From 8e1686ec6f0e54ba7d8cece693950e0175fa00fd Mon Sep 17 00:00:00 2001 From: Randolph Settgast Date: Tue, 3 Mar 2026 15:19:21 -0800 Subject: [PATCH 1/4] fix issues with spack on mac --- scripts/spack_configs/macOS/spack.yaml | 17 +++++++++++++++++ .../spack_packages/packages/geosx/package.py | 5 ++++- 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/scripts/spack_configs/macOS/spack.yaml b/scripts/spack_configs/macOS/spack.yaml index 6a0f0474..7f9bd45a 100644 --- a/scripts/spack_configs/macOS/spack.yaml +++ b/scripts/spack_configs/macOS/spack.yaml @@ -31,6 +31,13 @@ spack: operating_system: sequoia target: aarch64 modules: [] + environment: + set: + PATH: /usr/bin:/bin:/usr/sbin:/sbin:/opt/homebrew/bin:/opt/homebrew/sbin + AR: /usr/bin/ar + RANLIB: /usr/bin/ranlib + CMAKE_AR: /usr/bin/ar + CMAKE_RANLIB: /usr/bin/ranlib extra_rpaths: [] - compiler: spec: apple-clang@17.0.0 @@ -45,6 +52,13 @@ spack: operating_system: sequoia target: aarch64 modules: [] + environment: + set: + PATH: /usr/bin:/bin:/usr/sbin:/sbin:/opt/homebrew/bin:/opt/homebrew/sbin + AR: /usr/bin/ar + RANLIB: /usr/bin/ranlib + CMAKE_AR: /usr/bin/ar + CMAKE_RANLIB: /usr/bin/ranlib extra_rpaths: [] packages: @@ -57,6 +71,9 @@ spack: lapack: [openblas] variants: "~openmp" + geosx: + variants: "+addr2line" + openblas: buildable: False externals: diff --git a/scripts/spack_packages/packages/geosx/package.py b/scripts/spack_packages/packages/geosx/package.py index 91b7b6f0..8325aee6 100644 --- a/scripts/spack_packages/packages/geosx/package.py +++ b/scripts/spack_packages/packages/geosx/package.py @@ -177,6 +177,7 @@ class Geosx(CMakePackage, CudaPackage, ROCmPackage): with when("+trilinos"): trilinos_packages = '+aztec+stratimikos~amesos2~anasazi~belos~ifpack2~muelu~sacado+thyra+zoltan' depends_on("trilinos@16.1.0 cflags='-fPIC' cxxflags='-fPIC -include cstdint' fflags='-fPIC'" + trilinos_packages) + depends_on("trilinos fflags='-fsecond-underscore'", when="platform=darwin") depends_on("trilinos~openmp", when="~openmp") depends_on("trilinos+openmp", when="+openmp") @@ -213,6 +214,7 @@ class Geosx(CMakePackage, CudaPackage, ROCmPackage): # depends_on("mathpresso cxxflags='-fPIC'", when='+mathpresso') depends_on('grpc', when='+grpc') + depends_on('addr2line', when='+addr2line') # SPHINX_END_DEPENDS @@ -647,7 +649,7 @@ def geos_hostconfig(self, spec, prefix, py_site_pkgs_dir=None): cfg.write('# addr2line\n') cfg.write('#{0}\n\n'.format('-' * 80)) cfg.write(cmake_cache_option('ENABLE_ADDR2LINE', True)) - cfg.write(cmake_cache_entry('ADDR2LINE_EXEC ', '/usr/bin/addr2line')) + cfg.write(cmake_cache_entry('ADDR2LINE_EXEC', os.path.join(spec['addr2line'].prefix.bin, 'addr2line'))) cfg.write('#{0}\n'.format('-' * 80)) cfg.write('# Other\n') @@ -842,6 +844,7 @@ def lvarray_hostconfig(self, spec, prefix, py_site_pkgs_dir=None): cfg.write('# addr2line\n') cfg.write('#{0}\n\n'.format('-' * 80)) cfg.write(cmake_cache_option('ENABLE_ADDR2LINE', True)) + cfg.write(cmake_cache_entry('ADDR2LINE_EXEC', os.path.join(spec['addr2line'].prefix.bin, 'addr2line'))) def cmake_args(self): pass From d688f833a1980121fa7ec6a37ca121d33d47a6ea Mon Sep 17 00:00:00 2001 From: Sushma Yellapragada Date: Tue, 3 Mar 2026 18:35:23 -0600 Subject: [PATCH 2/4] Removing gcc-runtime due to missing files on TTE/pine (#341) * Update spack.yaml to comment out gcc-runtime Comment out gcc-runtime section due to missing libgcc_s.so.1 --- scripts/spack_configs/pine/spack.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/scripts/spack_configs/pine/spack.yaml b/scripts/spack_configs/pine/spack.yaml index 3941d5dc..6141aec7 100644 --- a/scripts/spack_configs/pine/spack.yaml +++ b/scripts/spack_configs/pine/spack.yaml @@ -1,7 +1,7 @@ # This is a Spack Environment file for Pine (Spack 1.0.2) # Run command from the top-level of the repository: # ./scripts/uberenv/uberenv.py \ -# --spec "~openmp~pygeosx~docs" \ +# --spec "~openmp~pygeosx~docs %gcc-11" \ # --spack-env-file=scripts/spack_configs/pine/spack.yaml \ # --project-json=.uberenv_config.json \ # --prefix ${GEOS_TPL_DIR} @@ -78,11 +78,12 @@ spack: extra_rpaths: [] buildable: false - gcc-runtime: - buildable: false - externals: - - spec: gcc-runtime@11.4.1 - prefix: /usr/lib/gcc/x86_64-redhat-linux/11 + # libgcc_s.so.1 is missing in /usr/lib/gcc/x86_64-redhat-linux/11 so removing it for now + # gcc-runtime: + # buildable: false + # externals: + # - spec: gcc-runtime@11.4.1 + # prefix: /usr/lib/gcc/x86_64-redhat-linux/11 gmp: externals: From d78583fc19a6dd952484e80e9a678ae29c604bdf Mon Sep 17 00:00:00 2001 From: Randolph Settgast Date: Tue, 3 Mar 2026 22:01:59 -0800 Subject: [PATCH 3/4] fix batch error --- scripts/setupLC-TPL-uberenv-helper.bash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/setupLC-TPL-uberenv-helper.bash b/scripts/setupLC-TPL-uberenv-helper.bash index 6ee12ca2..6f575f4b 100755 --- a/scripts/setupLC-TPL-uberenv-helper.bash +++ b/scripts/setupLC-TPL-uberenv-helper.bash @@ -52,7 +52,7 @@ echo "Building the TPLs on $MACHINE for $COMPILER to be installed at $INSTALL_DI ssh -t "${USER}@${MACHINE}.llnl.gov" " source /etc/profile && cd '${PWD}' && - ${GET_A_NODE} bash -c ' + ${GET_A_NODE} srun bash -c ' echo \"Start time: \$(date)\" ./scripts/uberenv/uberenv.py \ --spec ${SPEC} \ From b3584707b0997690e0600dafb3883a76cd649301 Mon Sep 17 00:00:00 2001 From: Randolph Settgast Date: Tue, 3 Mar 2026 