esmf@8.8.0b06 -> 8.8.0b10, configure LLVM 19.1.4 for Bounty, update customization of common packages for Derecho (#1409)

1. Update esmf from 8.8.0b06 to 8.8.0b10
2. Simplify/clean up modification of common packages in Derecho site config (move from openblas to intel-oneapi-mkl, since openblas no longer builds - neither 0.3.24 nor 0.3.28)
3. Configure LLVM 19.1.4 for Bounty; this requires updating openblas from 0.3.24 to 0.3.28, which we cannot do globally yet (waiting for #1384); there is also a build issue for ip that we can't work around, for now one has to manually replace ip with sp in spack-ext/path/to/my/env/package.py.

Author: climbfuji

configs/common/modules_lmod.yaml

@@ -132,8 +132,8 @@ modules:
           ^esmf@8.6.1+debug snapshot=none: 'esmf-8.6.1-debug'
           ^esmf@8.7.0~debug snapshot=none: 'esmf-8.7.0'
           ^esmf@8.7.0+debug snapshot=none: 'esmf-8.7.0-debug'
-          ^esmf@8.8.0b06~debug snapshot=b06: 'esmf-8.8.0b06'
-          ^esmf@8.8.0b06+debug snapshot=b06: 'esmf-8.8.0b06-debug'
+          ^esmf@8.8.0b10~debug snapshot=b10: esmf-8.8.0b10
+          ^esmf@8.8.0b10+debug snapshot=b10: esmf-8.8.0b10-debug
       openmpi:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -134,8 +134,8 @@ modules:
           ^esmf@8.6.1+debug snapshot=none: 'esmf-8.6.1-debug'
           ^esmf@8.7.0~debug snapshot=none: 'esmf-8.7.0'
           ^esmf@8.7.0+debug snapshot=none: 'esmf-8.7.0-debug'
-          ^esmf@8.8.0b06~debug snapshot=b06: 'esmf-8.8.0b06'
-          ^esmf@8.8.0b06+debug snapshot=b06: 'esmf-8.8.0b06-debug'
+          ^esmf@8.8.0b10~debug snapshot=b10: esmf-8.8.0b10
+          ^esmf@8.8.0b10+debug snapshot=b10: esmf-8.8.0b10-debug
       openmpi:
         environment:
           set:

configs/common/packages.yaml

@@ -55,7 +55,7 @@ packages:
   esmf:
     require:
     - '~xerces ~pnetcdf +shared +external-parallelio'
-    - any_of: ['@=8.6.1 snapshot=none', '@=8.8.0b06 snapshot=b06']
+    - any_of: ['@=8.6.1 snapshot=none', '@=8.8.0b10 snapshot=b10']
     - any_of: ['fflags="-fp-model precise" cxxflags="-fp-model precise"']
       when: "%intel"
       message: "Extra ESMF compile options for Intel"
@@ -177,8 +177,11 @@ packages:
   # ninja - when adding information here, also check Discover site config
   odc:
     require: '@1.5.2 ~fortran'
+  # Todo: update to 0.3.28 so that it builds with 'clang'. Check
+  # packages_clang.yaml where we are overwriting openblas for now.
   openblas:
-    require: '@0.3.24'
+    require:
+    - '@0.3.24'
   openmpi:
     require: '~internal-hwloc +two_level_namespace'
   openssl:

configs/common/packages_clang.yaml

@@ -0,0 +1,28 @@
+packages:
+  all:
+    providers:
+      blas: [openblas]
+      fftw-api: [fftw]
+      lapack: [openblas]
+  ectrans:
+    require:
+    - '~mkl +fftw'
+  gsibec:
+    require:
+    - '~mkl'
+  py-numpy:
+    require:
+    - '^openblas'
+  # clang@19 requires openblas@0.3.28 - with this, we can'this
+  # build all the Python dependencies as of 2024/12/11 due to
+  # version conflicts.
+  openblas:
+    require::
+    - '@0.3.28'
+  # ip@5 doesn't build with clang@19 compilers (flang-new)
+  # https://github.com/NOAA-EMC/NCEPLIBS-ip/issues/263
+  # but requiring %gcc doesn't work when using openblas
+  #ip:
+  #  require:
+  #  #- '~openmp'
+  #  - '%gcc'

configs/sites/tier1/derecho/packages.yaml

@@ -1,17 +1,18 @@
 packages:
   all:
     target: [core2]
+
 ### Modification of common packages
+  # Tell esmf that this is not a 'normal' Cray ...
   esmf:
-    variants: ~xerces ~pnetcdf snapshot=none ~shared +external-parallelio esmf_os=Linux esmf_comm=mpich
-  # Need to force spack to build python with ssl variant when using older openssl from OS
-  python:
-    require: "+ssl"
+    require:
+    - 'esmf_os=Linux esmf_comm=mpich'
   # py-scipy 1.12 does not build with intel on Derecho, pin to 1.11.4
   # use same version with gcc for consistency on the machine
   py-scipy:
     require:
     - '@1.11.4'
+
 ### All other external packages listed alphabetically
   autoconf:
     externals:

configs/sites/tier1/derecho/packages_intel.yaml

@@ -3,10 +3,6 @@ packages:
     compiler:: [intel@2021.10.0,gcc@11.2.0]
     providers:
       mpi:: [cray-mpich@8.1.25]
-      # Remove the next three lines to switch to intel-oneapi-mkl
-      blas:: [openblas]
-      fftw-api:: [fftw]
-      lapack:: [openblas]
   mpi:
     buildable: False
   cray-mpich:
@@ -18,25 +14,11 @@ packages:
       - libfabric/1.15.2.0
       - cray-pals/1.2.11
   intel-oneapi-mkl:
-    # Remove buildable: False and configure+uncomment externals section below to use intel-oneapi-mkl
-    # Note that on 2024/08/14, Dom H couldn't find any MKL installation on Derecho - keep using fftw
-    # and openblas, or find another provider (Cray stuff)?
-    buildable: False
-    #externals:
-    #- spec: intel-oneapi-mkl@2022.0.2%intel@2021.5.0
-    #  prefix: /apps/oneapi
+    # No intel-oneapi-mkl installed on Derecho, install via spack.
+    # Prefer the version that Intel releases with the above compiler
+    prefer:
+    - '@2023.2.0'
   # Newer versions of patchelf (tested 0.18.0) don't build with Intel on Derecho
   patchelf:
     version:: ['0.17.2']
-  # DH* Remove this section to switch to intel-oneapi-mkl
-  ectrans:
-    require::
-    - '@1.5.0 ~mkl +fftw'
-  gsibec:
-    require::
-    - '@1.2.1 ~mkl'
-  py-numpy:
-    require::
-    - '@:1.23 ^openblas'
-  # *DH
 

configs/sites/tier2/bounty/compilers.yaml

@@ -38,3 +38,18 @@ compilers:
     modules: []
     environment: {}
     extra_rpaths: []
+- compiler:
+    spec: clang@=19.1.4
+    paths:
+      cc: /home/dom/prod/llvm-19.1.4/bin/clang
+      cxx: /home/dom/prod/llvm-19.1.4/bin/clang++
+      f77: /home/dom/prod/llvm-19.1.4/bin/flang-new
+      fc: /home/dom/prod/llvm-19.1.4/bin/flang-new
+    flags: {}
+    operating_system: almalinux9
+    target: x86_64
+    modules: []
+    environment:
+      append_path:
+        LD_LIBRARY_PATH: /home/dom/prod/llvm-19.1.4/lib
+    extra_rpaths: [/home/dom/prod/llvm-19.1.4/lib] 

configs/sites/tier2/bounty/packages_clang.yaml

@@ -0,0 +1,5 @@
+packages:
+  all:
+    compiler:: [clang@19.1.4]
+    providers:
+      mpi:: [openmpi@5.0.5]

configs/templates/neptune-dev/spack.yaml

@@ -8,8 +8,8 @@ spack:
   definitions:
   - compilers: ['%aocc', '%apple-clang', '%gcc', '%intel', '%oneapi']
   - packages:
-      - neptune-env +espc                           ^esmf@=8.8.0b06
-      - neptune-python-env +xnrl ^neptune-env +espc ^esmf@=8.8.0b06
+      - neptune-env +espc                           ^esmf@=8.8.0b10
+      - neptune-python-env +xnrl ^neptune-env +espc ^esmf@=8.8.0b10
 
   specs:
     - matrix:

configs/templates/skylab-dev/spack.yaml

@@ -14,11 +14,11 @@ spack:
     - jedi-fv3-env
     - jedi-geos-env         ^esmf@=8.6.1
     - jedi-mpas-env
-    - jedi-neptune-env      ^esmf@=8.8.0b06
+    - jedi-neptune-env      ^esmf@=8.8.0b10
     - jedi-ufs-env          ^esmf@=8.6.1
     - jedi-um-env
-    - neptune-env           ^esmf@=8.8.0b06
-    - neptune-python-env    ^esmf@=8.8.0b06
+    - neptune-env           ^esmf@=8.8.0b10
+    - neptune-python-env    ^esmf@=8.8.0b10
     - soca-env
 
     # Various crtm tags (list all to avoid duplicate packages)
@@ -27,7 +27,7 @@ spack:
 
     # Various esmf tags (list all to avoid duplicate packages)
     - esmf@=8.6.1 snapshot=none
-    - esmf@=8.8.0b06 snapshot=b06
+    - esmf@=8.8.0b10 snapshot=b10
 
   specs:
   - matrix: