From 9e7f7cc6c17bf6d4aa6265ae6b5b817e33a00ade Mon Sep 17 00:00:00 2001 From: Matthew Thompson Date: Mon, 5 Oct 2026 10:41:13 -0400 Subject: [PATCH 1/3] Update hdf5 to 2.1.0 and parallel-netcdf to 1.14.1 --- configs/common/packages.yaml | 7 ++++--- configs/common/packages_oneapi.yaml | 3 --- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index b4dcfec9c..08aba3117 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -250,7 +250,7 @@ packages: - ~netcdf hdf5: require: - - '@1.14.5' + - '@2.1.0' - +hl - +fortran - +mpi @@ -389,10 +389,11 @@ packages: require: - '@2.6.2' - +pnetcdf - # DH* CAN WE UPDATE? NEED A NEW SHARED-INTEL PATCH? + # 1.14.1 fixes a GCC 15 build failure. The old oneAPI shared-intel + # linkage workaround applied only to 1.12.3 and is intentionally not used. parallel-netcdf: require: - - '@1.12.3' + - '@1.14.1' pflogger: require: - +mpi diff --git a/configs/common/packages_oneapi.yaml b/configs/common/packages_oneapi.yaml index a60141866..d48de7f6e 100644 --- a/configs/common/packages_oneapi.yaml +++ b/configs/common/packages_oneapi.yaml @@ -63,9 +63,6 @@ packages: oops: require: - +mkl - parallel-netcdf: - require: - - +shared-intel patchelf: require: - '%c=gcc' From 84db70a6f8ebf9655c56152789fd1bb3ff30ce5f Mon Sep 17 00:00:00 2001 From: Matthew Thompson Date: Mon, 5 Oct 2026 11:41:40 -0400 Subject: [PATCH 2/3] Remove parallel-netcdf update comments --- configs/common/packages.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index 08aba3117..696edcdce 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -389,8 +389,6 @@ packages: require: - '@2.6.2' - +pnetcdf - # 1.14.1 fixes a GCC 15 build failure. The old oneAPI shared-intel - # linkage workaround applied only to 1.12.3 and is intentionally not used. parallel-netcdf: require: - '@1.14.1' From 138d1996e8635d12dad007bc511e9ad07168c0f5 Mon Sep 17 00:00:00 2001 From: Dom Heinzeller Date: Wed, 7 Oct 2026 13:41:15 -0600 Subject: [PATCH 3/3] Remove util/check_libirc.sh and calls to it from GitHub workflows; force fixing libirc.so/libimf.so in intel-oneapi-runtime by requiring +fix_rt_linkage for intel-oneapi-compilers in configs/common/packages_oneapi.yaml --- .../ubuntu-ci-x86_64-oneapi-ifx.yaml | 6 ----- .../workflows/ubuntu-ci-x86_64-oneapi.yaml | 6 ----- configs/common/packages_oneapi.yaml | 4 +++ util/check_libirc.sh | 27 ------------------- 4 files changed, 4 insertions(+), 39 deletions(-) delete mode 100755 util/check_libirc.sh diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml index 182a8dd6c..2d021efae 100644 --- a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml +++ b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml @@ -174,9 +174,6 @@ jobs: spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.${ENVNAME}.all spack buildcache create -u local-binary - # Check for libirc.so in shared libraries (returns 1=error if found) - ${SPACK_STACK_DIR}/util/check_libirc.sh - # Remove buildcache config settings spack config remove config:install_tree:padded_length @@ -213,9 +210,6 @@ jobs: # Check shared libraries ${SPACK_STACK_DIR}/util/ldd_check.py $SPACK_ENV 2>&1 | tee log.ldd_check - # Check for libirc.so in shared libraries (returns 1=error if found) - ${SPACK_STACK_DIR}/util/check_libirc.sh - # Create modules spack clean -a spack module tcl refresh -y diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml b/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml index c6b9d436b..821cf9278 100644 --- a/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml +++ b/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml @@ -174,9 +174,6 @@ jobs: spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.${ENVNAME}.all spack buildcache create -u local-binary - # Check for libirc.so in shared libraries (returns 1=error if found) - ${SPACK_STACK_DIR}/util/check_libirc.sh - # Remove buildcache config settings spack config remove config:install_tree:padded_length @@ -213,9 +210,6 @@ jobs: # Check shared libraries ${SPACK_STACK_DIR}/util/ldd_check.py $SPACK_ENV 2>&1 | tee log.ldd_check - # Check for libirc.so in shared libraries (returns 1=error if found) - ${SPACK_STACK_DIR}/util/check_libirc.sh - # Create modules spack clean -a spack module tcl refresh -y diff --git a/configs/common/packages_oneapi.yaml b/configs/common/packages_oneapi.yaml index d48de7f6e..cd4aaba18 100644 --- a/configs/common/packages_oneapi.yaml +++ b/configs/common/packages_oneapi.yaml @@ -19,6 +19,10 @@ packages: lapack: require: - intel-oneapi-mkl + # Force fixing libirc.so/libimf.so in intel-oneapi-runtime + intel-oneapi-compilers: + require: + - +fix_rt_linkage # Individual package settings antlr: require: diff --git a/util/check_libirc.sh b/util/check_libirc.sh deleted file mode 100755 index 62e6f625a..000000000 --- a/util/check_libirc.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env bash - -ierror=0 - -searchfor="libirc.so" - -echo "Checking shared libraries for ${searchfor} ..." -for file in `find ${SPACK_ENV} -type f -iname '*.so*'`; do - # Return code from grep is 1 if not found, 0 if found - ldd $file 2>&1 | grep "${searchfor}" - if [[ $? -eq 0 ]]; then - echo "Found ${searchfor} linked in ${file}" - ierror=1 - fi -done - -echo "Checking executables for ${searchfor} ..." -for file in `find ${SPACK_ENV} -type f -executable`; do - # Return code from grep is 1 if not found, 0 if found - ldd $file 2>&1 | grep "${searchfor}" - if [[ $? -eq 0 ]]; then - echo "Found ${searchfor} linked in ${file}" - ierror=1 - fi -done - -exit ${ierror}