Move jet from tier1 to tier2 and update it (#1721)

Author: guoqing-noaa

configs/sites/tier1/jet/compilers.yaml

@@ -0,0 +1,48 @@
+compilers:
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/icc
+      cxx: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/icpc
+      f77: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
+      fc: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
+    flags: {}
+    operating_system: rocky8
+    modules:
+    - intel/2022.1.2
+    environment:
+      prepend_path:
+        PATH: '/apps/gnu/gcc-9.2.0/bin'
+        LD_LIBRARY_PATH: '/apps/gnu/gcc-9.2.0/lib64'
+        CPATH: '/apps/gnu/gcc-9.2.0/include'
+    extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /apps/gnu/gcc-13.2.0/bin/gcc
+      cxx: /apps/gnu/gcc-13.2.0/bin/g++
+      f77: /apps/gnu/gcc-13.2.0/bin/gfortran
+      fc:  /apps/gnu/gcc-13.2.0/bin/gfortran
+    flags: {}
+    operating_system: rocky8
+    modules:
+    - gnu/13.2.0
+    environment: {}
+    extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /apps/oneapi/compiler/2024.2/bin/icx
+      cxx: /apps/oneapi/compiler/2024.2/bin/icpx
+      f77: /apps/oneapi/compiler/2024.2/bin/ifort
+      fc: /apps/oneapi/compiler/2024.2/bin/ifort
+    flags: {}
+    operating_system: rocky8
+    modules:
+    - intel/2024.2.1
+    environment:
+      prepend_path:
+        PATH: '/apps/gnu/gcc-13.2.0/bin'
+        LD_LIBRARY_PATH: '/apps/gnu/gcc-13.2.0/lib64'
+        CPATH: '/apps/gnu/gcc-13.2.0/include'
+    extra_rpaths: []

configs/sites/tier1/jet/packages_gcc.yaml

@@ -1,15 +1,15 @@
 mirrors:
   local-source:
     fetch:
-      url: file:///mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/source-cache
+      url: file:///contrib/spack-stack/source-cache
       access_pair:
       - null
       - null
       access_token: null
       profile: null
       endpoint_url: null
     push:
-      url: file:///mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/source-cache
+      url: file:///lfs6/BMC/nrtrr/spack-stack/source-cache
       access_pair:
       - null
       - null

configs/sites/tier1/jet/packages_intel.yaml

@@ -42,10 +42,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  flex:
-    externals:
-    - spec: [email protected]+lex
-      prefix: /usr
   gawk:
     externals:
     - spec: [email protected]
@@ -66,10 +62,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  go:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   grep:
     externals:
     - spec: [email protected]
@@ -84,7 +76,7 @@ packages:
       prefix: /usr
   openjdk:
     externals:
-    - spec: [email protected].0_322-b06
+    - spec: [email protected].0_312-b07
       prefix: /usr
   krb5:
     externals:
@@ -97,10 +89,10 @@ packages:
   libxpm:
     externals:
     - spec: [email protected]
-      prefix: usr/
+      prefix: /usr
   lustre:
     externals:
-    - spec: lustre@2.12.6_ddn62
+    - spec: lustre@2.14.0_ddn168
       prefix: /usr
   m4:
     externals:
@@ -110,9 +102,13 @@ packages:
     buildable: False
     externals:
     - spec: [email protected]
-      prefix: /lfs4/HFIP/hfv3gfs/role.epic/apps/mysql-8.0.31
+      prefix: /contrib/spack-stack/installs/mysql-8.0.31
       modules:
       - mysql/8.0.31
+  ncurses:
+    externals:
+    - spec: [email protected]+termlib abi=5
+      prefix: /usr
   perl:
     externals:
     - spec: [email protected]~cpanm+shared+threads
@@ -122,7 +118,6 @@ packages:
     - spec: [email protected]
       prefix: /usr
   qt:
-    buildable: false
     externals:
     - spec: [email protected]
       prefix: /contrib/spack-stack/installs/qt-5.12.6/qtbase
@@ -146,10 +141,18 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  texlive:
+    externals:
+    - spec: texlive@20130530
+      prefix: /usr
   wget:
     externals:
     - spec: [email protected]
       prefix: /usr
+  xz:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   zip:
     externals:
     - spec: [email protected]

configs/sites/tier2/jet/compilers.yaml

@@ -0,0 +1,13 @@
+packages:
+  all:
+    compiler:: [[email protected]]
+    providers:
+      mpi:: [[email protected]]
+  mpi:
+    buildable: False
+  openmpi:
+    externals:
+    - spec: [email protected]~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java+legacylaunchers~lustre~memchecker~openshmem~orterunprefix+pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=ucx schedulers=slurm
+      modules:
+      - gnu/13.2.0
+      - openmpi/4.1.6

configs/sites/tier1/jet/config.yaml renamed to configs/sites/tier2/jet/config.yaml

@@ -0,0 +1,37 @@
+packages:
+  all:
+    compiler:: [[email protected],[email protected]]
+    providers:
+      mpi:: [[email protected]]
+      # Remove the next three lines to switch to intel-oneapi-mkl
+      blas:: [openblas]
+      fftw-api:: [fftw]
+      lapack:: [openblas]
+  mpi:
+    buildable: False
+  intel-oneapi-mpi:
+    externals:
+    - spec: [email protected]%[email protected] +classic-names
+      modules:
+      - impi/2022.1.2
+      prefix: /apps/oneapi
+  intel-oneapi-mkl:
+    # Remove buildable: False and uncomment externals section below to use intel-oneapi-mkl
+    buildable: False
+    #externals:
+    #- spec: [email protected]%[email protected]
+    #  prefix: /apps/oneapi
+  # DH* Remove this section to switch to intel-oneapi-mkl
+  ectrans:
+    require::
+    - '@1.2.0 ~mkl +fftw'
+  gsibec:
+    require::
+    - '@1.2.1 ~mkl'
+  py-numpy:
+    require::
+    - '^openblas'
+  # *DH
+  zlib-ng:
+    require:
+      - '~shared'