[feature/update_to_spack_v1] External zlib, external runtime libraries, MPI meta-modules updates, NRL site config updates round 2 of X (#1782)

This PR is for branch feature/update_to_spack_v1.

spack-packages submodule update for Intel oneAPI FPP bug affecting NASA packages, to allow for external Intel oneAPI runtime libraries, for ESMF bug (linking to MPI C++ libraries)
Numerous additional spack-packages updates from the authoritative repo (contributed by @AlexanderRichert-NOAA)
Return control over zlib libraries to site configs (can be external or spack-built)
Return control over runtime libraries to site configs (can be external or spack-built)
Updates to MPI meta-modules: set correct compiler wrapper and backend environment variables, set additional environment variables that define the MPI install prefix
NRL site config updates, second round (more to come in a follow-up PR)

Author: climbfuji

.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg

@@ -12,8 +12,7 @@
           cxx: /opt/intel/oneapi/compiler/2024.2/bin/icpx
           fortran: /opt/intel/oneapi/compiler/2024.2/bin/ifx
   intel-oneapi-runtime:
-    # LINK TO BUG REPORT HERE
-    #buildable: false
+    buildable: false
     externals:
     - spec: intel-oneapi-runtime@2024.2.0
       prefix: /opt/intel/oneapi

.github/workflows/ubuntu-ci-x86_64-oneapi.cfg

@@ -12,8 +12,7 @@
           cxx: /opt/intel/oneapi/compiler/2024.2/bin/icpx
           fortran: /opt/intel/oneapi/compiler/2024.2/bin/ifort
   intel-oneapi-runtime:
-    # LINK TO BUG REPORT HERE
-    #buildable: false
+    buildable: false
     externals:
     - spec: intel-oneapi-runtime@2024.2.0
       prefix: /opt/intel/oneapi

configs/common/packages.yaml

@@ -123,9 +123,6 @@ packages:
     g2tmpl:
       require:
       - '@1.13.0'
-    gcc-runtime:
-      require:
-      - '%gcc'
     # This version builds with Intel oneAPI compilers, newer/older versions don't
     gdal:
       require:

configs/common/packages_oneapi.yaml

@@ -48,10 +48,3 @@ packages:
     qt:
       require:
       - '%gcc'
-    # Prevent issues with fault Intel libraries
-    # when using tar etc by building zlib-api with gcc
-    zlib:
-      require:
-      - '%gcc'
-    zlib-ng:
-      buildable: False

configs/sites/tier1/atlantis/compilers.yaml.old

@@ -1,10 +1,7 @@
 packages:
   # Modification of common packages
-
-  ## Pin py-torch to 2.5.1 to avoid build errors with 2.6.0
-  #py-torch:
-  #  require:
-  #  - '@2.5.1'
+  zlib-api:
+    buildable: False
 
   # All other packages listed alphabetically
   autoconf:
@@ -74,11 +71,6 @@ packages:
     externals:
     - spec: openssh@8.0p1
       prefix: /usr
-  # Can no longer use, issues with py-cryptography
-  #openssl:
-  #  externals:
-  #  - spec: openssl@1.1.1k
-  #    prefix: /usr
   pkgconf:
     externals:
     - spec: pkgconf@1.4.2
@@ -103,7 +95,8 @@ packages:
     externals:
     - spec: wget@1.19.5
       prefix: /usr
-  #zlib:
-  #  externals:
-  #  - spec: zlib@1.2.11
-  #    prefix: /usr
+  zlib:
+    buildable: False
+    externals:
+    - spec: zlib@1.2.11
+      prefix: /usr

configs/sites/tier1/atlantis/packages.yaml

@@ -2,8 +2,14 @@ packages:
   mpi:
     buildable: False
     require:
-    - "openmpi@4.1.8"
+    - openmpi@4.1.8
+  gcc-runtime:
+    buildable: False
+    externals:
+    - spec: gcc-runtime@13.4.0%gcc@13.4.0
+      prefix: /gpfs/neptune/spack-stack/gcc-13.4.0
   gcc:
+    buildable: False
     externals:
     - spec: gcc@13.4.0 languages:='c,c++,fortran'
       prefix: /gpfs/neptune/spack-stack/gcc-13.4.0
@@ -14,11 +20,8 @@ packages:
           c: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/gcc
           cxx: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/g++
           fortran: /gpfs/neptune/spack-stack/gcc-13.4.0/bin/gfortran
-  gcc-runtime:
-    externals:
-    - spec: gcc-runtime@13.4.0%gcc@13.4.0
-      prefix: /gpfs/neptune/spack-stack/gcc-13.4.0
   openmpi:
+    buildable: False
     externals:
     - spec: openmpi@4.1.8
       prefix: /gpfs/neptune/spack-stack/openmpi-4.1.8/gcc-13.4.0

configs/sites/tier1/atlantis/packages_gcc-13.4.0.yaml

@@ -1,17 +1,24 @@
 packages:
   mpi:
-    buildable: False
+    buildable: false
     require:
-    - "intel-oneapi-mpi@2021.13"
-  intel-oneapi-compilers:
+    - intel-oneapi-mpi@2021.13
+  intel-oneapi-runtime:
+    buildable: false
     externals:
-    - spec: intel-oneapi-compilers@2024.2.1
+    - 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
-      - compiler/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
       extra_attributes:
         compilers:
           c: /cm/shared/apps/intel/oneapi-2024.2.1/compiler/2024.2/bin/icx
@@ -24,39 +31,13 @@ packages:
         extra_rpaths:
         - /cm/local/apps/gcc/11.2.0/lib64
         - /cm/local/apps/gcc/11.2.0/lib
-  intel-oneapi-mpi:
-    buildable: false
-    externals:
-    - spec: intel-oneapi-mpi@2021.13%oneapi@2024.2.1
-      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
-      modules:
-      - mpi/2021.13
-      - slurm
-  intel-oneapi-mkl:
-    buildable: false
-    externals:
-    - spec: intel-oneapi-mkl@2024.2
-      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
-      modules:
-      - mkl/2024.2
-  intel-oneapi-tbb:
+  gcc-runtime:
     buildable: false
     externals:
-    - spec: intel-oneapi-tbb@2021.13
-      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
-      modules:
-      - tbb/2021.13
-  intel-oneapi-runtime:
-    # LINK TO BUG REPORT HERE
-    #buildable: false
-    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: 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
@@ -65,7 +46,16 @@ packages:
           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
-  gcc-runtime:
+  intel-oneapi-mpi:
+    buildable: false
     externals:
-    - spec: gcc-runtime@11.2.0%gcc@11.2.0
-      prefix: /cm/local/apps/gcc/11.2.0
+    - spec: intel-oneapi-mpi@2021.13
+      prefix: /cm/shared/apps/intel/oneapi-2024.2.1
+      modules:
+      - mpi/2021.13
+      - slurm
+  intel-oneapi-mkl:
+    buildable: false
+    externals:
+    - spec: intel-oneapi-mkl@2024.2
+      prefix: /cm/shared/apps/intel/oneapi-2024.2.1