Update Atlantis and Nautilus: add [email protected] stack (#1707)

Update gcc@11 stacks on Atlantis and Nautilus to [email protected]. No changes are made for the gcc backend for Intel oneAPI. For both systems, the existing OpenMPI installations are used (provided by the system administrators).

Author: climbfuji

configs/common/packages.yaml

@@ -274,7 +274,7 @@ packages:
     require: '@69'
   py-setuptools-rust:
     require: '+rust_bootstrap'
-  # When making changes here, also check the tier2/blackpearl/packages.yaml
+  # When making changes here, also check the packages.yaml for atlantis, nautilus, blackpearl
   py-torch:
     require:
     - '+custom-protobuf ~mkldnn'

configs/sites/tier1/atlantis/compilers.yaml

@@ -31,7 +31,25 @@ compilers:
     modules:
     - gcc/11.2.0
     environment: {}
-    extra_rpaths: []
+    # For compiling parallel-netcdf; Bright must have removed some symbolic links required for OpenMPI 4.1.5a1 ...
+    extra_rpaths: [/gpfs/neptune/spack-stack/openmpi-4.1.5-fix-lib]
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/gcc
+      cxx: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/g++
+      f77: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/gfortran
+      fc: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules:
+    - gcc/13.4.0
+    environment:
+      prepend_path:
+        MODULEPATH: /gpfs/neptune/spack-stack/openmpi-5.0.6/gcc-13.4.0/modulefiles:/gpfs/neptune/spack-stack/gcc-13.4.0/modulefiles
+    # For compiling parallel-netcdf; Bright must have removed some symbolic links required for OpenMPI 4.1.5a1 ...
+    extra_rpaths: [/gpfs/neptune/spack-stack/openmpi-4.1.5-fix-lib]
 - compiler:
     spec: [email protected]
     paths:

configs/sites/tier1/atlantis/packages.yaml

@@ -11,6 +11,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  # Pin py-torch to 2.5.1 to avoid build errors with 2.6.0
+  py-torch:
+    require:
+        - '@2.5.1'
 
 # All other packages listed alphabetically
   autoconf:

configs/sites/tier1/atlantis/packages_gcc.yaml

@@ -1,14 +1,14 @@
 packages:
   all:
-    compiler:: [gcc@11.2.0]
+    compiler:: [gcc@13.4.0]
     providers:
       mpi:: [[email protected]]
   mpi:
     buildable: False
   openmpi:
     buildable: False
     externals:
-    - spec: [email protected]%gcc@=11.2.0~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath fabrics=ucx schedulers=slurm
+    - spec: [email protected] ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath fabrics=ucx schedulers=slurm %gcc@=13.4.0
       # Note: slurm must be loaded before openmpi on Atlantis
       modules:
       - slurm

configs/sites/tier1/nautilus/compilers.yaml

@@ -15,25 +15,6 @@ compilers::
     - amd/aocl/aocc/4.0
     environment: {}
     extra_rpaths: []
-- compiler:
-    spec: [email protected]
-    paths:
-      cc: /p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icc
-      cxx: /p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/icpc
-      f77: /p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
-      fc: /p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
-    flags: {}
-    operating_system: rhel8
-    target: x86_64
-    modules:
-    - slurm
-    - intel/compiler/2022.0.2
-    environment:
-      prepend_path:
-        PATH: '/opt/rh/gcc-toolset-11/root/usr/bin'
-        CPATH: '/opt/rh/gcc-toolset-11/root/usr/include'
-        LD_LIBRARY_PATH: '/opt/scyld/slurm/lib64:/opt/scyld/slurm/lib64/slurm:/p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/rh/gcc-toolset-11/root/usr/lib64:/opt/rh/gcc-toolset-11/root/usr/lib'
-    extra_rpaths: []
 - compiler:
     spec: [email protected]
     paths:
@@ -99,3 +80,20 @@ compilers::
     - scl/gcc-toolset-11
     environment: {}
     extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/bin/gcc
+      cxx: /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/bin/g++
+      f77: /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/bin/gfortran
+      fc: /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules:
+    - slurm
+    - gcc/13.4.0
+    environment:
+      prepend_path:
+        MODULEPATH: '/p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/modulefiles'
+    extra_rpaths: []

