release/2.0: Yet another Parallelworks update for site navy-aws

configs/sites/tier1/navy-aws/README.md

@@ -1,3 +1,134 @@
-# Provisiong NRL ParallelWorks AWS clusters
+# Preparing NRL ParallelWorks AWS clusters for spack-stack
 
-TODO UPDATE 20251208 !!!
+## Prerequisites
+
+### GNU 13.4.0
+
+Download and install:
+```
+module purge
+umask 0022
+
+mkdir -p /project/spack-stack/gcc-13.4.0/src
+cd /project/spack-stack/gcc-13.4.0/src
+wget https://github.com/gcc-mirror/gcc/archive/refs/tags/releases/gcc-13.4.0.tar.gz
+tar -xf gcc-13.4.0.tar.gz
+
+cd gcc-releases-gcc-13.4.0
+./contrib/download_prerequisites 2>&1 | tee log.download_prerequisites
+./configure \
+  --prefix=/project/spack-stack/gcc-13.4.0 \
+  --disable-multilib \
+  2>&1 | tee log.configure
+make -j48 2>&1 | tee log.make
+# Cannot run make check, because autogen is not installed
+#make check 2>&1 | tee log.check
+make install 2>&1 | tee log.install
+```
+
+Create modulefile `/project/spack-stack/gcc-13.4.0/modulefiles/gcc/13.4.0`:
+```
+mkdir -p /project/spack-stack/gcc-13.4.0/modulefiles/gcc
+cat << EOF > /project/spack-stack/gcc-13.4.0/modulefiles/gcc/13.4.0
+#%Module1.0
+
+module-whatis "Provides gcc-13.4.0 for use with spack."
+
+conflict gnu
+conflict gcc
+
+proc ModulesHelp { } {
+puts stderr "Provides gcc-13.4.0 for use with spack."
+}
+
+
+# Set this value
+set GCC_PATH "/project/spack-stack/gcc-13.4.0"
+
+prepend-path PATH "${GCC_PATH}/bin"
+prepend-path LD_LIBRARY_PATH "${GCC_PATH}/lib"
+prepend-path LD_LIBRARY_PATH "${GCC_PATH}/lib64"
+prepend-path LIBRARY_PATH "${GCC_PATH}/lib"
+prepend-path LIBRARY_PATH "${GCC_PATH}/lib64"
+prepend-path CPATH "${GCC_PATH}/include"
+prepend-path CMAKE_PREFIX_PATH "${GCC_PATH}"
+prepend-path PKG_CONFIG_PATH "${GCC_PATH}/usr/lib64/pkgconfig"
+prepend-path MANPATH "${GCC_PATH}/share/man"
+EOF
+```
+
+### OpenMPI 4.1.8
+
+Download and install:
+```
+module purge
+umask 0022
+
+module use /project/spack-stack/gcc-13.4.0/modulefiles
+module load gcc/13.4.0
+
+mkdir -p /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/src
+cd /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/src
+wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.8.tar.gz
+tar -xf openmpi-4.1.8.tar.gz
+
+cd openmpi-4.1.8
+./configure \
+  --prefix=/project/spack-stack/openmpi-4.1.8/gcc-13.4.0 \
+  2>&1 | tee log.configure
+make -j48 2>&1 | tee log.make
+make check 2>&1 | tee log.check
+make install 2>&1 | tee log.install
+```
+
+Create modulefile `/project/spack-stack/openmpi-4.1.8/gcc-13.4.0/modulefiles/openmpi/4.1.8`:
+```
+mkdir -p /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/modulefiles/openmpi
+cd /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/modulefiles/openmpi
+cat <<EOF > /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/modulefiles/openmpi/4.1.8
+#%Module1.0
+
+module-whatis "Provides openmpi-4.1.8 compiled with gcc-13.4.0 for use with spack."
+
+conflict gnu
+conflict gcc
+
+proc ModulesHelp { } {
+puts stderr "Provides openmpi-4.1.8 compiled with gcc-13.4.0 for use with spack."
+}
+
+
+# Set this value
+set OPENMPI_PATH "/project/spack-stack/openmpi-4.1.8/gcc-13.4.0"
+
+prepend-path PATH "${OPENMPI_PATH}/bin"
+prepend-path LD_LIBRARY_PATH "${OPENMPI_PATH}/lib"
+prepend-path LIBRARY_PATH "${OPENMPI_PATH}/lib"
+prepend-path CPATH "${OPENMPI_PATH}/include"
+prepend-path CMAKE_PREFIX_PATH "${OPENMPI_PATH}"
+prepend-path MANPATH "${OPENMPI_PATH}/share/man"
+EOF
+```
+
+### Intel oneAPI 2025.3.0
+
+Download and install:
+```
+module purge
+umask 022
+
+mkdir -p /project/spack-stack/oneapi-2025.3.0/src
+cd /project/spack-stack/oneapi-2025.3.0/src
+wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/66021d90-934d-41f4-bedf-b8c00bbe98bc/intel-oneapi-hpc-toolkit-2025.3.0.381_offline.sh
+
+sh ./intel-oneapi-hpc-toolkit-2025.3.0.381_offline.sh -a --silent --cli --eula accept
+```
+
+Select a custom installation of all components in `/project/spack-stack/oneapi-2025.3.0`. After the installation, create the modulefiles:
+```
+cd /project/spack-stack/oneapi-2025.3.0
+./modulefiles-setup.sh --ignore-latest --output-dir=/project/spack-stack/oneapi-2025.3.0/modulefiles
+
+# Fix non-ascii characters in modulefiles
+sed -i 's/®//g' `grep -lRe '®' modulefiles`
+```

configs/sites/tier1/navy-aws/packages_gcc-13.3.1.yaml → configs/sites/tier1/navy-aws/packages_gcc-13.4.0.yaml

@@ -5,15 +5,15 @@ packages:
     - "openmpi@4.1.8"
   gcc:
     externals:
-    - spec: gcc@13.3.1 languages:='c,c++,fortran'
-      prefix: /opt/rh/gcc-toolset-13/root
+    - spec: gcc@13.4.0 languages:='c,c++,fortran'
+      prefix: /project/spack-stack/gcc-13.4.0
       modules:
-      - gcc/13.3.1
+      - gcc/13.4.0
       extra_attributes:
         compilers:
-          c: /opt/rh/gcc-toolset-13/root/bin/gcc
-          cxx: /opt/rh/gcc-toolset-13/root/bin/g++
-          fortran: /opt/rh/gcc-toolset-13/root/bin/gfortran
+          c: /project/spack-stack/gcc-13.4.0/bin/gcc
+          cxx: /project/spack-stack/gcc-13.4.0/bin/g++
+          fortran: /project/spack-stack/gcc-13.4.0/bin/gfortran
     #- spec: gcc@11.5.0 languages:='c,c++,fortran'
     #  prefix: /usr
     #  extra_attributes:
@@ -23,12 +23,11 @@ packages:
     #      fortran: /usr/bin/gfortran
   gcc-runtime:
     externals:
-    - spec: gcc-runtime@13.3.1%gcc@13.3.1
-      prefix: /opt/rh/gcc-toolset-13/root
+    - spec: gcc-runtime@13.4.0%gcc@13.4.0
+      prefix: /project/spack-stack/gcc-13.4.0
   openmpi:
     externals:
     - spec: openmpi@4.1.8
-      prefix: /project/spack-stack/openmpi-4.1.8/gcc-13.3.1
+      prefix: /project/spack-stack/openmpi-4.1.8/gcc-13.4.0
       modules:
       - openmpi/4.1.8
-

util/nrl/batch_install.sh

@@ -145,7 +145,7 @@ case ${SPACK_STACK_BATCH_HOST} in
     SPACK_STACK_CARGO_MIRROR="/p/cwfs/projects/NEPTUNE/spack-stack/cargo-mirror"
     ;;
   navy-aws)
-    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.3.0" "gcc@=13.3.1")
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.3.0" "gcc@=13.4.0")
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "cylc-dev")
     SPACK_STACK_MODULE_CHOICE="tcl"
     SPACK_STACK_BOOTSTRAP_MIRROR="/project/spack-stack/bootstrap-mirror"
@@ -450,9 +450,9 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
         umask 0022
         module purge
         case ${compiler} in
-          gcc-13.3.1)
-            module use /project/spack-stack/gcc-13.3.1/modulefiles
-            module use /project/spack-stack/openmpi-4.1.8/gcc-13.3.1/modulefiles
+          gcc-13.4.0)
+            module use /project/spack-stack/gcc-13.4.0/modulefiles
+            module use /project/spack-stack/openmpi-4.1.8/gcc-13.4.0/modulefiles
 	    ;;
 	esac
         ;;