[skip ci] Updates for spack v1 at NAS

.github/workflows/ubuntu-ci-x86_64-gnu.yaml

@@ -112,7 +112,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -190,7 +190,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.yaml

@@ -128,7 +128,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -209,7 +209,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

.github/workflows/ubuntu-ci-x86_64-oneapi.yaml

@@ -128,7 +128,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -209,7 +209,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

configs/common/modules_lmod.yaml

@@ -142,6 +142,10 @@ modules:
           ^esmf@8.8.0+debug snapshot=none: 'esmf-8.8.0-debug'
           ^esmf@8.9.0~debug snapshot=none: 'esmf-8.9.0'
           ^esmf@8.9.0+debug snapshot=none: 'esmf-8.9.0-debug'
+      fms:
+        suffixes:
+          constants=GFS: 'gfs-constants'
+          constants=GEOS: 'geos-constants'
       openmpi:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -161,6 +161,10 @@ modules:
           ^esmf@8.8.0+debug snapshot=none: 'esmf-8.8.0-debug'
           ^esmf@8.9.0~debug snapshot=none: 'esmf-8.9.0'
           ^esmf@8.9.0+debug snapshot=none: 'esmf-8.9.0-debug'
+      fms:
+        suffixes:
+          constants=GFS: 'gfs-constants'
+          constants=GEOS: 'geos-constants'
       openmpi:
         environment:
           set:

configs/common/packages.yaml

@@ -107,7 +107,10 @@ packages:
     fms:
       require:
       - '@2024.02'
-      - precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io
+      - precision=32,64 +quad_precision +openmp +pic build_type=Release +deprecated_io
+      - any_of:
+        - +gfs_phys constants=GFS
+        - ~gfs_phys constants=GEOS
     fontconfig:
       require:
       - +pic
@@ -206,8 +209,6 @@ packages:
       require:
       - '@2.53'
       - ~shared ~f2py +pflogger
-    # Note: Please check the sites/tier1/nas/packages_gcc.yaml if
-    #       this is changed, as it has a custom variant combination
     met:
       require:
       - '@12.0.1'

configs/sites/tier1/nas/README.md

@@ -3,10 +3,15 @@
 In the commands below some will be run on login nodes (with internet access) and some
 on compute nodes as, at NAS, you aren't allowed more than 2 processes on a login node.
 
+## Machines
+
+For the below you will need to login to both an `afe01` node for one step. You'll
+also want to get a Rome compute node for the rest of the steps.
+
 ## Clone spack-stack
 
 ```
-git clone --recursive https://github.com/JCSDA/spack-stack.git -b release/1.9.0 spack-stack-1.9.3
+git clone --recurse-submodules https://github.com/mathomp4/spack-stack.git -b feature/nas_install_spack_v1 spack-stack-2.0.0-test
 ```
 
 ## Grab interactive node
@@ -23,7 +28,7 @@ We will start on a login node with internet access. This is mainly needed for th
 `spack mirror create` command which downloads all the source code for the packages.
 
 ```
-cd spack-stack-1.9.3
+cd spack-stack-2.0.0-test
 . setup.sh
 ```
 
@@ -37,7 +42,7 @@ are used to create the environments. You only need to do this once.
 To create the oneAPI environment, do:
 
 ```
-spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler oneapi
+spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler=oneapi-2024.2.0
 cd envs/ue-oneapi-2024.2.0
 ```
 
@@ -46,8 +51,8 @@ cd envs/ue-oneapi-2024.2.0
 To create the GCC environment, do:
 
 ```
-spack stack create env --name ue-gcc-12.3.0 --template unified-dev --site nas --compiler gcc
-cd envs/ue-gcc-12.3.0
+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
 ```
 
 ## Activate environment
@@ -67,41 +72,75 @@ below with this environment.
 spack concretize 2>&1 | tee log.concretize
 ```
 
+NOTE: The first time you do this on a new build, you should do it on a *LOGIN* node. This is because
+it might need to bootstrap things and so it will reach out to the internet.
+
 ## Create source cache (LOGIN NODE ONLY)
 
 Because this step downloads all the source code for all packages and all versions, it
 should be done on a login node with internet access.
 
 ```
-spack mirror create -a -d /nobackup/gmao_SIteam/spack-stack/source-cache
+spack mirror create -a -d /swbuild/gmao_SIteam/spack-stack/source-cache
 ```
 
 NOTE: Make sure you are in an environment when you run that `spack mirror create` command. Otherwise,
 you will download *EVERY* package and *EVERY* version in spack!
 
+## Pre-fetch cargo packages (LOGIN NODE ONLY)
+
+Some packages use Rust/Cargo for dependencies. These need internet access to build. So we pre-fetch them here.
+
+We need to set `CARGO_HOME` to a location where the Cargo deps have been downloaded
+
+```
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+../../util/fetch_cargo_deps.py
+```
+
+NOTE: `CARGO_HOME` should be set as well on the COMPUTE node!
+
 ## Install packages
 
 Our install process will actually have (at least) three steps. This is because of the `crtm` package
 which requires internet access at build time.
 
-### Install crtm dependencies (COMPUTE NODE)
+### Install Step 1: Dependencies of Rust codes and ecflow (COMPUTE NODE)
+
+We currently have some codes that use rust/cargo for dependencies. And, for some reason,
+even doing the "cargo dependencies" as above, they still need internet
+access to build/install. 
+
+As for ecflow, we built QT on a login node (as it was the only complete node), so we
+then have to build ecflow on a login node as well.
+
+So we first install all the dependencies of then codes.
 
 ```
-spack install -j 10 --verbose --fail-fast --show-log-on-error --no-check-signature --only dependencies crtm 2>&1 | tee log.install.crtm_dependencies
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+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
 ```
 
-### Install crtm (LOGIN NODE)
+### Install Step 2: Rust Codes and ecflow (AFE LOGIN NODE)
+
+NOTE: You *MUST* run this on an afe login node. The reason is the pfe login nodes are Sandy
+Bridge but we are building Spack with `x86_64_v3` and these are too old (`_v2`). So 
+you will get an illegal instruction error when the install below calls python3.
+
+So go back to an afe login node and run:
 
 ```
-spack install -j 2 --verbose --fail-fast --show-log-on-error --no-check-signature crtm 2>&1 | tee log.install.crtm
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+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
 ```
 
 Note we are only using 2 processes here because NAS limits you to 2 processes on a login node.
 
-### Install rest of packages (COMPUTE NODE)
+### Install Step 3: The rest (COMPUTE NODE)
 
 ```
-spack install -j 10 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install.after_crtm
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+spack install -j 16 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install.after-cargo
 ```
 
 NOTE: You might need to run the `spack install` command multiple times because sometimes
@@ -120,7 +159,7 @@ Then, once that package is built, you can go back to the compute node and run th
 ## Update module files and setup meta-modules
 
 ```
-spack module tcl refresh -y
+spack module tcl refresh -y --delete-tree
 spack stack setup-meta-modules
 ```
 
@@ -129,3 +168,13 @@ spack stack setup-meta-modules
 ```
 spack env deactivate
 ```
+
+# Debugging a package
+
+When things go wrong, a good way to debug a failure is:
+
+```
+spack clean
+spack stage <package>
+spack build-env <package> -- bash --norc --noprofile
+```

configs/sites/tier1/nas/config.yaml

@@ -1,2 +1,9 @@
 config:
   build_jobs: 6
+
+  # Overrides for spack build and staging areas to speed up builds
+  # and avoid errors with Lustre file locking and xattr issues
+  build_stage:  /swbuild/gmao_SIteam/spack-stack/cache/build_stage
+  test_stage:   /swbuild/gmao_SIteam/spack-stack/cache/test_stage
+  source_cache: /swbuild/gmao_SIteam/spack-stack/cache/source_cache
+  misc_cache:   /swbuild/gmao_SIteam/spack-stack/cache/misc_cache

configs/sites/tier1/nas/mirrors.yaml

@@ -1,18 +1,3 @@
 mirrors:
-  local-source:
-    fetch:
-      url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
-    push:
-      url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
+  local-source: file:///swbuild/gmao_SIteam/spack-stack/source-cache
+  local-binary: file:///swbuild/gmao_SIteam/spack-stack/binary-cache-spack-v1

configs/sites/tier1/nas/packages.yaml

@@ -7,6 +7,8 @@ packages:
     variants: ~shared
   met:
     variants: +python +grib2 +graphics +lidar2nc +modis
+  zlib-api:
+    buildable: False
 ### All other external packages listed alphabetically
   automake:
     externals:
@@ -20,6 +22,10 @@ packages:
     externals:
     - spec: bison@3.0.4
       prefix: /usr
+  cmake:
+    externals:
+    - spec: cmake@4.0.2
+      prefix: /nobackup/gmao_SIteam/cmake/cmake-4.0.2
   coreutils:
     externals:
     - spec: coreutils@8.30
@@ -45,10 +51,12 @@ packages:
     - spec: gh@2.78.0
       prefix: /nobackup/gmao_SIteam/gh/2.78.0
   git:
+    buildable: False
     externals:
     - spec: git@2.43.5~tcltk
       prefix: /usr
   git-lfs:
+    buildable: False
     externals:
     - spec: git-lfs@3.7.0
       prefix: /nobackup/gmao_SIteam/git-lfs/3.7.0
@@ -80,6 +88,11 @@ packages:
     externals:
     - spec: pkgconf@1.4.2
       prefix: /usr
+  qt:
+    buildable: False
+    externals:
+    - spec: qt@5.15.18
+      prefix: /nobackup/gmao_SIteam/qt5/5.15.18
   sed:
     externals:
     - spec: sed@4.5
@@ -97,6 +110,7 @@ packages:
     - spec: wget@1.19.5
       prefix: /usr
   zlib:
+    buildable: False
     externals:
     - spec: zlib@1.2.11
       prefix: /usr