JCSDA · climbfuji · Nov 3, 2025 · Jul 22, 2025 · Jul 22, 2025 · Jul 22, 2025
diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg
@@ -2,10 +2,6 @@
     externals:
     - spec: intel-oneapi-compilers@2024.2.0
       prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
-      - compiler-rt/2024.2.0
-      - compiler/2024.2.0
       extra_attributes:
         compilers:
           c: /opt/intel/oneapi/compiler/2024.2/bin/icx
@@ -16,27 +12,13 @@
     externals:
     - spec: intel-oneapi-runtime@2024.2.0
       prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
-      - compiler-rt/2024.2.0
-  intel-oneapi-tbb:
-    buildable: false
-    externals:
-    - spec: intel-oneapi-tbb@2021.13
-      prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
   intel-oneapi-mkl:
     buildable: false
     externals:
     - spec: intel-oneapi-mkl@2024.2
       prefix: /opt/intel/oneapi
-      modules:
-      - mkl/2024.2
   intel-oneapi-mpi:
     buildable: false
     externals:
     - spec: intel-oneapi-mpi@2021.13
       prefix: /opt/intel/oneapi
-      modules:
-      - mpi/2021.13
diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg
@@ -2,10 +2,6 @@
     externals:
     - spec: intel-oneapi-compilers@2024.2.0
       prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
-      - compiler-rt/2024.2.0
-      - compiler/2024.2.0
       extra_attributes:
         compilers:
           c: /opt/intel/oneapi/compiler/2024.2/bin/icx
@@ -16,27 +12,13 @@
     externals:
     - spec: intel-oneapi-runtime@2024.2.0
       prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
-      - compiler-rt/2024.2.0
-  intel-oneapi-tbb:
-    buildable: false
-    externals:
-    - spec: intel-oneapi-tbb@2021.13
-      prefix: /opt/intel/oneapi
-      modules:
-      - tbb/2021.13
   intel-oneapi-mkl:
     buildable: false
     externals:
     - spec: intel-oneapi-mkl@2024.2
       prefix: /opt/intel/oneapi
-      modules:
-      - mkl/2024.2
   intel-oneapi-mpi:
     buildable: false
     externals:
     - spec: intel-oneapi-mpi@2021.13
       prefix: /opt/intel/oneapi
-      modules:
-      - mpi/2021.13
diff --git a/configs/common/modules_lmod.yaml b/configs/common/modules_lmod.yaml
@@ -90,6 +90,11 @@ modules:
       - xtrans
       - xz
       - yaksa
+      # By default, do not create compiler modules
+      - apple-clang
+      - gcc
+      - intel-oneapi-compilers
+      - llvm
       # By default, do not create MPI modules
       - cray-mpich
       - intel-mpi

diff --git a/configs/common/modules_tcl.yaml b/configs/common/modules_tcl.yaml
@@ -88,6 +88,11 @@ modules:
       - xtrans
       - xz
       - yaksa
+      # By default, do not create compiler modules
+      - apple-clang
+      - gcc
+      - intel-oneapi-compilers
+      - llvm
       # By default, do not create MPI modules
       - cray-mpich
       - intel-mpi

diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml
@@ -263,6 +263,11 @@ packages:
     p4est:
       require:
       - '@2.8.7'
+    # Earlier versions of pango don't build on Blueback because of
+    # a bug in finding the correct Python interpreter from spack.
+    pango:
+      require:
+      - '@1.54:'
     parallelio:
       require:
       - '@2.6.2'
@@ -417,7 +422,7 @@ packages:
     # Need extradeps for grib-utils, enable by default to avoid duplicate packages
     w3emc:
       require:
-      - '@2.10.0'
+      - '@2.11.0'
       - precision=4,d,8 +extradeps
     w3nco:
       require:
@@ -426,6 +431,7 @@ packages:
     wgrib2:
       require:
       - '@3.6.0'
+      - +ipolates +netcdf
     wrf-io:
       require:
       - '@1.3.0'

diff --git a/configs/sites/tier1/atlantis/mirrors.yaml b/configs/sites/tier1/atlantis/mirrors.yaml
@@ -1,3 +1,3 @@
 mirrors:
   local-source: file:///neptune_diagnostics/spack-stack/source-cache
-  local-binary: file:///neptune_diagnostics/spack-stack/build-cache
+  local-binary: file:///neptune_diagnostics/spack-stack/build-cache-spack-v1
diff --git a/configs/sites/tier1/atlantis/packages.yaml b/configs/sites/tier1/atlantis/packages.yaml
@@ -1,5 +1,8 @@
 packages:
   # Modification of common packages
+  ewok-env:
+    require:
+    - '~ecflow'
   zlib-api:
     buildable: False
 

diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2024.2.1.yaml
@@ -8,17 +8,16 @@ packages:
     externals:
     - spec: intel-oneapi-runtime@2024.2.1
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
-      modules:
-      - intel-oneapi-2024.2.1
-      - tbb/2021.13
-      - compiler-rt/2024.2.1
   intel-oneapi-compilers:
     buildable: false
     externals:
     - spec: intel-oneapi-compilers@2024.2.1
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
       - intel-oneapi-2024.2.1
+      - tbb/2021.13
+      - compiler-rt/2024.2.1
+      - compiler/2024.2.1
       extra_attributes:
         compilers:
           c: /cm/shared/apps/intel/oneapi-2024.2.1/compiler/2024.2/bin/icx

diff --git a/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2025.3.0.yaml
@@ -0,0 +1,62 @@
+packages:
+  mpi:
+    buildable: false
+    require:
+    - intel-oneapi-mpi@2021.17
+  intel-oneapi-runtime:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-runtime@2025.3.0
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
+  intel-oneapi-compilers:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-compilers@2025.3.0
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
+      modules:
+      - umf/1.0.2
+      - tbb/2022.3
+      - compiler-rt/2025.3.0
+      - compiler/2025.3.0
+      extra_attributes:
+        compilers:
+          c: /gpfs/neptune/spack-stack/oneapi-2025.3.0/compiler/2025.3/bin/icx
+          cxx: /gpfs/neptune/spack-stack/oneapi-2025.3.0/compiler/2025.3/bin/icpx
+          fortran: /gpfs/neptune/spack-stack/oneapi-2025.3.0/compiler/2025.3/bin/ifx
+        environment:
+          prepend_path:
+            PATH: /cm/local/apps/gcc/11.2.0/bin
+            CPATH: /cm/local/apps/gcc/11.2.0/include
+        extra_rpaths:
+        - /cm/local/apps/gcc/11.2.0/lib64
+        - /cm/local/apps/gcc/11.2.0/lib
+  gcc-runtime:
+    buildable: false
+    externals:
+    - spec: gcc-runtime@11.2.0
+      prefix: /cm/local/apps/gcc/11.2.0
+  gcc:
+    buildable: false
+    externals:
+    - spec: gcc@11.2.0 languages:='c,c++'
+      prefix: /cm/local/apps/gcc/11.2.0
+      extra_attributes:
+        compilers:
+          c: /cm/local/apps/gcc/11.2.0/bin/gcc
+          cxx: /cm/local/apps/gcc/11.2.0/bin/g++
+          fortran: /cm/local/apps/gcc/11.2.0/bin/gfortran
+  intel-oneapi-mpi:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mpi@2021.17
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
+      modules:
+      - mpi/2021.17
+      - slurm
+  intel-oneapi-mkl:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mkl@2025.3
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.3.0
+      modules:
+      - mkl/2025.3
diff --git a/configs/sites/tier1/blueback/mirrors.yaml b/configs/sites/tier1/blueback/mirrors.yaml
@@ -1,3 +1,3 @@
 mirrors:
   local-source: file:///p/cwfs/projects/NEPTUNE/spack-stack/source-cache
-  local-binary: file:///p/cwfs/projects/NEPTUNE/spack-stack/build-cache
+  local-binary: file:///p/cwfs/projects/NEPTUNE/spack-stack/build-cache-spack-v1
diff --git a/configs/sites/tier1/blueback/packages.yaml b/configs/sites/tier1/blueback/packages.yaml
@@ -82,13 +82,11 @@ packages:
     externals:
     - spec: pkg-config@0.29.2
       prefix: /usr
-  # MISSING qt:
-  #  buildable: False
-  #  externals:
-  #  - spec: qt@5.15.2
-  #    prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
-  #    modules:
-  #    - qt/5.15.2
+  qt::
+    buildable: False
+    externals:
+    - spec: qt@5.15.2
+      prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
   sed:
     externals:
     - spec: sed@4.4