configs/sites/tier1/nautilus/packages.yaml

@@ -12,6 +12,11 @@ packages:
     - spec: [email protected]
       prefix: /usr
 
+  # Pin py-torch to 2.5.1 to avoid build errors with 2.6.0
+  py-torch:
+    require:
+        - '@2.5.1'
+
 # All other packages listed alphabetically
   autoconf:
     externals:

configs/sites/tier1/nautilus/packages_gcc.yaml

@@ -1,13 +1,13 @@
 packages:
   all:
-    compiler:: [gcc@11.2.1]
+    compiler:: [gcc@13.4.0]
     providers:
       mpi:: [[email protected]]
   mpi:
     buildable: False
   openmpi:
     externals:
-    - spec: [email protected]~cuda~java~memchecker~static~wrapper-rpath fabrics=ucx schedulers=slurm %gcc@11.2.1
+    - spec: [email protected]~cuda~java~memchecker~static~wrapper-rpath fabrics=ucx schedulers=slurm %gcc@13.4.0
       prefix: /p/app/penguin/openmpi/5.0.1/gcc-8.5.0
       modules:
       - penguin/openmpi/5.0.1/gcc-8.5.0

doc/source/PreConfiguredSites.rst

@@ -153,13 +153,19 @@ The following is required for building new spack environments with any supported
 NAVY HPCMP Nautilus
 ------------------------------
 
-The following is required for building new spack environments with any supported compiler on this platform.
+The following is required for building new spack environments with any supported compiler on this platform. For ``[email protected]``, see the additional instructions below.
 
 .. code-block:: console
 
    umask 0022
    module purge
 
+For ``[email protected]``, further run:
+
+.. code-block:: console
+
+   module use /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/modulefiles
+
 
 .. _Preconfigured_Sites_Blueback:
 

util/nrl/batch_install.sh

@@ -105,7 +105,7 @@ SPACK_STACK_BATCH_HOST=${SPACK_STACK_BATCH_HOST//[0-9]/}
 
 case ${SPACK_STACK_BATCH_HOST} in
   atlantis)
-    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.1" "oneapi@=2025.0.3" "gcc@=11.2.0" "clang@=20.1.5")
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.1" "oneapi@=2025.0.3" "gcc@=13.4.0" "clang@=20.1.5")
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "unified-dev" "cylc-dev")
     SPACK_STACK_MODULE_CHOICE="lmod"
     SPACK_STACK_BOOTSTRAP_MIRROR="/neptune_diagnostics/spack-stack/bootstrap-mirror"
@@ -133,7 +133,7 @@ case ${SPACK_STACK_BATCH_HOST} in
     SPACK_STACK_CARGO_MIRROR="/p/cwfs/projects/NEPTUNE/spack-stack/cargo-mirror"
     ;;
   nautilus)
-    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.1" "oneapi@=2025.1.1" "gcc@=11.2.1")
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.1" "oneapi@=2025.1.1" "gcc@=13.4.0")
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "unified-dev" "cylc-dev")
     SPACK_STACK_MODULE_CHOICE="tcl"
     SPACK_STACK_BOOTSTRAP_MIRROR="/p/cwfs/projects/NEPTUNE/spack-stack/bootstrap-mirror"
@@ -389,6 +389,9 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
             module use /gpfs/neptune/spack-stack/llvm-20.1.5/modulefiles
             module use /gpfs/neptune/spack-stack/openmpi-5.0.6/llvm-20.1.5/modulefiles
             ;;
+          gcc@=13.4.0)
+            module use /gpfs/neptune/spack-stack/gcc-13.4.0/modulefiles
+            ;;
         esac
         ;;
       blueback)
@@ -412,6 +415,11 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
       nautilus)
         umask 0022
         module purge
+        case ${compiler} in
+          gcc@=13.4.0)
+            module use /p/app/projects/NEPTUNE/spack-stack/gcc-13.4.0/modulefiles
+            ;;
+        esac
         ;;
       tusk)
         umask 0022