Merge release/1.6.0 into develop

.gitmodules

@@ -3,7 +3,8 @@
   #url = https://github.com/spack/spack
   #branch = develop
   url = https://github.com/jcsda/spack
-  branch = jcsda_emc_spack_stack
+  #branch = jcsda_emc_spack_stack
+  branch = feature/merge_rel160_into_develop
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
   url = https://github.com/noaa-emc/cmakemodules

configs/common/modules_lmod.yaml

@@ -71,7 +71,6 @@ modules:
       - openssl
       - perl
       - pkgconf
-      - qhull
       - qt
       - randrproto
       - readline

configs/common/modules_tcl.yaml

@@ -73,7 +73,6 @@ modules:
       - openssl
       - perl
       - pkgconf
-      - qhull
       - qt
       - randrproto
       - readline

configs/containers/specs/jedi-ci.yaml

@@ -1,4 +1,4 @@
-  ### spack-stack-1.6.0 / skylab-7.0.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
+  ### 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,
     [email protected], [email protected] +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,

configs/sites/aws-pcluster/config.yaml

@@ -1,9 +1,8 @@
 config:
-  build_jobs: 24
+  build_jobs: 8
 
   # Overrides for spack build and staging areas to speed up builds
   # by using a local directory instead of the EFS shared filesystem
-
   build_stage: /tmp/spack-stack/cache/build_stage
   test_stage: /tmp/spack-stack/cache/test_stage
   source_cache: /tmp/spack-stack/cache/source_cache

configs/sites/derecho/packages.yaml

@@ -36,32 +36,22 @@ packages:
 ### All other external packages listed alphabetically
   autoconf:
     externals:
-    - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: [email protected]
       prefix: /usr
   automake:
     externals:
-    - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: [email protected]
       prefix: /usr
   binutils:
     externals:
     - spec: [email protected]
       prefix: /usr
-  cmake:
-    externals:
-    - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/spack/opt/spack/cmake/3.26.3/gcc/7.5.0/k34x
   coreutils:
     externals:
     - spec: [email protected]
       prefix: /usr
   curl:
     externals:
-    - spec: [email protected]+nghttp2
-      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: [email protected]+gssapi+ldap+nghttp2
       prefix: /usr
   cvs:
@@ -83,24 +73,20 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  flex:
-    externals:
-    - spec: [email protected]+lex
-      prefix: /glade/u/apps/derecho/23.09/opt/view
   gawk:
     externals:
     - spec: [email protected]
       prefix: /usr
   git:
     externals:
     - spec: [email protected]+tcltk
-      prefix: /glade/u/apps/derecho/23.09/opt/view
+      prefix: /glade/u/apps/derecho/23.09/spack/opt/spack/git/2.41.0/gcc/7.5.0/jgni
     - spec: [email protected]+tcltk
       prefix: /usr
   git-lfs:
     externals:
     - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/opt/view
+      prefix: /glade/u/apps/derecho/23.09/spack/opt/spack/git-lfs/3.3.0/gcc/7.5.0/u3kh
   gmake:
     externals:
     - spec: [email protected]
@@ -113,21 +99,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr/lib/mit
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/opt/view
-    - spec: [email protected]
-      prefix: /usr
   m4:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Automatically detected, but don't use - missing "ninja" dependency
-  #meson:
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /glade/u/apps/derecho/23.09/opt/view
   mysql:
     buildable: False
     externals:
@@ -147,6 +122,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   subversion:
     externals:
     - spec: [email protected]
@@ -157,8 +136,6 @@ packages:
       prefix: /usr
   texinfo:
     externals:
-    - spec: [email protected]
-      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: [email protected]
       prefix: /usr
   wget:

configs/sites/discover/packages.yaml

@@ -121,10 +121,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libxpm:
     externals:
     - spec: [email protected]

configs/sites/gaea-c5/packages.yaml

@@ -122,10 +122,6 @@ packages:
       prefix: /usr
   libtirpc:
     variants: ~gssapi
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   # This package is currently incomplete (no headers), but still works
   libxaw:
     externals:

configs/sites/hera/packages.yaml

@@ -124,10 +124,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libxpm:
     externals:
     - spec: [email protected]

configs/sites/hercules/compilers.yaml

@@ -11,7 +11,10 @@ compilers:
     target: x86_64
     modules:
     - intel-oneapi-compilers/2023.1.0
-    environment: {}
+    environment:
+      set:
+        # https://github.com/ufs-community/ufs-weather-model/issues/2015#issuecomment-1864438186
+        I_MPI_EXTRA_FILESYSTEM: 'ON'
     extra_rpaths: []
 - compiler:
     spec: [email protected]

configs/sites/hercules/packages.yaml

@@ -3,6 +3,8 @@ packages:
     compiler:: [[email protected], [email protected]]
     providers:
       mpi:: [[email protected], [email protected]]
+      # Alternative [email protected] with [email protected] for testing
+      #mpi:: [[email protected]]
 
 ### MPI, Python, MKL
   mpi:
@@ -20,11 +22,17 @@ packages:
       modules:
       - gcc/12.2.0
       - mvapich2/2.3.7
+  # Alternative [email protected] with [email protected] for testing
+  #openmpi:
+  #  externals:
+  #  - spec: [email protected]%[email protected]~cuda~cxx~cxx_exceptions~java~memchecker+pmi+static~wrapper-rpath
+  #      schedulers=slurm
+  #    prefix: /work/noaa/epic/role-epic/spack-stack/hercules/openmpi-4.1.6/gcc-12.2.0-spack
+  #    modules:
+  #    - gcc/12.2.0
+  #    - openmpi/4.1.6-gcc-12.2.0-spack
 
 ### Modifications of common packages
-  # DH* TRY IF THIS IS STILL TRUE # Version 2.0.8 doesn't compile on Hercules
-  # DH* TRY IF THIS IS STILL TRUE wgrib2:
-  # DH* TRY IF THIS IS STILL TRUE   version:: ['3.1.1']
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -84,10 +92,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   m4:
     externals:
     - spec: [email protected]
@@ -109,6 +113,10 @@ packages:
       prefix: /apps/spack-managed/gcc-11.3.1/qt-5.15.8-d47tsna6f5dylcpblkfgw4gpn2cucihd
       modules:
       - qt/5.15.8
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   subversion:
     externals:
     - spec: [email protected]

configs/sites/jet/packages.yaml

@@ -129,10 +129,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libxpm:
     externals:
     - spec: [email protected]

configs/sites/narwhal/compilers.yaml

@@ -11,6 +11,7 @@ compilers::
       modules:
       - PrgEnv-intel/8.3.2
       - intel-classic/2021.4.0
+      - node.js/20.10.0
       environment:
         prepend_path:
           PATH: '/opt/cray/pe/gcc/10.3.0/snos/bin'
@@ -31,6 +32,7 @@ compilers::
       modules:
       - PrgEnv-gnu/8.3.2
       - gcc/10.3.0
+      - node.js/20.10.0
       environment:
         prepend_path:
           LD_LIBRARY_PATH: '/opt/cray/pe/libsci/22.08.1.1/GNU/9.1/x86_64/lib'

configs/sites/narwhal/packages.yaml

@@ -115,6 +115,10 @@ packages:
       prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
       modules:
       - qt/5.15.2
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   subversion:
     externals:
     - spec: [email protected]

configs/sites/nautilus/packages.yaml

@@ -103,10 +103,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   m4:
     externals:
     - spec: [email protected]
@@ -125,6 +121,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   tar:
     externals:
     - spec: [email protected]

configs/sites/noaa-aws/compilers.yaml

@@ -16,20 +16,6 @@ compilers:
         PATH: '/apps/gnu/gcc-9.2.0/bin'
         LD_LIBRARY_PATH: '/apps/oneapi/compiler/2021.3.0/linux/compiler/lib/intel64_lin:/apps/gnu/gcc-9.2.0/lib64'
     extra_rpaths: []
-- compiler:
-    spec: [email protected]
-    paths:
-      cc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/icc
-      cxx: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/icpc
-      f77: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
-      fc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
-    flags: {}
-    operating_system: centos7
-    target: x86_64
-    modules:
-    - intel/18.0.5.274
-    environment: {}
-    extra_rpaths: []
 - compiler:
     spec: [email protected]
     paths:

configs/sites/noaa-aws/packages.yaml

@@ -1,10 +1,8 @@
 packages:
   all:
     compiler:: [[email protected], [email protected]]
-    #compiler:: [[email protected]]
     providers:
       mpi:: [[email protected], [email protected]]
-      #mpi:: [[email protected]]
 
 ### MPI, Python, MKL
   mpi:
@@ -15,12 +13,6 @@ packages:
       prefix: /apps/oneapi
       modules:
       - impi/2021.3.0
-  intel-mpi:
-    externals:
-    - spec: [email protected]%[email protected]
-      prefix: /apps/intel/compilers_and_libraries_2018
-      modules:
-      - impi/2018.4.274
   openmpi:
     externals:
     - spec: [email protected]%[email protected]

configs/sites/noaa-azure/compilers.yaml

@@ -16,20 +16,6 @@ compilers:
         PATH: '/apps/gnu/gcc-9.2.0/bin'
         LD_LIBRARY_PATH: '/apps/oneapi/compiler/2021.3.0/linux/compiler/lib/intel64_lin:/apps/gnu/gcc-9.2.0/lib64'
     extra_rpaths: []
-- compiler:
-    spec: [email protected]
-    paths:
-      cc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/icc
-      cxx: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/icpc
-      f77: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
-      fc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
-    flags: {}
-    operating_system: centos7
-    target: x86_64
-    modules:
-    - intel/18.0.5.274
-    environment: {}
-    extra_rpaths: []
 - compiler:
     spec: [email protected]
     paths: