[arch-commits] Commit in med-openmpi/repos/community-x86_64 (PKGBUILD hdf5-1.12.patch)

Alexander Rødseth arodseth at gemini.archlinux.org
Sat Aug 6 17:37:24 UTC 2022


    Date: Saturday, August 6, 2022 @ 17:37:24
  Author: arodseth
Revision: 1260456

archrelease: copy trunk to community-x86_64

Added:
  med-openmpi/repos/community-x86_64/PKGBUILD
    (from rev 1260455, med-openmpi/trunk/PKGBUILD)
  med-openmpi/repos/community-x86_64/hdf5-1.12.patch
    (from rev 1260455, med-openmpi/trunk/hdf5-1.12.patch)

-----------------+
 PKGBUILD        |   53 +++++++++++++++
 hdf5-1.12.patch |  189 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 242 insertions(+)

Copied: med-openmpi/repos/community-x86_64/PKGBUILD (from rev 1260455, med-openmpi/trunk/PKGBUILD)
===================================================================
--- PKGBUILD	                        (rev 0)
+++ PKGBUILD	2022-08-06 17:37:24 UTC (rev 1260456)
@@ -0,0 +1,53 @@
+# Maintainer: Alexander F. Rødseth <xyproto at archlinux.org>
+# Contributor: Guilhem Saurel <guilhem at saurel.me>
+# Contributor: Michel Zou
+# Contributor: Oliver Goethel
+# Contributor: Gustavo Alvarez <sl1pkn07 at gmail.com>
+
+pkgname=med-openmpi
+pkgver=4.1.1
+pkgrel=1
+pkgdesc='Generic pre- and post-processing platform for numerical simulation'
+url="https://www.salome-platform.org/downloads"
+license=(LGPL)
+arch=(x86_64)
+provides=(med)
+conflicts=(med)
+replaces=(med)
+depends=(hdf5-openmpi python tk)
+makedepends=(cmake gcc-fortran ninja openmpi swig)
+source=("https://files.salome-platform.org/Salome/other/med-$pkgver.tar.gz"
+        hdf5-1.12.patch)
+b2sums=('fb9bc3239c18c53fa42c5dd1101559746e8d38db2a3cb5fb47d1bf0cb578facc4ab95409af8524f5c20251848842cc1a331f6a816ce0754e9a6c95f507174ed1'
+        '998958970918d98724b80f7b5ff09558f7abea39cdac5e558b66410c4d8d1476b0407295f3745ece5586482bf76db3eef0139918d27d1bbc3eb166ed7ab4745a')
+
+prepare() {
+  cd med-${pkgver}_SRC
+  patch -p1 -i ../hdf5-1.12.patch # Fix build with hdf5 1.12 (Fedora)
+  sed -i 's/if H5_VERS_MINOR > 10/if 0/g' src/ci/MEDfileCompatibility.c
+}
+
+build() {
+  export CPPFLAGS+=' -DH5_USE_110_API'
+  cmake \
+    -B build \
+    -D CMAKE_BUILD_TYPE=Release \
+    -D CMAKE_INSTALL_PREFIX=/usr \
+    -D CMAKE_SKIP_RPATH=ON \
+    -D MEDFILE_BUILD_PYTHON=ON \
+    -D MEDFILE_BUILD_TESTS=OFF \
+    -D MEDFILE_INSTALL_DOC=OFF \
+    -D MEDFILE_USE_MPI=ON \
+    -G Ninja \
+    -S med-${pkgver}_SRC
+  ninja -C build
+}
+
+check() {
+  cd build
+  LD_LIBRARY_PATH="$srcdir/build/src" ctest -E '._Python' --output-on-failure
+}
+
+package() {
+  DESTDIR="$pkgdir" ninja -C build install
+}