diff --git a/configs/sites/tier1/blueback/packages_gcc-13.3.0.yaml b/configs/sites/tier1/blueback/packages_gcc-13.3.0.yaml
@@ -34,3 +34,7 @@ packages:
       - libfabric/1.22.0
       - craype-network-ofi
       - cray-mpich/8.1.32
+      extra_attributes:
+        environment:
+          prepend_path:
+            CMAKE_PREFIX_PATH: /p/app/projects/NEPTUNE/spack-stack/cmake-findmpi
diff --git a/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml b/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml
@@ -61,6 +61,10 @@ packages:
       - libfabric/1.22.0
       - craype-network-ofi
       - cray-mpich/8.1.32
+      extra_attributes:
+        environment:
+          prepend_path:
+            CMAKE_PREFIX_PATH: /p/app/projects/NEPTUNE/spack-stack/cmake-findmpi
   intel-oneapi-mkl:
     buildable: false
     externals:

diff --git a/configs/sites/tier1/blueback/packages_oneapi-2025.2.1.yaml.donotuse b/configs/sites/tier1/blueback/packages_oneapi-2025.2.1.yaml.donotuse
@@ -61,7 +61,10 @@ packages:
       - libfabric/1.22.0
       - craype-network-ofi
       - cray-mpich/8.1.32
-      - craype-network-ofi
+      extra_attributes:
+        environment:
+          prepend_path:
+            CMAKE_PREFIX_PATH: /p/app/projects/NEPTUNE/spack-stack/cmake-findmpi
   intel-oneapi-mkl:
     buildable: false
     externals:

diff --git a/configs/sites/tier1/hera/packages.yaml b/configs/sites/tier1/hera/packages.yaml
@@ -1,7 +1,8 @@
 packages:
   all:
+    # https://github.com/JCSDA/spack-stack/issues/1781
     # To support hecflow01
-    target: [haswell]
+    #target: [haswell]
     providers:
       zlib-api:: [zlib]
   zlib-api:
@@ -110,10 +111,10 @@ packages:
   mysql:
     buildable: False
     externals:
-    - spec: mysql@8.0.31
-      prefix: /scratch1/NCEPDEV/global/spack-stack/apps/mysql-8.0.31
+    - spec: mysql@8.0.36
+      prefix: /contrib/spack-stack/installs/mysql/8.0.36
       modules:
-      - mysql/8.0.31
+      - mysql/8.0.36
   ncurses:
     externals:
     - spec: ncurses@5.9.20130511+termlib abi=5
@@ -129,7 +130,7 @@ packages:
   qt:
     externals:
     - spec: qt@5.12.6
-      prefix: /scratch1/NCEPDEV/nems/role.epic/installs/qt-5.12.6/qtbase
+      prefix: /contrib/spack-stack/installs/qt-5.12.6/qtbase
   rsync:
     externals:
     - spec: rsync@3.1.2

diff --git a/configs/sites/tier1/hera/packages_oneapi.yaml b/configs/sites/tier1/hera/packages_oneapi.yaml
@@ -1,6 +1,6 @@
 packages:
   all:
-    compiler:: [oneapi@2024.2.1]
+    compiler:: [oneapi@2024.2.1, gcc@13.3.0]
     providers:
       mpi:: [intel-oneapi-mpi@2021.13]
       # Remove the next three lines to switch to intel-oneapi-mkl

diff --git a/configs/sites/tier1/hercules/compilers.yaml b/configs/sites/tier1/hercules/compilers.yaml
@@ -10,11 +10,15 @@ compilers:
     operating_system: rocky9
     target: x86_64
     modules:
+    - spack-managed-x86-64_v3
     - intel-oneapi-compilers/2024.2.1
     environment:
       set:
         # https://github.com/ufs-community/ufs-weather-model/issues/2015#issuecomment-1864438186
         I_MPI_EXTRA_FILESYSTEM: 'ON'
+        # Override system module settings for FC and F77 (they're set to ifx)
+        F77: '/apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort'
+        FC: '/apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort'
       prepend_path:
         PATH: /usr/bin
         LD_LIBRARY_PATH: /usr/lib:/usr/lib64

diff --git a/configs/sites/tier1/hercules/packages_oneapi.yaml b/configs/sites/tier1/hercules/packages_oneapi.yaml
@@ -15,6 +15,8 @@ packages:
     - spec: intel-oneapi-mpi@2021.13%oneapi@2024.2.1
       prefix: /apps/spack-managed-x86_64_v3-v1.0/oneapi-2024.2.1/intel-oneapi-mpi-2021.13.1-3pv63eugwmse2xpeglxib4dr2oeb42g2
       modules:
+      - spack-managed-x86-64_v3
+      - intel-oneapi-compilers/2024.2.1
       - intel-oneapi-mpi/2021.13.1
 
   intel-oneapi-mkl:
@@ -23,13 +25,15 @@ packages:
     - spec: intel-oneapi-mkl@2024.2.1
       prefix: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-mkl-2024.2.1-aeiool3i5jj4newwifvkhow5almp67rt
       modules:
+      - spack-managed-x86-64_v3
       - intel-oneapi-mkl/2024.2.1
 
   intel-oneapi-runtime:
     externals:
     - spec: intel-oneapi-runtime@2024.2.1%oneapi@2024.2.1
       prefix: /apps/spack-managed-x86_64_v3-v1.0/oneapi-2024.2.1/intel-oneapi-runtime-2024.2.1-hl5zgdjaldynq35dq3yotclfy2vblybx
       modules:
+      - spack-managed-x86-64_v3
       - intel-oneapi-compilers/2024.2.1
       - intel-oneapi-runtime/2024.2.1
 
@@ -49,3 +53,6 @@ packages:
   py-scipy:
     require:
     - '%gcc'
+  zlib-ng:
+    require:
+    - '~shared'
diff --git a/configs/sites/tier1/narwhal/mirrors.yaml b/configs/sites/tier1/narwhal/mirrors.yaml
@@ -1,3 +1,3 @@
 mirrors:
   local-source: file:///p/cwfs/projects/NEPTUNE/spack-stack/source-cache
-  local-binary: file:///p/cwfs/projects/NEPTUNE/spack-stack/build-cache
+  local-binary: file:///p/cwfs/projects/NEPTUNE/spack-stack/build-cache-spack-v1
diff --git a/configs/sites/tier1/narwhal/packages.yaml b/configs/sites/tier1/narwhal/packages.yaml
@@ -81,13 +81,11 @@ packages:
     externals:
     - spec: pkg-config@0.29.2
       prefix: /usr
-  qt:
+  qt::
     buildable: False
     externals:
     - spec: qt@5.15.2
       prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
-      modules:
-      - qt/5.15.2
   sed:
     externals:
     - spec: sed@4.4