From 75bd6d7e1f00333ee817441e288dc6ecee97e140 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 23 Jun 2025 15:46:17 +0000 Subject: [PATCH 1/4] #84 tweak hdf5 paths --- scripts/custom/install_hdf5.sh | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh index 6def052..0f014ee 100755 --- a/scripts/custom/install_hdf5.sh +++ b/scripts/custom/install_hdf5.sh @@ -69,31 +69,30 @@ fi mkdir -p ${base_dir}/src/hdf5 cd ${base_dir}/src/hdf5 -URL_HDF5= +src_dir=$(pwd)/hdf5-${version} +mkdir -p ${src_dir} + if (version_ge "${version}" '1.10.0' && version_lt "${version}" '1.10.12') || # HDF5 >=1.10.0, <1.10.12 (version_ge "${version}" '1.12.0' && version_lt "${version}" '1.12.2') # HDF5 >=1.12.0, <1.12.2 then - URL_HDF5=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${major}.${minor}/hdf5-${version}/src/hdf5-${version}.tar.gz + wget -nc https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${major}.${minor}/hdf5-${version}/src/hdf5-${version}.tar.gz + tar -xzf hdf5-${version}.tar.gz elif (version_ge "${version}" '1.12.2' && version_lt "${version}" '1.12.4') || # HDF5 >=1.12.2, <1.12.4 (version_ge "${version}" '1.14.0' && version_lt "${version}" '1.14.4') # HDF5 >=1.14.0, <1.14.4 then - URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${ver_si_on}.tar.gz + wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${ver_si_on}.tar.gz + tar -xzf hdf5-${ver_si_on}.tar.gz -C ${src_dir} --strip-components=1 else # HDF5 >=1.10.12, <1.11 # HDF5 >=1.12.4, <1.13 # HDF5 >=1.14.4, <1.15 # + catch-all - URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${version}.tar.gz + wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${version}.tar.gz + tar -xzf hdf5-${version}.tar.gz -C ${src_dir} --strip-components=1 fi -src_dir=$(pwd)/hdf5-${version} -mkdir -p ${src_dir} - -wget -nc ${URL_HDF5} -tar -xzf $(basename ${URL_HDF5}) -C ${src_dir} --strip-components=1 - # Build and install install_dir=${base_dir}/opt/hdf5/${version} mkdir -p ${install_dir} @@ -105,6 +104,7 @@ cd build CC=mpicc cmake \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX=${install_dir} \ + -DHDF5_BUILD_HL_LIB=OFF \ -DHDF5_BUILD_TOOLS=OFF \ -DHDF5_ENABLE_PARALLEL=ON \ -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \ From a3e2d8ed47c7ed1f86e6366721ca25de1ad56372 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 23 Jun 2025 15:46:38 +0000 Subject: [PATCH 2/4] #84 Tweak petsc debug option --- scripts/custom/install_petsc.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/custom/install_petsc.sh b/scripts/custom/install_petsc.sh index 9c88c79..6be5851 100755 --- a/scripts/custom/install_petsc.sh +++ b/scripts/custom/install_petsc.sh @@ -128,6 +128,7 @@ case ${arch} in --download-parmetis=1 \ --with-cc=mpicc \ --with-cxx=mpicxx \ + --with-debugging=0 \ --with-fc=0 \ --with-shared-libraries \ --with-ssl=false \ From 455f170899e8c2c6a732d753c3afffceae630e71 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 23 Jun 2025 15:47:42 +0000 Subject: [PATCH 3/4] #84 Link issue to petsc_hdf5 compatibility todos --- scripts/custom/install_petsc_hdf5.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/custom/install_petsc_hdf5.sh b/scripts/custom/install_petsc_hdf5.sh index de88580..4f07260 100755 --- a/scripts/custom/install_petsc_hdf5.sh +++ b/scripts/custom/install_petsc_hdf5.sh @@ -2,6 +2,7 @@ # TODO: This script adds a PETSc/HDF5 modulefile as a temporary workaround for backwards compatibility. # Remove once the combined PETSc/HDF5 module is no longer needed. +# See https://github.com/Chaste/dependency-modules/issues/84 usage() { From 360179ac7fe6d540b455a66ea3b84afa0a615f41 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 23 Jun 2025 15:48:13 +0000 Subject: [PATCH 4/4] #84 Link issue to petsc_hdf5 compatibility todos --- Dockerfile.custom | 1 + scripts/system/install_modulefiles.sh | 2 ++ 2 files changed, 3 insertions(+) diff --git a/Dockerfile.custom b/Dockerfile.custom index b69f812..5907b87 100755 --- a/Dockerfile.custom +++ b/Dockerfile.custom @@ -109,6 +109,7 @@ RUN source /etc/profile.d/modules.sh && \ # TODO: This RUN section is a temporary workaround for backwards compatibility. # Remove once the combined PETSc/HDF5 module is no longer needed. +# See https://github.com/Chaste/dependency-modules/issues/84 RUN source /etc/profile.d/modules.sh && \ module use ${MODULES_DIR}/modulefiles && \ install_petsc_hdf5.sh \ diff --git a/scripts/system/install_modulefiles.sh b/scripts/system/install_modulefiles.sh index c44d0b5..7e4c1f3 100755 --- a/scripts/system/install_modulefiles.sh +++ b/scripts/system/install_modulefiles.sh @@ -130,6 +130,8 @@ EOF # TODO: This adds PETSc/HDF5 modulefile stub as a temporary workaround for backwards compatibility. # Remove once the combined PETSc/HDF5 module is no longer needed. +# See https://github.com/Chaste/dependency-modules/issues/84 + mkdir -p ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version} cd ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version}