Updates for spack-stack: gsibec, fms, pfunit

configs/common/packages.yaml

@@ -155,13 +155,12 @@ packages:
       - '@2.6.4'
     fms:
       require:
-      - '@2024.02'
+      - '@2025.03'
       - precision=32,64
       - +quad_precision
       - +openmp
       - +pic
       - build_type=Release
-      - +deprecated_io
       - any_of:
         - +gfs_phys constants=GFS
         - ~gfs_phys constants=GEOS
@@ -196,7 +195,7 @@ packages:
       - '@1.4.0'
     gsibec:
       require:
-      - '@1.2.1'
+      - '@1.4.1'
     gsi-ncdiag:
       require:
       - '@1.1.2'
@@ -346,6 +345,10 @@ packages:
     pflogger:
       require:
       - +mpi
+    pfunit:
+      require:
+      - +mpi
+      - +fhamcrest
     pixman:
       require:
       - +pic
@@ -480,10 +483,6 @@ packages:
     snappy:
       require:
       - +shared
-    sp:
-      require:
-      - '@2.5.0'
-      - precision=4,d,8
     udunits:
       require:
       - '@2.2.28'

configs/containers/specs/jedi-ci.yaml

@@ -21,7 +21,7 @@
     fms@2024.02,
     g2@3.5.1,
     g2tmpl@1.17.0,
-    gsibec@1.2.1,
+    gsibec@1.4.1,
     hdf@4.2.15,
     hdf5@1.14.5,
     ip@5.4.0,

configs/sites/tier1/acorn/packages_intel-19.1.3.304.yaml

@@ -91,7 +91,7 @@ packages:
   go:
     require: ['%gcc']
   gsibec:
-    require: ['@1.2.1']
+    require: ['@1.4.1']
   harfbuzz:
     require: ['%gcc']
   libffi:

configs/sites/tier1/acorn/packages_oneapi-2024.2.1.yaml

@@ -76,7 +76,7 @@ packages:
   glib:
     require: ['%gcc']
   gsibec:
-    require: ['@1.2.1']
+    require: ['@1.4.1']
   libtiff:
     require: ['build_system=cmake']
   nco:

configs/sites/tier1/aws-pcluster/packages_intel.yaml

@@ -28,7 +28,7 @@ packages:
     - '@1.2.0 ~mkl +fftw'
   gsibec:
     require::
-    - '@1.2.1 ~mkl'
+    - '@1.4.1 ~mkl'
   py-numpy:
     require::
     - '^openblas'

configs/sites/tier1/hera/packages_intel.yaml

@@ -27,7 +27,7 @@ packages:
     - '@1.2.0 ~mkl +fftw'
   gsibec:
     require::
-    - '@1.2.1 ~mkl'
+    - '@1.4.1 ~mkl'
   py-numpy:
     require::
     - '^openblas'

configs/sites/tier1/hera/packages_oneapi.yaml

@@ -29,7 +29,7 @@ packages:
     - '@1.2.0 ~mkl +fftw'
   gsibec:
     require::
-    - '@1.2.1 ~mkl'
+    - '@1.4.1 ~mkl'
   py-numpy:
     require::
     - '@1.26'

