Tweak PETSc and HDF5 installation

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 \

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 \

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 \

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()
 {

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}