Various updates for GMAO, NAS, and NCCS

.gitignore

@@ -7,3 +7,8 @@ doc/build
 deploy_logs/
 logs/
 log.*
+spack-install.*
+tmp-bootstrap-mirror/
+spack.nas.*
+spack.nas-toss5.*
+spack.discover*

configs/common/packages.yaml

@@ -261,7 +261,7 @@ packages:
       - generator=make
     libpng:
       require:
-      - '@1.6.37'
+      - '@1.6.55'
       - +pic
     # libtirpc +gssapi doesn't build with oneapi@2025
     # https://github.com/JCSDA/spack-stack/issues/1441
@@ -414,7 +414,8 @@ packages:
     # https://github.com/JCSDA/spack-stack/issues/1276
     py-matplotlib:
       require:
-      - '@3.7.4'
+      - '@3.10.8'
+      #- '@3.7.4'
       #- '@3.8.0'
     # https://github.com/JCSDA/spack-stack/issues/1971
     py-netcdf4:

configs/sites/tier1/discover/mirrors.yaml

@@ -0,0 +1,8 @@
+mirrors:
+  local-source:
+    url: file:///discover/swdev/jcsda/spack-stack/source-cache
+    binary: false
+  local-binary:
+    url: file:///discover/swdev/jcsda/spack-stack/build-cache
+    binary: true
+

configs/sites/tier1/discover-scu17/packages.yaml → configs/sites/tier1/discover/packages.yaml

@@ -31,8 +31,10 @@ packages:
       prefix: /usr
   cmake:
     externals:
-    - spec: cmake@3.28.2
-      prefix: /usr/local/other/cmake/3.28.2
+    - spec: cmake@3.30.3
+      prefix: /usr/local/other/cmake/3.30.3
+    - spec: cmake@4.3.0
+      prefix: /usr/local/other/cmake/4.3.0
   coreutils:
     externals:
     - spec: coreutils@8.32
@@ -69,15 +71,10 @@ packages:
     externals:
     - spec: git@2.35.3+tcltk
       prefix: /usr
-    - spec: git@2.42.0+tcltk
-      prefix: /usr/local/other/git/2.42.0/gcc-7.5.0
+    - spec: git@2.49.0+tcltk
+      prefix: /usr/local/other/git/2.49.0/gcc-7.5.0
       modules:
-      - git/2.42.0
-    # DH*
-    #- spec: git@2.42.0~tcltk
-    #  prefix: /usr/local/other/git/2.42.0/gcc-7.5.0/libexec/git-core
-    #  modules:
-    #  - git/2.42.0
+      - git/2.49.0
   git-lfs:
     externals:
     - spec: git-lfs@3.4.0
@@ -143,3 +140,12 @@ packages:
     externals:
     - spec: texinfo@6.5
       prefix: /usr
+  wget:
+    externals:
+    - spec: wget@1.20.3
+      prefix: /usr
+  zlib:
+    buildable: False
+    externals:
+    - spec: zlib@1.2.11
+      prefix: /usr

configs/sites/tier1/discover/packages_gcc-14.2.0.yaml

@@ -0,0 +1,48 @@
+packages:
+  all:
+    require:
+    - any_of: ['%gcc@=14.2.0']
+      when: '%gcc'
+  mpi:
+    buildable: false
+    require:
+    - "openmpi@4.1.6"
+  gcc:
+    buildable: false
+    externals:
+    - spec: gcc@14.2.0 languages:='c,c++,fortran'
+      prefix: /usr/local/other/gcc/gcc-14.2.0
+      modules:
+      - comp/gcc/14.2.0
+      extra_attributes:
+        compilers:
+          c: /usr/local/other/gcc/gcc-14.2.0/bin/gcc
+          cxx: /usr/local/other/gcc/gcc-14.2.0/bin/g++
+          fortran: /usr/local/other/gcc/gcc-14.2.0/bin/gfortran
+  openmpi:
+    buildable: false
+    externals:
+    - spec: openmpi@4.1.6 ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath+lustre~internal-hwloc+two_level_namespace fabrics=ucx schedulers=slurm %gcc@14.2.0
+      prefix: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0
+      modules:
+      - mpi/openmpi/4.1.6/gcc-14.2.0
+      extra_attributes:
+        environment:
+          set:
+            OMPI_MCA_orte_tmpdir_base: /tmp
+            OMP_STACKSIZE: 1G
+            OMPI_MCA_mca_base_component_show_load_errors: 0
+            PMIX_MCA_mca_base_component_show_load_errors: 0
+            OMPI_MCA_coll_hcoll_enable: 0
+            OPENMPI: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0
+          prepend_path:
+            PATH: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0/bin
+            LIBRARY_PATH: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0/lib
+            LD_LIBRARY_PATH: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0/lib
+            INCLUDE: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0/include
+            MANPATH: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-14.2.0
+
+  # Testing shows we now need to pass in -lm for GCC
+  p4est:
+    require:
+    - 'ldflags="-lm"'

