JCSDA · climbfuji · Jan 7, 2025 · Jan 2, 2025 · Jan 2, 2025 · Jan 2, 2025
diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml
@@ -145,6 +145,10 @@ packages:
     require: '@2.1.0'
   libpng:
     require: '@1.6.37 +pic'
+  # libtirpc +gssapi doesn't build with oneapi@2025
+  # https://github.com/JCSDA/spack-stack/issues/1441
+  libtirpc:
+    require: '~gssapi'
   # Newest version of magics needed for oneapi compilers
   magics:
     require: "@4.15.3:"

diff --git a/configs/sites/tier1/atlantis/compilers.yaml b/configs/sites/tier1/atlantis/compilers.yaml
@@ -54,3 +54,26 @@ compilers:
       append_path:
         CPATH: /cm/shared/apps/intel/oneapi-2024.2.1/compiler/2024.2/opt/compiler/include/intel64/
     extra_rpaths: []
+#- compiler:
+#    spec: oneapi@2025.0.3
+#    paths:
+#      cc: /gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0/bin/icx
+#      cxx: /gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0/bin/icpx
+#      f77: /gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0/bin/ifx
+#      fc: /gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0/bin/ifx
+#    flags: {}
+#    operating_system: rhel8
+#    target: x86_64
+#    modules:
+#    - umf/0.9.1
+#    - compiler-rt/2025.0.1
+#    - tbb/2022.0
+#    - compiler-intel-llvm/2025.0.1
+#    environment:
+#      prepend_path:
+#        PATH: /cm/local/apps/gcc/11.2.0/bin
+#        CPATH: /cm/local/apps/gcc/11.2.0/include
+#        LD_LIBRARY_PATH: /cm/shared/apps/slurm/21.08.8/lib64:/cm/shared/apps/slurm/21.08.8/lib64/slurm:/gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0
+#      append_path:
+#        CPATH: /gpfs/neptune/spack-stack/oneapi-2025.0.3/compiler/2025.0/opt/compiler/include/intel64
+#    extra_rpaths: []
diff --git a/configs/sites/tier1/atlantis/packages.yaml b/configs/sites/tier1/atlantis/packages.yaml
@@ -1,4 +1,18 @@
 packages:
+# Modification of common packages
+  # Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    - spec: zlib@1.2.11
+      prefix: /usr
+
+# All other packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.69
@@ -41,12 +55,12 @@ packages:
       prefix: /usr
   git:
     externals:
-    - spec: git@2.39.2+tcltk
-      prefix: /software8/depot/git-2.39.2
+    - spec: git@2.43.5+tcltk
+      prefix: /usr
   git-lfs:
     externals:
-    - spec: git-lfs@3.3.0
-      prefix: /software8/depot/git-2.39.2
+    - spec: git-lfs@3.4.1
+      prefix: /usr
   gmake:
     externals:
     - spec: gmake@4.2.1
@@ -59,10 +73,11 @@ packages:
     externals:
     - spec: groff@1.22.3
       prefix: /usr
-  libtool:
-    externals:
-    - spec: libtool@2.4.6
-      prefix: /usr
+  # Do not use external libtool, incomplete install
+  #libtool:
+  #  externals:
+  #  - spec: libtool@2.4.6
+  #    prefix: /usr
   m4:
     externals:
     - spec: m4@1.4.18

diff --git a/configs/sites/tier1/atlantis/packages_oneapi.yaml b/configs/sites/tier1/atlantis/packages_oneapi.yaml
@@ -1,8 +1,10 @@
 packages:
   all:
     compiler:: [oneapi@2024.2.1,gcc@11.2.0]
+    #compiler:: [oneapi@2025.0.3, gcc@11.2.0]
     providers:
       mpi:: [intel-oneapi-mpi@2021.13]
+      #mpi:: [intel-oneapi-mpi@2021.14]
   mpi:
     buildable: False
   intel-oneapi-mpi:
@@ -12,15 +14,41 @@ packages:
       modules:
       - mpi/2021.13
       - slurm
+    #- spec: intel-oneapi-mpi@2021.14%oneapi@2025.0.3
+    #  prefix: /gpfs/neptune/spack-stack/oneapi-2025.0.3
+    #  modules:
+    #  - mpi/2021.14
+    #  - slurm
   intel-oneapi-mkl:
     externals:
     - spec: intel-oneapi-mkl@2024.2
+      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
       - mkl/2024.2
-      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
+    #- spec: intel-oneapi-mkl@2025.0
+    #  prefix: /gpfs/neptune/spack-stack/oneapi-2025.0.3
+    #  modules:
+    #  - mkl/2025.0
   intel-oneapi-tbb:
     externals:
     - spec: intel-oneapi-tbb@2021.13
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
       - tbb/2021.13
+    #- spec: intel-oneapi-tbb@2022.0
+    #  prefix: /gpfs/neptune/spack-stack/oneapi-2025.0.3
+    #  modules:
+    #  - tbb/2022.0
+  intel-oneapi-runtime:
+    externals:
+    - spec: intel-oneapi-runtime@2024.2.1%oneapi@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
+    #- spec: intel-oneapi-runtime@2025.0.0%oneapi@2025.0.0
+    #  prefix: /gpfs/neptune/spack-stack/oneapi-2025.0.3
+    #  modules:
+    #  - tbb/2022.0
+    #  - compiler-rt/2025.0.1
diff --git a/configs/sites/tier1/blueback/packages.yaml b/configs/sites/tier1/blueback/packages.yaml
@@ -1,4 +1,22 @@
 packages:
+# Modification of common packages
+  # Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    # For TDS tusk
+    - spec: zlib@1.2.11
+      prefix: /usr
+    # For TDS cole
+    #- spec: zlib@1.2.13
+    #  prefix: /usr
+
+# All other packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.69

diff --git a/configs/sites/tier1/narwhal/packages.yaml b/configs/sites/tier1/narwhal/packages.yaml
@@ -1,4 +1,18 @@
 packages:
+# Modification of common packages
+  # Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    - spec: zlib@1.2.11
+      prefix: /usr
+
+# All other packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.69

diff --git a/configs/sites/tier1/narwhal/packages_gcc.yaml b/configs/sites/tier1/narwhal/packages_gcc.yaml
@@ -2,12 +2,12 @@ packages:
   all:
     compiler:: [gcc@10.3.0]
     providers:
-      mpi:: [cray-mpich@8.1.21]
+      mpi:: [cray-mpich@8.1.26]
   mpi:
     buildable: False
   cray-mpich:
     externals:
-    - spec: cray-mpich@8.1.21%gcc@10.3.0 ~wrappers
+    - spec: cray-mpich@8.1.26%gcc@10.3.0 ~wrappers
       modules:
-      - cray-mpich-ucx/8.1.21
+      - cray-mpich-ucx/8.1.26
       - craype-network-ucx
diff --git a/configs/sites/tier1/narwhal/packages_intel.yaml b/configs/sites/tier1/narwhal/packages_intel.yaml
@@ -2,14 +2,14 @@ packages:
   all:
     compiler:: [intel@2021.10.0,gcc@10.3.0]
     providers:
-      mpi:: [cray-mpich@8.1.21]
+      mpi:: [cray-mpich@8.1.26]
   mpi:
     buildable: False
   cray-mpich:
     externals:
-    - spec: cray-mpich@8.1.21%intel@2021.10.0 ~wrappers
+    - spec: cray-mpich@8.1.26%intel@2021.10.0 ~wrappers
       modules:
-      - cray-mpich-ucx/8.1.21
+      - cray-mpich-ucx/8.1.26
       - craype-network-ucx
   intel-oneapi-mkl:
     externals:

diff --git a/configs/sites/tier1/narwhal/packages_oneapi.yaml b/configs/sites/tier1/narwhal/packages_oneapi.yaml
@@ -2,14 +2,14 @@ packages:
   all:
     compiler:: [oneapi@2024.2.0,gcc@10.3.0]
     providers:
-      mpi:: [cray-mpich@8.1.21]
+      mpi:: [cray-mpich@8.1.26]
   mpi:
     buildable: False
   cray-mpich:
     externals:
-    - spec: cray-mpich@8.1.21%oneapi@2024.2.0 ~wrappers
+    - spec: cray-mpich@8.1.26%oneapi@2024.2.0 ~wrappers
       modules:
-      - cray-mpich-ucx/8.1.21
+      - cray-mpich-ucx/8.1.26
       - craype-network-ucx
   intel-oneapi-mkl:
     externals:

diff --git a/configs/sites/tier1/nautilus/packages.yaml b/configs/sites/tier1/nautilus/packages.yaml
@@ -1,4 +1,18 @@
 packages:
+# Modification of common packages
+  # Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    - spec: zlib@1.2.11
+      prefix: /usr
+
+# All other packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.69

diff --git a/configs/sites/tier2/bounty/compilers.yaml b/configs/sites/tier2/bounty/compilers.yaml
@@ -52,4 +52,20 @@ compilers:
     environment:
       append_path:
         LD_LIBRARY_PATH: /home/dom/prod/llvm-19.1.4/lib
-    extra_rpaths: [/home/dom/prod/llvm-19.1.4/lib] 
+    extra_rpaths: [/home/dom/prod/llvm-19.1.4/lib]
+- compiler:
+    spec: aocc@=5.0.0
+    paths:
+      cc: /home/dom/prod/aocc-5.0.0/bin/clang
+      cxx: /home/dom/prod/aocc-5.0.0/bin/clang++
+      f77: /home/dom/prod/aocc-5.0.0/bin/flang
+      fc: /home/dom/prod/aocc-5.0.0/bin/flang
+    flags: {}
+    operating_system: almalinux9
+    target: x86_64
+    modules: []
+    environment: {}
+      #append_path:
+        # For libquadmath etc
+        # NEEDED? LD_LIBRARY_PATH: /usr/lib/gcc/x86_64-redhat-linux/11
+    extra_rpaths: []
diff --git a/configs/templates/neptune-dev/spack.yaml b/configs/templates/neptune-dev/spack.yaml
@@ -15,3 +15,9 @@ spack:
     - matrix:
       - [$packages]
       - [$compilers]
+      exclude:
+      # Skip neptune-python-env with Intel Classic due to problems
+      # with new versions of py-numpy, py-scipy, ...
+      - neptune-python-env%intel
+      # Same for LLVM compilers
+      - neptune-python-env%clang
diff --git a/doc/source/PreConfiguredSites.rst b/doc/source/PreConfiguredSites.rst
@@ -160,14 +160,14 @@ The following is required for building new spack environments with Intel on this
    module unload cray-mpich
    module unload craype-network-ofi
    # Warning. Do not load craype-network-ucx
-   # or cray-mpich-ucx/8.1.21!
+   # or cray-mpich-ucx/8.1.26!
    # There is a bug in the modulefile that prevents
    # spack from setting the environment for its
    # build steps when the module is already
    # loaded. Instead, let spack load it when the
    # package requires it.
    #module load craype-network-ucx
-   #module load cray-mpich-ucx/8.1.21
+   #module load cray-mpich-ucx/8.1.26
    module load libfabric/1.12.1.2.2.1
    module unload cray-libsci
    module load cray-libsci/23.05.1.4
@@ -184,14 +184,14 @@ The following is required for building new spack environments with Intel oneAPI
    module unload cray-mpich
    module unload craype-network-ofi
    # Warning. Do not load craype-network-ucx
-   # or cray-mpich-ucx/8.1.21!
+   # or cray-mpich-ucx/8.1.26!
    # There is a bug in the modulefile that prevents
    # spack from setting the environment for its
    # build steps when the module is already
    # loaded. Instead, let spack load it when the
    # package requires it.
    #module load craype-network-ucx
-   #module load cray-mpich-ucx/8.1.21
+   #module load cray-mpich-ucx/8.1.26
    module load libfabric/1.12.1.2.2.1
    module unload cray-libsci
    module load cray-libsci/23.05.1.4
@@ -208,14 +208,14 @@ The following is required for building new spack environments with GNU on this p
    module unload cray-mpich
    module unload craype-network-ofi
    # Warning. Do not load craype-network-ucx
-   # or cray-mpich-ucx/8.1.21!
+   # or cray-mpich-ucx/8.1.26!
    # There is a bug in the modulefile that prevents
    # spack from setting the environment for its
    # build steps when the module is already
    # loaded. Instead, let spack load it when the
    # package requires it.
    #module load craype-network-ucx
-   #module load cray-mpich-ucx/8.1.21
+   #module load cray-mpich-ucx/8.1.26
    module load libfabric/1.12.1.2.2.1
    module unload cray-libsci
    module load cray-libsci/23.05.1.4

diff --git a/spack b/spack
+6 −2		share/spack/qa/run-style-tests
+8 −1		var/spack/repos/builtin/packages/freetype/package.py