Copied: med-openmpi/repos/community-x86_64/hdf5-1.12.patch (from rev 1260455, med-openmpi/trunk/hdf5-1.12.patch)
===================================================================
--- hdf5-1.12.patch	                        (rev 0)
+++ hdf5-1.12.patch	2022-08-06 17:37:24 UTC (rev 1260456)
@@ -0,0 +1,189 @@
+diff -rupN med-4.1.0/config/cmake_files/medMacros.cmake med-4.1.0-new/config/cmake_files/medMacros.cmake
+--- med-4.1.0/config/cmake_files/medMacros.cmake	2021-12-03 09:35:30.675827163 +0100
++++ med-4.1.0-new/config/cmake_files/medMacros.cmake	2021-12-03 09:32:31.894994147 +0100
+@@ -447,7 +447,7 @@ MACRO(MED_FIND_HDF5)
+     ##
+     ## Requires 1.10.x version
+     ##
+-    IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++    IF (HDF5_VERSION VERSION_LESS 1.10.2)
+         MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+     ENDIF()
+     ##
+diff -rupN med-4.1.0/src/ci/MEDfileCompatibility.c med-4.1.0-new/src/ci/MEDfileCompatibility.c
+--- med-4.1.0/src/ci/MEDfileCompatibility.c	2021-12-03 09:35:30.676827162 +0100
++++ med-4.1.0-new/src/ci/MEDfileCompatibility.c	2021-12-03 09:33:26.292942149 +0100
+@@ -71,7 +71,7 @@ MEDfileCompatibility(const char* const f
+   _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+   /* ISCRUTE(_hversionMMR); */
+   /* ISCRUTE(HDF_VERSION_NUM_REF); */
+-  if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++  if (_hversionMMR >= HDF_VERSION_NUM_REF) *hdfok = MED_TRUE;
+ 
+   /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+      à la version mineure de la bibliothèque HDF utilisée :
+@@ -113,7 +113,7 @@ MEDfileCompatibility(const char* const f
+ #if MED_NUM_MAJEUR != 4
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+ #error "Cf. _MEDfileCreate ..."
+ #endif
+diff -rupN med-4.1.0/src/hdfi/_MEDattributeNumWrByName.c med-4.1.0-new/src/hdfi/_MEDattributeNumWrByName.c
+--- med-4.1.0/src/hdfi/_MEDattributeNumWrByName.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDattributeNumWrByName.c	2021-12-03 09:33:08.851958696 +0100
+@@ -68,7 +68,7 @@ med_err _MEDattributeNumWrByName(med_idt
+ 
+   if  ( (_attid=H5Aopen_by_name( pid, path, attname, H5P_DEFAULT, H5P_DEFAULT )) >= 0 ) {
+ 
+-    if ( H5Oget_info( pid, &_oinfo ) <0) {
++    if ( H5Oget_info( pid, &_oinfo, H5O_INFO_ALL ) <0) {
+ 	MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info");
+ 	goto ERROR;
+     }
+diff -rupN med-4.1.0/src/hdfi/_MEDattributeNumWr.c med-4.1.0-new/src/hdfi/_MEDattributeNumWr.c
+--- med-4.1.0/src/hdfi/_MEDattributeNumWr.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDattributeNumWr.c	2021-12-03 09:33:11.840955852 +0100
+@@ -77,7 +77,7 @@ med_err _MEDattributeNumWr(med_idt pid,
+ 
+   if  ( (_attid=H5Aopen( pid, attname, H5P_DEFAULT )) >= 0 ) {
+ 
+-    if ( H5Oget_info( pid, &_oinfo ) <0) {
++    if ( H5Oget_info( pid, &_oinfo, H5O_INFO_ALL ) <0) {
+ 	MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info");
+ 	goto ERROR;
+     }
+diff -rupN med-4.1.0/src/hdfi/_MEDcheckAttributeStringFunc.c med-4.1.0-new/src/hdfi/_MEDcheckAttributeStringFunc.c
