGER(SIZE_T), INTENT(IN) :: buf_size",
"INTEGER(SIZE_T), INTENT(OUT) :: buf_size",
"fortran/src/H5Fff.F90",
string=True,
ignore_absent=True,
)
filter_file(
"INTEGER(SIZE_T), INTENT(IN) :: buf_size",
"INTEGER(SIZE_T), INTENT(OUT) :: buf_size",
"fortran/src/H5Fff_F03.f90",
string=True,
ignore_absent=True,
)
if self.run_tests:
# hdf5 has ~2200 CPU-intensive tests, some of them have races:
# Often, these loop endless(at least on one Xeon and one EPYC).
# testphdf5 fails indeterministic. This fixes finishing the tests
filter_file(
"REMOVE_ITEM H5P_TESTS",
"REMOVE_ITEM H5P_TESTS t_bigio t_shapesame testphdf5",
"testpar/CMakeTests.cmake",
)
# The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
# compiler wrappers and do not need to be changed.
# These do not exist on Windows.
# Enable only for supported target platforms.
if sys.platform != "win32":
filter_compiler_wrappers(
"h5cc", "h5hlcc", "h5fc", "h5hlfc", "h5c++", "h5hlc++", relative_root="bin"
)
def url_for_version(self, version):
url = "https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
return url.format(version.up_to(2), version)
def flag_handler(self, name, flags):
spec = self.spec
cmake_flags = []
if name == "cflags":
if (
spec.satisfies("%gcc")
or spec.satisfies("%clang")
or spec.satisfies("%apple-clang")
or spec.satisfies("%oneapi")
):
# Quiet warnings/errors about implicit declaration of functions
# in C99:
cmake_flags.append("-Wno-error=implicit-function-declaration")
# Note that this flag will cause an error if building %nvhpc.
if spec.satisfies("@:1.8.12~shared"):
# More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
# True and build with PIC flags.
cmake_flags.append(self.compiler.cc_pic_flag)
if spec.satisfies("@1.8.21 %oneapi@2023.0.0"):
cmake_flags.append("-Wno-error=int-conversion")
elif name == "cxxflags":
if spec.satisfies("@:1.8.12+cxx~shared"):
cmake_flags.append(self.compiler.cxx_pic_flag)
elif name == "fflags":
if spec.satisfies("+fortran%cce"):
# Cray compiler generates module files with uppercase names by
# default, which is not handled by the CMake scripts. The
# following flag forces the compiler to produce module files
# with lowercase names.
cmake_flags.append("-ef")
if spec.satisfies("@:1.8.12+fortran~shared"):
cmake_flags.append(self.compiler.fc_pic_flag)
elif name == "ldlibs":
if spec.satisfies("+fortran %fj"):
cmake_flags.extend(["-lfj90i", "-lfj90f", "-lfjsrcinfo", "-lelf"])
return flags, None, (cmake_flags or None)
@property
def libs(self):
"""HDF5 can be queried for the following parameters:
- "hl": high-level interface
- "cxx": C++ APIs
- "fortran": Fortran APIs
- "java": Java APIs
:return: list of matching libraries
"""
query_parameters = self.spec.last_query.extra_parameters
shared = self.spec.satisfies("+shared")
# This map contains a translation from query_parameters
# to the libraries needed
query2libraries = {
tuple(): ["libhdf5"],
("cxx", "fortran", "hl", "java"): [
# When installed with Autotools, the basename of the real
# library file implementing the High-level Fortran interface is
# 'libhdf5hl_fortran'. Starting versions 1.8.22, 1.10.5 and
# 1.12.0, the Autotools installation also produces a symbolic
# link 'libhdf5_hl_fortran.<so/a>' to
# 'libhdf5hl_fortran.<so/a>'. Note that in the case of the
# dynamic library, the latter is a symlink to the real sonamed
# file 'libhdf5_fortran.so.<abi-version>'. This means that all
# dynamically linked executables/libraries of the dependent
# packages need 'libhdf5_fortran.so.<abi-version>' with the same
# DT_SONAME entry. However, the CMake installation (at least
# starting version 1.8.10) does not produce it. Instead, the
# basename of the library file is 'libhdf5_hl_fortran'. Which
# means that switching to CMake requires rebuilding of all
# dependant packages that use the High-level Fortran interface.
# Therefore, we do not try to preserve backward compatibility
# with Autotools installations by creating symlinks. The only
# packages that could benefit from it would be those that
# hardcode the library name in their building systems. Such
# packages should simply be patched.
"libhdf5_hl_fortran",
"libhdf5_hl_f90cstub",
"libhdf5_hl_cpp",
"libhdf5_hl",
"libhdf5_fortran",
"libhdf5_f90cstub",
"libhdf5_java",
"libhdf5",
],
("cxx", "hl"): ["libhdf5_hl_cpp", "libhdf5_hl", "libhdf5"],
("fortran", "hl"): [
"libhdf5_hl_fortran",
"libhdf5_hl_f90cstub",
"libhdf5_hl",
"libhdf5_fortran",
"libhdf5_f90cstub",
"libhdf5",
],
("hl",): ["libhdf5_hl", "libhdf5"],
("cxx", "fortran"): ["libhdf5_fortran", "libhdf5_f90cstub", "libhdf5_cpp", "libhdf5"],
("cxx",): ["libhdf5_cpp", "libhdf5"],
("fortran",): ["libhdf5_fortran", "libhdf5_f90cstub", "libhdf5"],
("java",): ["libhdf5_java", "libhdf5"],
}
# Turn the query into the appropriate key
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
return find_libraries(libraries, root=self.prefix, shared=shared, recursive=True)
@classmethod
def determine_version(cls, exe):
output = Executable(exe)("-showconfig", output=str, error=str)
match = re.search(r"HDF5 Version: (\d+\.\d+\.\d+)(\D*\S*)", output)
return match.group(1) if match else None
@classmethod
def determine_variants(cls, exes, version):
def is_enabled(text):
return text.lower() in ["t", "true", "enabled", "yes", "1", "on"]
results = []
for exe in exes:
variants = []
output = Executable(exe)("-showconfig", output=str, error=os.devnull)
match = re.search(r"High-level library: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+hl")
else:
variants.append("~hl")
match = re.search(r"Parallel HDF5: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+mpi")
else:
variants.append("~mpi")
match = re.search(r"C\+\+: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+cxx")
else:
variants.append("~cxx")
match = re.search(r"Fortran: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+fortran")
else:
variants.append("~fortran")
match = re.search(r"Java: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+java")
else:
variants.append("~java")
match = re.search(r"Threadsafety: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+threadsafe")
else:
variants.append("~threadsafe")
match = re.search(r"Build HDF5 Tools: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+tools")
else:
variants.append("~tools")
match = re.search(r"I/O filters \(external\): \S*(szip\(encoder\))\S*", output)
if match:
variants.append("+szip")
else:
variants.append("~szip")
match = re.search(r"Default API mapping: (\S+)", output)
if match and match.group(1) in set(["v200", "v114", "v112", "v110", "v18", "v16"]):
variants.append("api={0}".format(match.group(1)))
results.append(" ".join(variants))
return results
@when("@:1.8.21,1.10.0:1.10.5+szip")
def setup_build_environment(self, env: EnvironmentModifications) -> None:
env.set("SZIP_INSTALL", self.spec["szip"].prefix)
def cmake_args(self):
spec = self.spec
if spec.satisfies("@:1.8.15+shared"):
tty.warn("hdf5@:1.8.15+shared does not produce static libraries")
args = [
# Speed-up the building by skipping the examples:
self.define("HDF5_BUILD_EXAMPLES", False),
self.define(
"BUILD_TESTING",
self.run_tests or
# Version 1.8.22 fails to build the tools when shared libraries
# are enabled but the tests are disabled.
spec.satisfies("@1.8.22+shared+tools"),
),
self.define_from_variant("HDF5_ENABLE_SUBFILING_VFD", "subfiling"),
self.define_from_variant("HDF5_ENABLE_MAP_API", "map"),
self.define_from_variant("HDF5_ENABLE_SZIP_SUPPORT", "szip"),
self.define_from_variant("HDF5_ENABLE_SZIP_ENCODING", "szip"),
self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
self.define("ONLY_SHARED_LIBS", False),
self.define_from_variant("HDF5_ENABLE_PARALLEL", "mpi"),
self.define_from_variant("HDF5_ENABLE_THREADSAFE", "threadsafe"),
self.define_from_variant("HDF5_BUILD_HL_LIB", "hl"),
self.define_from_variant("HDF5_BUILD_CPP_LIB", "cxx"),
self.define_from_variant("HDF5_BUILD_FORTRAN", "fortran"),
self.define_from_variant("HDF5_BUILD_JAVA", "java"),
self.define_from_variant("HDF5_BUILD_TOOLS", "tools"),
]
# Always enable this option. This does not actually enable any
# features: it only *allows* the user to specify certain combinations
# of other arguments that would normally be rejected as unsupported
# configurations.
# Note: This option was renamed from ALLOW_UNSUPPORTED to
# HDF5_ALLOW_UNSUPPORTED in HDF5 2.0.0 as part of the standardization
# of CMake option naming.
if self.spec.satisfies("@2.0.0:"):
args.append(self.define("HDF5_ALLOW_UNSUPPORTED", True))
else:
args.append(self.define("ALLOW_UNSUPPORTED", True))
# The name of option HDF5_ENABLE_Z_LIB_SUPPORT was also changed
# to HDF5_ENABLE_ZLIB_SUPPORT.
if self.spec.satisfies("@2.0.0:"):
args.append(self.define("HDF5_ENABLE_ZLIB_SUPPORT", True))
else:
args.append(self.define("HDF5_ENABLE_Z_LIB_SUPPORT", True))
# The name of option DEFAULT_API_VERSION was also changed to
# HDF5_DEFAULT_API_VERSION
api = spec.variants["api"].value
if api != "default":
if self.spec.satisfies("@2.0.0:"):
args.append(self.define("HDF5_DEFAULT_API_VERSION", api))
else:
args.append(self.define("DEFAULT_API_VERSION", api))
# MSMPI does not provide compiler wrappers
# and pointing these variables at the MSVC compilers
# breaks CMake's mpi detection for MSMPI.
if spec.satisfies("+mpi") and "msmpi" not in spec:
if spec.satisfies("+cxx"):
args.append(self.define("MPI_CXX_COMPILER", spec["mpi"].mpicxx))
args.append(self.define("MPI_C_COMPILER", spec["mpi"].mpicc))
if spec.satisfies("+fortran"):
args.append(self.define("MPI_Fortran_COMPILER", spec["mpi"].mpifc))
# work-around for https://github.com/HDFGroup/hdf5/issues/1320
if spec.satisfies("@1.10.8,1.13.0"):
args.append(self.define("HDF5_INSTALL_CMAKE_DIR", "share/cmake/hdf5"))
# AOCC does not support _Float16
if spec.satisfies("@1.14.4: %aocc"):
args.append(self.define("HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16", False))
return args
@run_after("install")
def ensure_parallel_compiler_wrappers(self):
# When installed with Autotools and starting at least version 1.8.10,
# the package produces C compiler wrapper called either 'h5cc' (when MPI
# support is disabled) or 'h5pcc' (when MPI support is enabled). The
# CMake installation produces the wrapper called 'h5cc' (regardless of
# whether MPI support is enabled) only starting versions 1.8.21, 1.10.2
# and 1.12.0. The current develop versions also produce 'h5pcc' when MPI
# support is enabled and the file is identical to 'h5cc'. Here, we make
# sure that 'h5pcc' is available when MPI support is enabled (only for
# versions that generate 'h5cc').
if self.spec.satisfies("@1.8.21:1.8.22,1.10.2:1.10.7,1.12.0+mpi"):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink("h5cc", "h5pcc")