configs/sites/tier1/discover-scu17/packages_oneapi.yaml → configs/sites/tier1/discover/packages_oneapi-2024.2.0.yaml

@@ -1,13 +1,16 @@
 packages:
   all:
-    prefer:
-    - '%oneapi'
-    providers:
-      mpi:: [intel-oneapi-mpi@2021.13]
+    require:
+    - any_of: ['%intel-oneapi-compilers@=2024.2.0']
+      when: '%intel-oneapi-compilers'
+    - any_of: ['%gcc@=12.3.0']
+      when: '%gcc'
   mpi:
-    buildable: False
+    buildable: false
+    require:
+    - "intel-oneapi-mpi@2021.13"
   intel-oneapi-compilers:
-    buildable: False
+    buildable: false
     externals:
     - spec: intel-oneapi-compilers@2024.2.0
       prefix: /usr/local/intel/oneapi/2024
@@ -18,32 +21,18 @@ packages:
           c: /usr/local/intel/oneapi/2024/compiler/2024.2/bin/icx
           cxx: /usr/local/intel/oneapi/2024/compiler/2024.2/bin/icpx
           fortran: /usr/local/intel/oneapi/2024/compiler/2024.2/bin/ifort
-          f77: /usr/local/intel/oneapi/2024/compiler/2024.2/bin/ifort
         environment:
-          set:
-            # Force ifort not ifx
-            INTEL_COMPILER_TYPE: 'RECOMMENDED'
           prepend_path:
             PATH: /usr/local/other/gcc/12.3.0/bin
             CPATH: /usr/local/other/gcc/12.3.0/include
-            LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2024/compiler/2024.2/lib/:/usr/local/other/gcc/12.3.0/lib64'
+            LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2024/compiler/2024.2/compiler/lib:/usr/local/other/gcc/12.3.0/lib64'
         extra_rpaths:
         - /usr/local/other/gcc/12.3.0/lib64
-  intel-oneapi-mpi:
-    buildable: False
-    externals:
-    - spec: intel-oneapi-mpi@2021.13
-      prefix: /usr/local/intel/oneapi/2024
-      modules:
-      - mpi/impi/2021.13
-  intel-oneapi-mkl:
-    buildable: false
-    externals:
-    - spec: intel-oneapi-mkl@2024.2.0
-      prefix: /usr/local/intel/oneapi/2024
+        - /usr/local/other/gcc/12.3.0/lib
   gcc:
+    buildable: false
     externals:
-    - spec: gcc@12.3.0 languages:='c,c++,fortran'
+    - spec: gcc@12.3.0 languages:='c,c++'
       prefix: /usr/local/other/gcc/12.3.0
       modules:
       - comp/gcc/12.3.0
@@ -52,6 +41,15 @@ packages:
           c: /usr/local/other/gcc/12.3.0/bin/gcc
           cxx: /usr/local/other/gcc/12.3.0/bin/g++
           fortran: /usr/local/other/gcc/12.3.0/bin/gfortran
-        flags: {}
-        environment: {}
-        extra_rpaths: []
+  intel-oneapi-mpi:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mpi@2021.13
+      prefix: /usr/local/intel/oneapi/2024
+      modules:
+      - mpi/impi/2021.13
+  intel-oneapi-mkl:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mkl@2024.2
+      prefix: /usr/local/intel/oneapi/2024