+--- med-4.1.0/src/hdfi/_MEDcheckAttributeStringFunc.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDcheckAttributeStringFunc.c	2021-12-03 09:33:14.266953546 +0100
+@@ -40,7 +40,7 @@ med_err _MEDcheckAttributeStringFunc(med
+     oinfo.type=H5G_LINK;
+     break;
+   case H5L_TYPE_HARD:
+-    if ( H5Oget_info_by_name( id, lname, &oinfo, H5P_DEFAULT ) <0) {
++    if ( H5Oget_info_by_name( id, lname, &oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+       MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+       SSCRUTE(lname);
+     }
+diff -rupN med-4.1.0/src/hdfi/_MEDchecknSublinkFunc.c med-4.1.0-new/src/hdfi/_MEDchecknSublinkFunc.c
+--- med-4.1.0/src/hdfi/_MEDchecknSublinkFunc.c	2020-03-11 10:36:36.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDchecknSublinkFunc.c	2021-12-03 09:33:16.487951437 +0100
+@@ -41,7 +41,7 @@ med_err _MEDchecknSublinkFunc(med_idt id
+     oinfo.type=H5G_LINK;
+     break;
+   case H5L_TYPE_HARD:
+-    if ( H5Oget_info_by_name( id, lname, &oinfo, H5P_DEFAULT ) <0) {
++    if ( H5Oget_info_by_name( id, lname, &oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+       MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+       SSCRUTE(lname);
+     }
+diff -rupN med-4.1.0/src/hdfi/_MEDdatagroupExist.c med-4.1.0-new/src/hdfi/_MEDdatagroupExist.c
+--- med-4.1.0/src/hdfi/_MEDdatagroupExist.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDdatagroupExist.c	2021-12-03 09:33:18.742949298 +0100
+@@ -45,7 +45,7 @@ med_err _MEDdatagroupExist(const med_idt
+ 
+     case H5L_TYPE_HARD:
+       *isasoftlink  = MED_FALSE;
+-      if ( H5Oget_info_by_name( gid, datagroupname, &_oinfo, H5P_DEFAULT ) <0) {
++      if ( H5Oget_info_by_name( gid, datagroupname, &_oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+ 	MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+ 	SSCRUTE( datagroupname);
+       }
+diff -rupN med-4.1.0/src/hdfi/_MEDdatasetExist.c med-4.1.0-new/src/hdfi/_MEDdatasetExist.c
+--- med-4.1.0/src/hdfi/_MEDdatasetExist.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDdatasetExist.c	2021-12-03 09:33:24.158944167 +0100
+@@ -47,7 +47,7 @@ med_err _MEDdatasetExist(const med_idt
+ 
+     case H5L_TYPE_HARD:
+       *isasoftlink  = MED_FALSE;
+-      if ( H5Oget_info_by_name( gid, datasetname, &_oinfo, H5P_DEFAULT ) <0) {
++      if ( H5Oget_info_by_name( gid, datasetname, &_oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+ 	MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+ 	SSCRUTE( datasetname);
+       }
+diff -rupN med-4.1.0/src/hdfi/_MEDfileCreate.c med-4.1.0-new/src/hdfi/_MEDfileCreate.c
+--- med-4.1.0/src/hdfi/_MEDfileCreate.c	2021-12-03 09:35:30.677827161 +0100
++++ med-4.1.0-new/src/hdfi/_MEDfileCreate.c	2021-12-03 09:32:31.894994147 +0100
+@@ -159,7 +159,7 @@ med_idt _MEDfileCreate(const char * cons
+    * En HDF5-1.10.0p1 cela n'a aucun effet ! 
+    * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+    */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+    
+diff -rupN med-4.1.0/src/hdfi/_MEDfileOpen.c med-4.1.0-new/src/hdfi/_MEDfileOpen.c
+--- med-4.1.0/src/hdfi/_MEDfileOpen.c	2021-12-03 09:35:30.677827161 +0100
++++ med-4.1.0-new/src/hdfi/_MEDfileOpen.c	2021-12-03 09:32:31.894994147 +0100
+@@ -72,7 +72,7 @@ med_idt _MEDfileOpen(const char * const
+ 
+    •   The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order). 
+   */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5 
+diff -rupN med-4.1.0/src/hdfi/_MEDlinkObjs.c med-4.1.0-new/src/hdfi/_MEDlinkObjs.c
+--- med-4.1.0/src/hdfi/_MEDlinkObjs.c	2020-03-11 10:36:37.000000000 +0100
++++ med-4.1.0-new/src/hdfi/_MEDlinkObjs.c	2021-12-03 09:33:21.096947067 +0100
+@@ -62,7 +62,7 @@ med_err _MEDlinkobjs(med_idt id,const ch
+        sur un lien hard
+        Sur un lien soft H5O_TYPE_UNKNOWN
+     */
+-    if ( H5Oget_info_by_name( id, lname, &oinfo, H5P_DEFAULT ) <0) {
++    if ( H5Oget_info_by_name( id, lname, &oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+       MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+       SSCRUTE(lname);
+     }
+diff -rupN med-4.1.0/src/hdfi/_MEDmemFileOpen.c med-4.1.0-new/src/hdfi/_MEDmemFileOpen.c
+--- med-4.1.0/src/hdfi/_MEDmemFileOpen.c	2021-12-03 09:35:30.678827160 +0100
++++ med-4.1.0-new/src/hdfi/_MEDmemFileOpen.c	2021-12-03 09:32:31.894994147 +0100
+@@ -434,7 +434,7 @@ med_idt _MEDmemFileOpen(const char * con
+     goto ERROR;
+   }
+ 
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+   if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+diff -rupN med-4.1.0/src/hdfi/_MEDparFileCreate.c med-4.1.0-new/src/hdfi/_MEDparFileCreate.c
+--- med-4.1.0/src/hdfi/_MEDparFileCreate.c	2021-12-03 09:35:30.678827160 +0100
++++ med-4.1.0-new/src/hdfi/_MEDparFileCreate.c	2021-12-03 09:32:31.894994147 +0100
+@@ -64,7 +64,7 @@ med_idt _MEDparFileCreate(const char * c
+    * En HDF5-1.10.0p1 cela n'a aucun effet ! 
+    * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+    */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+    
+diff -rupN med-4.1.0/src/hdfi/_MEDparFileOpen.c med-4.1.0-new/src/hdfi/_MEDparFileOpen.c
+--- med-4.1.0/src/hdfi/_MEDparFileOpen.c	2021-12-03 09:35:30.679827159 +0100
++++ med-4.1.0-new/src/hdfi/_MEDparFileOpen.c	2021-12-03 09:32:31.894994147 +0100
+@@ -55,7 +55,7 @@ med_idt _MEDparFileOpen(const char * con
+     MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_PARALLEL_MSG);
+     goto ERROR;
+   }
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+   if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+diff -rupN med-4.1.0/tools/medimport/2.3.6/_MEDconvertStringDatasets.c med-4.1.0-new/tools/medimport/2.3.6/_MEDconvertStringDatasets.c
+--- med-4.1.0/tools/medimport/2.3.6/_MEDconvertStringDatasets.c	2020-03-11 10:36:40.000000000 +0100
++++ med-4.1.0-new/tools/medimport/2.3.6/_MEDconvertStringDatasets.c	2021-12-03 09:34:42.715870908 +0100
+@@ -52,7 +52,7 @@ med_err _MEDconvertStringDatasets(med_id
+     oinfo.type=(H5O_type_t) H5G_LINK;
+     break;
+   case H5L_TYPE_HARD:
+-    if ( H5Oget_info_by_name( id, lname, &oinfo, H5P_DEFAULT ) <0) {
++    if ( H5Oget_info_by_name( id, lname, &oinfo, H5O_INFO_ALL, H5P_DEFAULT ) <0) {
+       MED_ERR_(_ret,MED_ERR_CALL,MED_ERR_API,"H5Oget_info_by_name");
+       SSCRUTE(lname);
+     }



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