# The same as for 'h5pcc'. However, the CMake installation produces the
# Fortran compiler wrapper called 'h5fc' only starting versions 1.8.22,
# 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
# at all. Here, we make sure that 'h5pfc' is available when Fortran and
# MPI support are enabled (only for versions that generate 'h5fc').
if self.spec.satisfies("@1.8.22:1.8,1.10.6:1.10.9,1.12.0:1.12.2+fortran+mpi"):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink("h5fc", "h5pfc")
@run_after("install")
def fix_package_config(self):
# We need to fix the pkg-config files, which are also used by the
# compiler wrappers. The files are created starting versions 1.8.21,
# 1.10.2 and 1.12.0. However, they are broken (except for the version
# 1.8.22): the files are named <name>-<version>.pc but reference <name>
# packages. This was fixed in the develop versions at some point: the
# files started referencing <name>-<version> packages but got broken
# again: the files got names <name>.pc but references had not been
# updated accordingly. Another issue, which we address here, is that
# some Linux distributions install pkg-config files named hdf5.pc and we
# want to override them. Therefore, the following solution makes sure
# that each <name>-<version>.pc file is symlinked by <name>.pc and all
# references to <name>-<version> packages in the original files are
# replaced with references to <name> packages.
pc_files = find(self.prefix.lib.pkgconfig, "hdf5*.pc", recursive=False)
if not pc_files:
# This also tells us that the pkgconfig directory does not exist.
return
# Replace versioned references in all pkg-config files:
filter_file(
r"(Requires(?:\.private)?:.*)(hdf5[^\s,]*)(?:-[^\s,]*)(.*)",
r"\1\2\3",
*pc_files,
backup=False,
)
# Create non-versioned symlinks to the versioned pkg-config files:
with working_dir(self.prefix.lib.pkgconfig):
for f in pc_files:
src_filename = os.path.basename(f)
version_sep_idx = src_filename.find("-")
if version_sep_idx > -1:
tgt_filename = src_filename[:version_sep_idx] + ".pc"
if not os.path.exists(tgt_filename):
symlink(src_filename, tgt_filename)
@run_after("install")
def link_debug_libs(self):
# When build_type is Debug, the hdf5 build appends _debug to all library names.
# Dependents of hdf5 (netcdf-c etc.) can't handle those, thus make symlinks.
if self.spec.satisfies("build_type=Debug"):
libs = find(self.prefix.lib, "libhdf5*_debug.*", recursive=False)
with working_dir(self.prefix.lib):
for lib in libs:
libname = os.path.split(lib)[1]
symlink(libname, libname.replace("_debug", ""))
@run_after("install")
def symlink_to_h5hl_wrappers(self):
if self.spec.satisfies("+hl"):
with working_dir(self.prefix.bin):
# CMake's FindHDF5 relies only on h5cc so it doesn't find the HL
# component unless it uses h5hlcc so we symlink h5cc to h5hlcc etc
symlink_files = {"h5cc": "h5hlcc", "h5c++": "h5hlc++"}
for old, new in symlink_files.items():
if os.path.isfile(old):
os.remove(old)
symlink(new, old)
@run_after("install")
def symlink_mpi_libs(self):
"""Compatibility layer to support projects looking for the MPI suffix"""
if not self.spec.satisfies("+mpi"):
return
mpi_libs = ["libhdf5{mpi_suffix}", "libhdf5{mpi_suffix}_hl"]
for lib_f in mpi_libs:
src_name = lib_f.format(mpi_suffix="")
dst_name = lib_f.format(mpi_suffix="_mpi")
libs = find_libraries(src_name, root=self.prefix, recursive=True)
for lib_path in libs:
prefix = os.path.dirname(lib_path)
src_lib = os.path.basename(lib_path)
dst_lib = dst_name.join(src_lib.rsplit(src_name, 1))
with working_dir(prefix):
symlink(src_lib, dst_lib)
@property
@memoized
def _output_version(self):
spec_vers_str = str(self.spec.version.up_to(3))
if "develop" in spec_vers_str:
# Remove 'develop-' from the version in spack for checking
# version against the version in the HDF5 code.
spec_vers_str = spec_vers_str.partition("-")[2]
return spec_vers_str
@run_after("install")
@on_package_attributes(run_tests=True)
def check_install(self):
self.test_check_prog()
def test_check_prog(self):
"""build, run and check output of check.c"""
print("Checking HDF5 installation...")
prog = "check.c"
spec = self.spec
checkdir = "spack-check"
# Because the release number in a develop branch is not fixed,
# only the major and minor version numbers are compared.
# Otherwise all 3 numbers are checked.
fmt = "%d.%d %u.%u"
arg_line1 = "H5_VERS_MAJOR, H5_VERS_MINOR"
arg_line2 = "majnum, minnum"
if not spec.version.isdevelop():
fmt = "%d." + fmt + ".%u"
arg_line2 = "H5_VERS_RELEASE, " + arg_line2 + ", relnum"
source = r"""
#include <hdf5.h>
#include <assert.h>
#include <stdio.h>
int main(int argc, char **argv) {{
unsigned majnum, minnum, relnum;
herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
assert(!herr);
printf("HDF5 version {}\n", {},
{});
return 0;
}}
"""
expected = f"HDF5 version {self._output_version} {self._output_version}\n"
with working_dir(checkdir, create=True):
with open(prog, "w") as f:
f.write(source.format(fmt, arg_line1, arg_line2))
cc = Executable(os.environ["CC"])
cc(*(["-c", "check.c"] + spec["hdf5"].headers.cpp_flags.split()))
cc(*(["-o", "check", "check.o"] + spec["hdf5"].libs.ld_flags.split()))
try:
check = Executable("./check")
output = check(output=str)
except ProcessError:
output = ""
success = output == expected
if not success:
print("Produced output does not match expected output.")
print("Expected output:")
print("-" * 80)
print(expected)
print("-" * 80)
print("Produced output:")
print("-" * 80)
print(output)
print("-" * 80)
raise RuntimeError("HDF5 install check failed")
shutil.rmtree(checkdir)
def test_version(self):
"""Perform version checks on selected installed package binaries."""
expected = f"Version {self._output_version}"
exes = [
"h5copy",
"h5diff",
"h5dump",
"h5format_convert",
"h5ls",
"h5mkgrp",
"h5repack",
"h5stat",
"h5unjam",
]
use_short_opt = ["h52gif", "h5repart", "h5unjam"]
for exe in exes:
reason = f"ensure version of {exe} is {self._output_version}"
option = "-V" if exe in use_short_opt else "--version"
with test_part(self, f"test_version_{exe}", purpose=reason):
path = join_path(self.prefix.bin, exe)
if not os.path.isfile(path):
raise SkipTest(f"{path} is not installed")
prog = which(path, required=True)
output = prog(option, output=str.split, error=str.split)
assert expected in output
def test_example(self):
"""copy, dump, and diff example hdf5 file"""
test_data_dir = self.test_suite.current_test_data_dir
with working_dir(test_data_dir, create=True):
filename = "spack.h5"
h5dump = which(self.prefix.bin.h5dump, required=True)
out = h5dump(filename, output=str.split, error=str.split)
expected = get_escaped_text_output("dump.out")
check_outputs(expected, out)
h5copy = which(self.prefix.bin.h5copy, required=True)
copyname = "test.h5"
options = ["-i", filename, "-s", "Spack", "-o", copyname, "-d", "Spack"]
h5copy(*options)
h5diff = which(self.prefix.bin.h5diff, required=True)
h5diff(filename, copyname)

43
tools/spack/spack_repo/cp2k_dev/packages/hdf5/pre-c99-comments.patch Normal file
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@ -0,0 +1,43 @@
diff --git a/test/th5s.c b/test/th5s.c
index 462bc36..8e18fad 100644
--- a/test/th5s.c
+++ b/test/th5s.c
@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
CHECK(ret, FAIL, "H5Pset_chunk");
- // ret = H5Pset_alloc_time(plist_id, alloc_time);
- // CHECK(ret, FAIL, "H5Pset_alloc_time");
+ /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
+ /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
CHECK(dset1, FAIL, "H5Dcreate2");
diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
index ee6de5e..3ed6045 100644
--- a/tools/h5dump/h5dump_ddl.c
+++ b/tools/h5dump/h5dump_ddl.c
@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
string_dataformat.do_escape = display_escape;
outputformat = &string_dataformat;
- //attr_name = attr + j + 1;
- // need to replace escape characters
+ /* attr_name = attr + j + 1; */
+ /* need to replace escape characters */
attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 9ce3524..3b4e5e7 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
}
-// ctx->need_prefix = 0;
+/* ctx->need_prefix = 0; */
}
/*-------------------------------------------------------------------------

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