configs/sites/tier1/discover/packages_oneapi-2025.3.0.yaml

@@ -0,0 +1,55 @@
+packages:
+  all:
+    require:
+    - any_of: ['%intel-oneapi-compilers@=2025.3.0']
+      when: '%intel-oneapi-compilers'
+    - any_of: ['%gcc@=12.3.0']
+      when: '%gcc'
+  mpi:
+    buildable: false
+    require:
+    - "intel-oneapi-mpi@2021.17"
+  intel-oneapi-compilers:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-compilers@2025.3.0
+      prefix: /usr/local/intel/oneapi/2025
+      modules:
+      - comp/intel/2025.3.0
+      extra_attributes:
+        compilers:
+          c: /usr/local/intel/oneapi/2025/compiler/2025.3/bin/icx
+          cxx: /usr/local/intel/oneapi/2025/compiler/2025.3/bin/icpx
+          fortran: /usr/local/intel/oneapi/2025/compiler/2025.3/bin/ifx
+        environment:
+          prepend_path:
+            PATH: /usr/local/other/gcc/12.3.0/bin
+            CPATH: /usr/local/other/gcc/12.3.0/include
+            LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2025/compiler/2025.3/compiler/lib:/usr/local/other/gcc/12.3.0/lib64'
+        extra_rpaths:
+        - /usr/local/other/gcc/12.3.0/lib64
+        - /usr/local/other/gcc/12.3.0/lib
+  gcc:
+    buildable: false
+    externals:
+    - spec: gcc@12.3.0 languages:='c,c++'
+      prefix: /usr/local/other/gcc/12.3.0
+      modules:
+      - comp/gcc/12.3.0
+      extra_attributes:
+        compilers:
+          c: /usr/local/other/gcc/12.3.0/bin/gcc
+          cxx: /usr/local/other/gcc/12.3.0/bin/g++
+          fortran: /usr/local/other/gcc/12.3.0/bin/gfortran
+  intel-oneapi-mpi:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mpi@2021.17
+      prefix: /usr/local/intel/oneapi/2025
+      modules:
+      - mpi/impi/2021.17
+  intel-oneapi-mkl:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mkl@2025.3
+      prefix: /usr/local/intel/oneapi/2025

configs/sites/tier1/nas-toss5/README.md

@@ -161,7 +161,7 @@ spack mirror create -a -d /swbuild/gmao_SIteam/spack-stack/source-cache
 Rust packages frequently require network access during build. Pre-fetch their dependencies:
 
 ```bash
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 ../../util/fetch_cargo_deps.py
 ```
 
@@ -174,7 +174,7 @@ export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
 Run installation on a **compute node**:
 
 ```bash
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install ; bell
 ```
 
@@ -229,17 +229,17 @@ Typical commands were:
 
 ```bash
 # Step 1 (compute node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature \
   --only dependencies py-cryptography py-maturin py-rpds-py ecflow 2>&1 | tee log.install.deps-for-rust-and-ecflow ; bell
 
 # Step 2 (athfe login node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 2 -p 1 --verbose --fail-fast --show-log-on-error --no-check-signature \
   py-cryptography py-maturin py-rpds-py ecflow 2>&1 | tee log.install.rust-and-ecflow ; bell
 
 # Step 3 (compute node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install.after-cargo ; bell
 ```
 

configs/sites/tier1/nas/README.md

@@ -113,8 +113,8 @@ cd envs/ue-oneapi-2024.2.0
 ### GCC Environment
 
 ```bash
-spack stack create env --name ue-gcc-13.2.0 --template unified-dev --site nas --compiler=gcc-13.2.0
-cd envs/ue-gcc-13.2.0
+spack stack create env --name ue-gcc-14.2.0 --template unified-dev --site nas --compiler=gcc-14.2.0
+cd envs/ue-gcc-14.2.0
 ```
 
 ---
@@ -163,7 +163,7 @@ spack mirror create -a -d /swbuild/gmao_SIteam/spack-stack/source-cache
 Rust packages frequently require network access during build. Pre-fetch their dependencies:
 
 ```bash
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 ../../util/fetch_cargo_deps.py
 ```
 
@@ -176,7 +176,7 @@ export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
 Run installation on a **compute node**:
 
 ```bash
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install ; bell
 ```
 
@@ -231,17 +231,17 @@ Typical commands were:
 
 ```bash
 # Step 1 (compute node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature \
   --only dependencies py-cryptography py-maturin py-rpds-py ecflow 2>&1 | tee log.install.deps-for-rust-and-ecflow ; bell
 
 # Step 2 (afe login node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 2 -p 1 --verbose --fail-fast --show-log-on-error --no-check-signature \
   py-cryptography py-maturin py-rpds-py ecflow 2>&1 | tee log.install.rust-and-ecflow ; bell
 
 # Step 3 (compute node)
-export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-mirror
 spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install.after-cargo ; bell
 ```