22:24:04 -0800 Subject: [PATCH 4/4] fix scheduling commands again --- scripts/setupLC-TPL-uberenv-helper.bash | 2 +- scripts/setupLC-TPL-uberenv.bash | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/setupLC-TPL-uberenv-helper.bash b/scripts/setupLC-TPL-uberenv-helper.bash index 6f575f4b..6ee12ca2 100755 --- a/scripts/setupLC-TPL-uberenv-helper.bash +++ b/scripts/setupLC-TPL-uberenv-helper.bash @@ -52,7 +52,7 @@ echo "Building the TPLs on $MACHINE for $COMPILER to be installed at $INSTALL_DI ssh -t "${USER}@${MACHINE}.llnl.gov" " source /etc/profile && cd '${PWD}' && - ${GET_A_NODE} srun bash -c ' + ${GET_A_NODE} bash -c ' echo \"Start time: \$(date)\" ./scripts/uberenv/uberenv.py \ --spec ${SPEC} \ diff --git a/scripts/setupLC-TPL-uberenv.bash b/scripts/setupLC-TPL-uberenv.bash index e0b0555c..27974a6e 100755 --- a/scripts/setupLC-TPL-uberenv.bash +++ b/scripts/setupLC-TPL-uberenv.bash @@ -88,7 +88,7 @@ function launch_jobs() { # Note: The max time allowed on the debug queue is 1h. If we need more, switch to pbatch case "$machine" in dane) - ALLOC_CMD="salloc -N 1 --exclusive -p pdebug -t 60 -A vortex" + ALLOC_CMD="srun -N 1 --exclusive -p pdebug -t 60 -A vortex" "${UBERENV_HELPER}" "$INSTALL_DIR" dane gcc-12 "+docs %%gcc-12 ${COMMON}" "${ALLOC_CMD}" "$@" & "${UBERENV_HELPER}" "$INSTALL_DIR" dane gcc-13 "+docs %%gcc-13 ${COMMON}" "${ALLOC_CMD}" "$@" & "${UBERENV_HELPER}" "$INSTALL_DIR" dane llvm-14 "+docs %%clang-14 ${COMMON}" "${ALLOC_CMD}" "$@" & @@ -96,7 +96,7 @@ function launch_jobs() { ;; matrix) - ALLOC_CMD="salloc -N 1 --exclusive -p pdebug -t 60 -A vortex" + ALLOC_CMD="srun -N 1 --exclusive -p pdebug -t 60 -A vortex" "${UBERENV_HELPER}" "$INSTALL_DIR" matrix gcc-12-cuda-12.6 "+cuda~uncrustify cuda_arch=90 %%gcc-12 ^cuda@12.6.0+allow-unsupported-compilers ${COMMON}" "${ALLOC_CMD}" "$@" & "${UBERENV_HELPER}" "$INSTALL_DIR" matrix gcc-13-cuda-12.9 "+cuda~uncrustify cuda_arch=90 %%gcc-13 ^cuda@12.9.1+allow-unsupported-compilers ${COMMON}" "${ALLOC_CMD}" "$@" & "${UBERENV_HELPER}" "$INSTALL_DIR" matrix llvm-14-cuda-12.6 "+cuda~uncrustify cuda_arch=90 %%clang-14 ^cuda@12.6.0+allow-unsupported-compilers ${COMMON}" "${ALLOC_CMD}" "$@" & @@ -104,7 +104,7 @@ function launch_jobs() { ;; tuo|tuolumne) - ALLOC_CMD="salloc -N 1 --exclusive -p pdebug -t 60 -A vortex" + ALLOC_CMD="flux run -N 1 -x -t 60m --bank=vortex" "${UBERENV_HELPER}" "$INSTALL_DIR" tuolumne cce-20-rocm-6.4.3 "+rocm~pygeosx~trilinos~petsc~docs amdgpu_target=gfx942 %%cce-20 ${COMMON}" "${ALLOC_CMD}" "$@" & "${UBERENV_HELPER}" "$INSTALL_DIR" tuolumne llvm-amdgpu-6.4.3 "+rocm~pygeosx~trilinos~petsc~docs amdgpu_target=gfx942 %%llvm-amdgpu_6_4_3 ${COMMON}" "${ALLOC_CMD}" "$@" & ;;