Updates for spack-stack: gsibec, fms, pfunit (#1908)

This PR has updates for spack-stack v2.1. It's mainly involved with:

* Add pFUnit 4.15.0 ([INSTALL]: pfunit 4.15.0 #1840)
* Add FMS 2025.03 ([INSTALL]: for spack-stack-2.0, update to fms@2025.03 #1547)
* Add gsibec 1.4.2 ([INSTALL]: for spack-stack-2.1, update to gsibec@1.4.2 #1648)
* Remove sp library (Remove sp library in spack-stack-1.9.0 --> spack-stack-2.1.0 #1330)

I've also added a new ifx testing stack/setup for NAS as well as my testing for NAS-TOSS5 (see #1905 and #1907 )

Author: mathomp4

configs/common/packages.yaml

@@ -158,13 +158,12 @@ 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
@@ -199,7 +198,7 @@ packages:
       - '@1.4.0'
     gsibec:
       require:
-      - '@1.2.1'
+      - '@1.4.2'
     gsi-ncdiag:
       require:
       - '@1.1.2'
@@ -349,6 +348,10 @@ 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@1.4.2,
     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: ['@1.4.2']
   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: ['@1.4.2']
   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'
+    - '@1.4.2 ~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'
+    - '@1.4.2 ~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'
+    - '@1.4.2 ~mkl'
   py-numpy:
     require::
     - '@1.26'

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

@@ -0,0 +1,246 @@
+# How to Build **spack-stack** at NAS on TOSS5
+
+This guide documents how to build **spack-stack** on NASA NAS TOSS5 systems. The previous install process used three stages across compute and login nodes, but recent testing shows installation can now be done directly on a compute node.
+
+---
+
+## 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 - ifx Environment](#oneapi---ifx-environment)
+  - [oneAPI - ifort Environment](#oneapi---ifort-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 (COMPUTE NODE)](#install-packages-compute-node)
+- [Update Module Files](#update-module-files)
+- [Deactivate the Environment](#deactivate-the-environment)
+- [Debugging Package Builds](#debugging-package-builds)
+- [Deprecated: Legacy Three-Step Install](#deprecated-legacy-three-step-install)
+
+---
+
+## Overview
+
+NAS login nodes and compute nodes have different constraints:
+
+- **Login nodes**:
+  - Have internet access
+  - Limited to **2 processes**
+
+- **Compute nodes** (Turin):
+  - No internet access
+  - Allow parallel builds
+
+Use login nodes for setup steps that require internet access (e.g., concretization, mirroring sources, pre-fetching Cargo dependencies), then run installation on a compute node.
+
+The install step itself is now a single compute-node command.
+
+---
+
+## Machines Required
+
+You will need:
+
+- **A login node**
+  Used for setup steps that require internet access.
+
+- **A Turin compute node**
+  Used for package installation with higher parallelism.
+
+---
+
+## 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
+```
+
+> ⚠️ **Set `CARGO_HOME` on compute nodes** before running `spack install`.
+
+---
+
+## Install Packages (COMPUTE NODE)
+
+Run installation on a **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 ; bell
+```
+
+This replaces the former compute → login → compute install sequence.
+
+> **Note:** You may need to re-run this command multiple times. Some builds fail intermittently but succeed on retry.
+
+---
+
+## Update Module Files
+
+After installation completes, run:
+
+```bash
+spack module tcl refresh -y --delete-tree ; bell
+spack stack setup-meta-modules
+```
+
+---
+
+## 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.
+
+---
+
+## Deprecated: Legacy Three-Step Install
+
+> ⚠️ **Deprecated:** Keep this only as historical reference. Prefer the single compute-node install above.
+
+Older workflows used three stages:
+
+1. Compute node: build dependencies for Rust-related Python packages and ecFlow.
+2. `athfe` login node: build `py-cryptography`, `py-maturin`, `py-rpds-py`, and `ecflow` with `-j 2`.
+3. Compute node: run full `spack install` to finish remaining packages.
+
+Typical commands were:
+
+```bash
+# Step 1 (compute node)
+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 (athfe login node)
+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
+
+# Step 3 (compute node)
+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
+```
+
+---

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
+