JCSDA · climbfuji · Jul 22, 2025 · Jul 22, 2025 · Jul 22, 2025 · Jul 23, 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/.gitmodules b/.gitmodules
@@ -10,5 +10,7 @@
   branch = v1.3.0
 [submodule "repos/builtin"]
   path = repos/builtin
-  url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  #url = https://github.com/jcsda/spack-packages
+  #branch = spack-stack-dev
+  url = https://github.com/climbfuji/spack-packages
+  branch = bugfixes/kiwisolver_cartopy_ectrans
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
@@ -426,6 +426,7 @@ packages:
     wgrib2:
       require:
       - '@3.6.0'
+      - +ipolates +netcdf
     wrf-io:
       require:
       - '@1.3.0'

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-2025.2.1.yaml b/configs/sites/tier1/atlantis/packages_oneapi-2025.2.1.yaml
@@ -0,0 +1,62 @@
+packages:
+  mpi:
+    buildable: false
+    require:
+    - intel-oneapi-mpi@2021.16
+  intel-oneapi-runtime:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-runtime@2025.2.1
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.2.1
+  intel-oneapi-compilers:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-compilers@2025.2.1
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.2.1
+      modules:
+      - umf/0.11.0
+      - tbb/2022.2
+      - compiler-rt/2025.2.1
+      - compiler/2025.2.1
+      extra_attributes:
+        compilers:
+          c: /gpfs/neptune/spack-stack/oneapi-2025.2.1/compiler/2025.2/bin/icx
+          cxx: /gpfs/neptune/spack-stack/oneapi-2025.2.1/compiler/2025.2/bin/icpx
+          fortran: /gpfs/neptune/spack-stack/oneapi-2025.2.1/compiler/2025.2/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@2021.16
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.2.1
+      modules:
+      - mpi/2021.16
+      - slurm
+  intel-oneapi-mkl:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mkl@2025.2
+      prefix: /gpfs/neptune/spack-stack/oneapi-2025.2.1
+      modules:
+      - mkl/2025.2
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/packages_gcc-12.2.0.yaml b/configs/sites/tier1/narwhal/packages_gcc-12.2.0.yaml
@@ -8,9 +8,6 @@ packages:
     externals:
     - spec: gcc-runtime@12.2.0
       prefix: /opt/cray/pe/gcc/12.2.0/snos
-      modules:
-      - PrgEnv-gnu/8.4.0
-      - gcc/12.2.0
   gcc:
     buildable: false
     externals:
@@ -27,15 +24,24 @@ packages:
         environment:
           set:
             CONFIG_SITE: ''
+        extra_rpaths:
+        - /opt/cray/libfabric/1.22.0/lib64
+        - /opt/cray/pe/gcc/12.2.0/snos/lib64
+        - /opt/cray/pe/gcc/12.2.0/snos/lib
   cray-mpich:
     buildable: false
     externals:
     - spec: cray-mpich@8.1.26
       prefix: /opt/cray/pe/mpich/8.1.26/ofi/gnu/9.1
       modules:
-      - libfabric/1.12.1.2.2.1
       - craype-network-ucx
       - cray-mpich-ucx/8.1.26
+      - libfabric/1.22.0
+      extra_attributes:
+        extra_rpaths:
+        - /opt/cray/libfabric/1.22.0/lib64
+        # - /opt/cray/pe/mpich/8.1.26/ofi/gnu/9.1/lib
+
   # Require node-js earlier than 21 to prevent compile
   # errors with Cray GNU compiler 12.2.0
   #node-js: