Merge remote-tracking branch 'jcsda/develop' into feature/MET_METp_3.1.1

* jcsda/develop: Bump Python to 3.11.7 (JCSDA#1217) Add a clause in the cleanup to fix directory permissions (JCSDA#1273) Bug fix: configure neptune-env variants in three templates: neptune-dev, skylab-dev, unified-dev (JCSDA#1268) Update site configs for Atlantis, Narwhal, Nautilus (JCSDA#1266) Configuration for [email protected] and [email protected] (JCSDA#1240)
DavidHuber-NOAA · Aug 26, 2024 · edbe999 · edbe999
2 parents 22e5218 + ac43a4c
commit edbe999
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diff --git a/.github/workflows/macos-ci-aarch64.yaml b/.github/workflows/macos-ci-aarch64.yaml
@@ -20,6 +20,7 @@ jobs:
         run: |
           pwd
           ls -lart
+          find ./* -type d -exec chmod u+xw {} \;
           rm -fr *
 
       - name: checkout

diff --git a/.github/workflows/ubuntu-ci-x86_64-gnu.yaml b/.github/workflows/ubuntu-ci-x86_64-gnu.yaml
@@ -20,6 +20,7 @@ jobs:
         run: |
           pwd
           ls -lart
+          find ./* -type d -exec chmod u+xw {} \;
           rm -fr *
 
       - name: checkout

diff --git a/.github/workflows/ubuntu-ci-x86_64-intel.yaml b/.github/workflows/ubuntu-ci-x86_64-intel.yaml
@@ -20,6 +20,7 @@ jobs:
         run: |
           pwd
           ls -lart
+          find ./* -type d -exec chmod u+xw {} \;
           rm -fr *
 
       - name: checkout

diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml b/.github/workflows/ubuntu-ci-x86_64-oneapi.yaml
@@ -20,6 +20,7 @@ jobs:
         run: |
           pwd
           ls -lart
+          find ./* -type d -exec chmod u+xw {} \;
           rm -fr *
 
       - name: checkout

diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml
@@ -20,6 +20,8 @@ packages:
     require: '@1.84 ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=17 visibility=hidden'
   bufr:
     require: '@12.1.0 +python'
+  bufr-query:
+    require: '@0.0.2 +python'
   cairo:
     require: '+pic'
   cdo:
@@ -37,7 +39,7 @@ packages:
   ecflow:
     require: '@5.11.4 +ui'
   eckit:
-    require: '@1.24.5 linalg=eigen,lapack compression=lz4,bzip2'
+    require: '@1.27.0 linalg=eigen,lapack compression=lz4,bzip2'
   ecmwf-atlas:
     require: '@0.38.1 +fckit +trans +tesselation +fftw'
   ectrans:

diff --git a/configs/containers/specs/jedi-ci.yaml b/configs/containers/specs/jedi-ci.yaml
@@ -1,7 +1,7 @@
   ### spack-stack-1.6.0 / skylab-7.x.y containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
   specs: [[email protected], [email protected], [email protected], [email protected],
-    [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], ecflow@5,
-    eckit@1.24.5, [email protected] +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,
+    [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], ecflow@5,
+    eckit@1.27.0, [email protected] +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,
     [email protected], [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected], [email protected],

diff --git a/configs/sites/tier1/atlantis/packages.yaml b/configs/sites/tier1/atlantis/packages.yaml
@@ -122,10 +122,11 @@ packages:
     externals:
     - spec: [email protected]+lex
       prefix: /usr
-  openssl:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
+  # Can no longer use, issues with py-cryptography
+  #openssl:
+  #  externals:
+  #  - spec: [email protected]
+  #    prefix: /usr
   gawk:
     externals:
     - spec: [email protected]

diff --git a/configs/sites/tier1/narwhal/compilers.yaml b/configs/sites/tier1/narwhal/compilers.yaml
@@ -14,27 +14,30 @@ compilers::
       modules:
       - PrgEnv-intel/8.3.3
       - intel-classic/2023.2.0
+      - cray-libsci/23.05.1.4
       - libfabric/1.12.1.2.2.1
       environment:
         prepend_path:
           PATH: '/opt/cray/pe/gcc/10.3.0/snos/bin'
           CPATH: '/opt/cray/pe/gcc/10.3.0/snos/include'
-          LD_LIBRARY_PATH: '/opt/cray/libfabric/1.12.1.2.2.1/lib64:/opt/cray/pe/libsci/22.11.1.2/INTEL/19.0/x86_64/lib:/opt/cray/pe/gcc/10.3.0/snos/lib:/opt/cray/pe/gcc/10.3.0/snos/lib64'
+          LD_LIBRARY_PATH: '/opt/cray/libfabric/1.12.1.2.2.1/lib64:/opt/cray/pe/libsci/23.05.1.4/INTEL/2022.2/x86_64/lib:/opt/cray/pe/gcc/10.3.0/snos/lib:/opt/cray/pe/gcc/10.3.0/snos/lib64'
         set:
           CRAYPE_LINK_TYPE: 'dynamic'
       extra_rpaths: []
   - compiler:
       spec: [email protected]
       paths:
-        cc: cc
-        cxx: CC
-        f77: ftn
-        fc: ftn
+        cc: /opt/cray/pe/gcc/10.3.0/bin/gcc
+        cxx: /opt/cray/pe/gcc/10.3.0/bin/g++
+        f77: /opt/cray/pe/gcc/10.3.0/bin/gfortran
+        fc: /opt/cray/pe/gcc/10.3.0/bin/gfortran
       flags: {}
       operating_system: sles15
       modules:
       - PrgEnv-gnu/8.3.3
       - gcc/10.3.0
+      - cray-libsci/22.11.1.2
+      - libfabric/1.12.1.2.2.1
       environment:
         prepend_path:
           LD_LIBRARY_PATH: '/opt/cray/libfabric/1.12.1.2.2.1/lib64:/opt/cray/pe/libsci/22.11.1.2/GNU/9.1/x86_64/lib'

diff --git a/configs/sites/tier1/narwhal/packages_gcc.yaml b/configs/sites/tier1/narwhal/packages_gcc.yaml
@@ -7,7 +7,7 @@ packages:
     buildable: False
   cray-mpich:
     externals:
-    - spec: [email protected]%[email protected] ~wrappers
+    - spec: [email protected]%[email protected] +wrappers
       modules:
       - cray-mpich-ucx/8.1.21
       - craype-network-ucx
diff --git a/configs/sites/tier1/nautilus/packages_gcc.yaml b/configs/sites/tier1/nautilus/packages_gcc.yaml
@@ -1,8 +1,17 @@
 packages:
+# On Nautilus, use intel-oneapi-mkl as provider
+# for blas, lapack, fftw-api with GNU because of
+# problems using openblas in downstream applications
+# (e.g. py-pandas):
+# ELF load command address/offset not properly aligned" when loading libopenblas.so
+# https://github.com/OpenMathLib/OpenBLAS/wiki/Faq#ELFoffset
   all:
     compiler:: [[email protected]]
     providers:
       mpi:: [[email protected]]
+      blas:: [intel-oneapi-mkl]
+      fftw-api:: [intel-oneapi-mkl]
+      lapack:: [intel-oneapi-mkl]
   mpi:
     buildable: False
   openmpi:
@@ -12,3 +21,14 @@ packages:
       modules:
       - penguin/openmpi/5.0.1/gcc-8.5.0
       - slurm
+  openblas:
+    buildable: False
+  ectrans:
+    require::
+    - '@1.2.0 +mkl ~fftw'
+  gsibec:
+    require::
+    - '@1.2.1 +mkl'
+  py-numpy:
+    require::
+    - '@:1.25 ^intel-oneapi-mkl'
diff --git a/configs/templates/neptune-dev/spack.yaml b/configs/templates/neptune-dev/spack.yaml
@@ -8,7 +8,7 @@ spack:
   definitions:
   - compilers: ['%aocc', '%apple-clang', '%gcc', '%intel', '%oneapi']
   - packages:
-      - neptune-env +python ^[email protected] snapshot=b11
+      - neptune-env +espc +python +xnrl ^[email protected] snapshot=b11
 
   specs:
     - matrix:

diff --git a/configs/templates/skylab-dev/spack.yaml b/configs/templates/skylab-dev/spack.yaml
@@ -17,6 +17,7 @@ spack:
     - jedi-neptune-env      ^esmf@=8.7.0b11 snapshot=b11
     - jedi-ufs-env          ^esmf@=8.6.1
     - jedi-um-env
+    - neptune-env ~espc +python ~xnrl ^esmf@=8.7.0b11 snapshot=b11
     - soca-env
 
     # Various crtm tags (list all to avoid duplicate packages)

diff --git a/configs/templates/unified-dev/spack.yaml b/configs/templates/unified-dev/spack.yaml
@@ -21,7 +21,7 @@ spack:
     - jedi-tools-env
     - jedi-ufs-env          ^esmf@=8.6.1
     - jedi-um-env
-    - neptune-env ~python   ^esmf@=8.7.0b11 snapshot=b11
+    - neptune-env ~espc +python ~xnrl ^esmf@=8.7.0b11 snapshot=b11
     - soca-env
     - ufs-srw-app-env       ^esmf@=8.6.1
     - ufs-weather-model-env ^esmf@=8.6.1

diff --git a/doc/source/PreConfiguredSites.rst b/doc/source/PreConfiguredSites.rst
@@ -253,8 +253,12 @@ With Intel, the following is required for building new spack environments and fo
    module unload intel
    module load intel-classic/2023.2.0
    module unload cray-mpich
-   module load cray-mpich/8.1.21
+   module unload craype-network-ofi
+   module load craype-network-ucx
+   module load cray-mpich-ucx/8.1.21
    module load libfabric/1.12.1.2.2.1
+   module unload cray-libsci
+   module load cray-libsci/23.05.1.4
 
 THIS SECTION IS OUT OF DATE, REFER TO 1.7.0 RELEASE DOCUMENTATION -  - For ``spack-stack-1.7.0`` with Intel, proceed with loading the following modules:
 
@@ -279,8 +283,12 @@ With GNU, the following is required for building new spack environments and for
    module unload gcc
    module load gcc/10.3.0
    module unload cray-mpich
-   module load cray-mpich/8.1.21
+   module unload craype-network-ofi
+   module load craype-network-ucx
+   module load cray-mpich-ucx/8.1.21
    module load libfabric/1.12.1.2.2.1
+   module unload cray-libsci
+   module load cray-libsci/22.11.1.2
 
 THIS SECTION IS OUT OF DATE, REFER TO 1.7.0 RELEASE DOCUMENTATION - For ``spack-stack-1.7.0`` with GNU, proceed with loading the following modules:
 

diff --git a/spack b/spack
diff --git a/spack-ext/repos/spack-stack/packages/jedi-base-env/package.py b/spack-ext/repos/spack-stack/packages/jedi-base-env/package.py
@@ -20,12 +20,14 @@ class JediBaseEnv(BundlePackage):
     # Need to find a free fftw provider for fftw-api ...
     variant("fftw", default=True, description="Build fftw")
     variant("hdf4", default=True, description="Build hdf4 library and python hdf module")
+    variant("bufrquery", default=True, description="Build bufr-query library")
 
     depends_on("base-env", type="run")
     depends_on("bison", type="run")
     depends_on("blas", type="run")
     depends_on("boost", type="run")
     depends_on("bufr", type="run")
+    depends_on("bufr-query", when="+bufrquery", type="run")
     # Force users to load manually
     # depends_on("[email protected]", type="run")
     depends_on("ecbuild", type="run")