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

@@ -0,0 +1,264 @@
+# How to Build **spack-stack** at NAS on TOSS5
+
+This guide documents how to build **spack-stack** on NASA NAS TOSS5 systems, where login nodes have internet access but are CPU-restricted, while compute nodes allow parallel builds but have *no* internet access. Several packages (Rust/Cargo, ecFlow, CRTM) require special handling due to these constraints.
+
+---
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Machines Required](#machines-required)
+- [Clone spack-stack](#clone-spack-stack)
+- [Obtain an Interactive Compute Node](#obtain-an-interactive-compute-node)
+- [Setup spack-stack](#setup-spack-stack)
+- [Create Environments](#create-environments)
+  - [oneAPI Environment](#oneapi-environment)
+  - [GCC Environment](#gcc-environment)
+- [Activate the Environment](#activate-the-environment)
+- [Concretize the Environment](#concretize-the-environment)
+- [Create Source Cache (LOGIN NODE ONLY)](#create-source-cache-login-node-only)
+- [Pre-Fetch Cargo Dependencies (LOGIN NODE ONLY)](#pre-fetch-cargo-dependencies-login-node-only)
+- [Install Packages](#install-packages)
+  - [Step 1 — Dependencies of Rust codes and ecFlow (COMPUTE NODE)](#step-1--dependencies-of-rust-codes-and-ecflow-compute-node)
+  - [Step 2 — Rust codes and ecFlow (ATHFE LOGIN NODE)](#step-2--rust-codes-and-ecflow-athfe-login-node)
+  - [Step 3 — Remaining Packages (COMPUTE NODE)](#step-3--remaining-packages-compute-node)
+  - [Packages Requiring Internet](#packages-requiring-internet)
+- [Update Module Files](#update-module-files)
+- [Deactivate the Environment](#deactivate-the-environment)
+- [Debugging Package Builds](#debugging-package-builds)
+
+---
+
+## Overview
+
+Due to NAS system architecture and network restrictions:
+
+- **Login nodes**:  
+  - Have internet  
+  - Limited to **2 processes**  
+
+- **Compute nodes** (Turnin):
+  - No internet  
+  - Allow parallel builds  
+
+Some packages (Cargo/Rust, ecFlow, CRTM) require internet or newer CPU features, so the install is broken into multiple steps across different node types.
+
+---
+
+## Machines Required
+
+You will need:
+
+- **An `athfe` login node**
+  Supports x86_64_v3 binaries → required for building Rust packages and ecFlow.
+
+- **A Turnin compute node**
+  Used for the main installation with multiple cores.
+
+---
+
+## Clone spack-stack
+
+Use the appropriate branch or tag:
+
+```bash
+git clone --recurse-submodules https://github.com/JCSDA/spack-stack.git -b spack-stack-2.1.0 spack-stack-2.1.0
+```
+
+---
+
+## Obtain an Interactive Compute Node
+
+NAS login nodes allow only **2 processes**, so use:
+
+```bash
+qsub -I -V -X -l select=1:ncpus=128:mpiprocs=128:model=tur_ath -l walltime=12:00:00 -W group_list=s1873 -m b -N Interactive
+```
+
+This gives a Turin** compute node for up to 12 hours. 
+
+---
+
+## Setup spack-stack
+
+Run on a **login node with internet**:
+
+```bash
+cd spack-stack-2.1.0
+. setup.sh
+```
+
+---
+
+## Create Environments
+
+You only need to create each environment once.
+
+### oneAPI - ifx Environment
+
+```bash
+spack stack create env --name ue-oneapi-2025.3.0 --template unified-dev --site nas-toss5 --compiler=oneapi-2025.3.0
+cd envs/ue-oneapi-2025.3.0
+```
+
+### oneAPI - ifort Environment
+
+```bash
+spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas-toss5 --compiler=oneapi-2024.2.0
+cd envs/ue-oneapi-2024.2.0
+```
+
+### GCC Environment
+
+```bash
+spack stack create env --name ue-gcc-14.2.1 --template unified-dev --site nas-toss5 --compiler=gcc-14.2.1
+cd envs/ue-gcc-14.2.1
+```
+
+---
+
+## Activate the Environment
+
+```bash
+spack env activate .
+```
+
+> **Important:** Run this in *every* terminal where you plan to run Spack commands.
+
+---
+
+## Concretize the Environment
+
+Run on a **login node** (internet required for bootstrapping Clingo and other tools):
+
+```bash
+spack concretize 2>&1 | tee log.concretize ; bell
+```
+
+### Optional `bell` helper
+
+```bash
+bell() { tput bel ; printf "\nFinished at: " ; date; }
+```
+
+---
+
+## Create Source Cache (LOGIN NODE ONLY)
+
+This downloads all source tarballs for your environment:
+
+```bash
+spack mirror create -a -d /swbuild/gmao_SIteam/spack-stack/source-cache
+```
+
+> ⚠️ **Do not run this outside an activated environment.**  
+> Otherwise Spack will attempt to mirror **every** known package/version.
+
+---
+
+## Pre-Fetch Cargo Dependencies (LOGIN NODE ONLY)
+
+Rust packages frequently require network access during build. Pre-fetch their dependencies:
+
+```bash
+export CARGO_HOME=/swbuild/gmao_SIteam/spack-stack/cargo-cache
+../../util/fetch_cargo_deps.py
+```
+
+> ⚠️ **You must also set `CARGO_HOME` on compute nodes** before building.
+
+---
+
+## Install Packages
+
+Installation requires three stages:
+
+| Step | Node Type | Why |
+|------|-----------|-----|
+| Step 1 | Compute | Build dependencies in parallel, avoids CPU limits |
+| Step 2 | `athfe` login | Needed for x86_64_v3 Python and internet access |
+| Step 3 | Compute | Finish main installation at high parallelism |
+
+---
+
+### Step 1 — Dependencies of Rust codes and ecFlow (COMPUTE NODE)
+
+```bash
+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 ; bell
+```
+
+---
+
+### Step 2 — Rust codes and ecFlow (ATHFE LOGIN NODE)
+
+```bash
+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 ; bell
+```
+
+NAS limits login nodes to 2 processes, hence `-j 2`.
+
+---
+
+### Step 3 — Remaining Packages (COMPUTE NODE)
+
+```bash
+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 ; bell
+```
+
+> **Note:** You may need to re-run this command multiple times. Some builds fail intermittently but succeed on retry.
+
+---
+
+### Packages Requiring Internet (ATHFE LOGIN NODE)
+
+If you encounter another package that insists on network access:
+
+```bash
+spack install -j 2 --verbose --fail-fast --show-log-on-error --no-check-signature <package> |& tee log.install.<package> ; bell
+```
+
+Again, this must be done on an **athfe** login node because of the CPU architecture.
+
+Once built, return to the compute node and resume the full installation.
+
+---
+
+## Update Module Files (ATHFE LOGIN NODE)
+
+After installation completes, on an **athfe** login node run:
+
+```bash
+spack module tcl refresh -y --delete-tree ; bell
+spack stack setup-meta-modules
+```
+
+Apparently, spack modulefile generation might use code that spack built for `x86_64_v3`.
+
+---
+
+## Deactivate the Environment
+
+```bash
+spack env deactivate
+```
+
+---
+
+## Debugging Package Builds
+
+```bash
+spack clean
+spack stage <package>
+spack build-env <package> -- bash --norc --noprofile
+```
+
+This drops you into a clean build environment with the package’s full compiler/runtime environment loaded.
+
+---
+
+

configs/sites/tier1/nas-toss5/config.yaml

@@ -0,0 +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-toss5/mirrors.yaml

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

configs/sites/tier1/nas-toss5/modules.yaml

@@ -0,0 +1,8 @@
+modules:
+  default:
+    enable::
+    - tcl
+    tcl:
+      include:
+      # List of packages for which we need modules that are blacklisted by default
+      - python