Merge pull request #1312 from RatkoVasic-NOAA/update-1.6.0-rocky-OS

Update changes to 1.6.0 for machines that switched to Rocky OS

configs/common/modules_lmod.yaml

@@ -190,7 +190,7 @@ modules:
             'TOCGRIB': '{prefix}/bin/tocgrib'
             'TOCGRIB2': '{prefix}/bin/tocgrib2'
             'TOCGRIB2SUPER': '{prefix}/bin/tocgrib2super'
-            'WGRIB': '{prefix}/bin/wgrib2'
+            'WGRIB': '{prefix}/bin/wgrib'
       landsfcutil:
         environment:
           set:
@@ -259,6 +259,8 @@ modules:
 
       hierarchy:
       - mpi
+      - g2virt
+      - g2tmplvirt
 
     prefix_inspections:
       bin:

configs/common/modules_tcl.yaml

@@ -192,7 +192,7 @@ modules:
             'TOCGRIB': '{prefix}/bin/tocgrib'
             'TOCGRIB2': '{prefix}/bin/tocgrib2'
             'TOCGRIB2SUPER': '{prefix}/bin/tocgrib2super'
-            'WGRIB': '{prefix}/bin/wgrib2'
+            'WGRIB': '{prefix}/bin/wgrib'
       landsfcutil:
         environment:
           set:

configs/sites/hera/compilers.yaml

@@ -7,7 +7,7 @@ compilers:
       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: centos7
+    operating_system: rocky8
     modules:
     - intel/2022.1.2
     environment:
@@ -24,7 +24,7 @@ compilers:
       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
+    operating_system: rocky8
     modules:
     - intel/18.0.5.274
 - compiler:
@@ -35,7 +35,7 @@ compilers:
       f77: /apps/gnu/gcc-9.2.0/bin/gfortran
       fc:  /apps/gnu/gcc-9.2.0/bin/gfortran
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - gnu/9.2.0
     environment: {}

configs/sites/hera/packages.yaml

@@ -45,10 +45,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  bzip2:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   cpio:
     externals:
     - spec: [email protected]
@@ -116,10 +112,6 @@ packages:
     externals:
     - spec: [email protected]_312-b07
       prefix: /usr
-  krb5:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libfuse:
     externals:
     - spec: [email protected]
@@ -183,11 +175,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  xz:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   zip:
     externals:
     - spec: [email protected]
       prefix: /usr
+
+  zlib:
+    require: ["~shared"]

configs/sites/jet/compilers.yaml

@@ -7,7 +7,7 @@ compilers:
       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: centos7
+    operating_system: rocky8
     modules:
     - intel/2022.1.2
     environment:
@@ -24,7 +24,7 @@ compilers:
       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
+    operating_system: rocky8
     modules:
     - intel/18.0.5.274
 - compiler:
@@ -35,7 +35,7 @@ compilers:
       f77: /apps/gnu/gcc-9.2.0/bin/gfortran
       fc:  /apps/gnu/gcc-9.2.0/bin/gfortran
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - gnu/9.2.0
     environment: {}

configs/sites/jet/packages.yaml

@@ -46,10 +46,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  bzip2:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   cpio:
     externals:
     - spec: [email protected]
@@ -121,10 +117,6 @@ packages:
     externals:
     - spec: [email protected]_322-b06
       prefix: /usr
-  krb5:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libfuse:
     externals:
     - spec: [email protected]
@@ -145,13 +137,11 @@ 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=6
-      prefix: /lfs4/HFIP/hfv3gfs/Kyle.Gerheiser/miniconda/miniconda-3.9.7
     - spec: [email protected]+termlib abi=5
       prefix: /usr
   perl:
@@ -186,11 +176,9 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  xz:
-    externals:
-    - spec: [email protected]
-      prefix: /lfs4/HFIP/hfv3gfs/Kyle.Gerheiser/miniconda/miniconda-3.9.7
   zip:
     externals:
     - spec: [email protected]
       prefix: /usr
+  zlib:
+    require: ["~shared"]

configs/sites/noaa-aws/README.md

@@ -52,24 +52,14 @@ exit
 
 # Build external packages for spack-stack
 
-mkdir -p /contrib/spack-stack
+mkdir -p /contrib/spack-stack-rocky8
 mkdir /contrib/spack-stack/modulefiles
-cd /contrib/spack-stack/
-
-mkdir -p git-lfs-2.4.1/src
-cd git-lfs-2.4.1/src
-wget http://mirror.centos.org/centos/7/sclo/x86_64/rh/Packages/r/rh-git218-git-lfs-2.4.1-3.el7.x86_64.rpm
-rpm2cpio rh-git218-git-lfs-2.4.1-3.el7.x86_64.rpm | cpio -idmv
-mv opt/rh/rh-git218/root/usr/* ..
-rm -fr opt
-cd /contrib/spack-stack/modulefiles
-mkdir git-lfs
+
 # Create the modulefile from the template in doc/modulefile_templates
 
-cd /contrib/spack-stack/
+cd /contrib/spack-stack-rocky8
 mkdir -p mysql-8.0.31/src
 cd mysql-8.0.31/src
-ldd --version
 wget https://dev.mysql.com/get/Downloads/MySQL-8.0/mysql-8.0.31-linux-glibc2.17-x86_64-minimal.tar.xz
 tar -xvf mysql-8.0.31-linux-glibc2.17-x86_64-minimal.tar.xz
 mv mysql-8.0.31-linux-glibc2.17-x86_64-minimal/* ..
@@ -78,37 +68,20 @@ cd /contrib/spack-stack/modulefiles
 mkdir mysql
 # Create the modulefile from the template in doc/modulefile_templates
 
-cd /contrib/spack-stack/
-mkdir -p cmake-3.27.2/src
-cd cmake-3.27.2/src
-wget https://github.com/Kitware/CMake/releases/download/v3.27.2/cmake-3.27.2-linux-x86_64.tar.gz
-tar -xvzf cmake-3.27.2-linux-x86_64.tar.gz
-mv cmake-3.27.2-linux-x86_64/* ..
-rmdir cmake-3.27.2-linux-x86_64
-cd /contrib/spack-stack/modulefiles
-mkdir cmake
-# Create the modulefile from the template in doc/modulefile_templates
 
 # Set up basic modules for building the external ecflow package
-module unuse /opt/cray/craype/default/modulefiles
-module unuse /opt/cray/modulefiles
-
-module purge
-module load gnu/9.2.0
-module use /contrib/spack-stack/modulefiles
-module load cmake/3.27.2
-
-mkdir -p /contrib/spack-stack/ecflow-5.8.4/src
-cd /contrib/spack-stack/ecflow-5.8.4/src
+mkdir -p /contrib/spack-stack-rocky8/ecflow-5.8.4/src
+cd /contrib/spack-stack-rocky8/ecflow-5.8.4/src
 wget https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-5.8.4-Source.tar.gz?api=v2
 wget https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.tar.gz
 mv ecFlow-5.8.4-Source.tar.gz\?api\=v2 ecFlow-5.8.4-Source.tar.gz
 tar -xvzf boost_1_78_0.tar.gz
 tar -xvzf ecFlow-5.8.4-Source.tar.gz
-export WK=/contrib/spack-stack/ecflow-5.8.4/src/ecFlow-5.8.4-Source
-export BOOST_ROOT=/contrib/spack-stack/ecflow-5.8.4/src/boost_1_78_0
+export WK=/contrib/spack-stack-rocky8/ecflow-5.8.4/src/ecFlow-5.8.4-Source
+export BOOST_ROOT=/contrib/spack-stack-rocky8/ecflow-5.8.4/src/boost_1_78_0
 
 # Build static boost (to not interfere with spack-stack boost)
+# Note that the default compiler supplied with the OS is used
 cd $BOOST_ROOT
 ./bootstrap.sh 2>&1 | tee bootstrap.log
 $WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log
@@ -117,21 +90,51 @@ $WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log
 cd $WK
 mkdir build
 cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=/contrib/spack-stack/ecflow-5.8.4 2>&1 | tee log.cmake
+cmake .. -DPython3_EXECUTABLE=`which python3` -DCMAKE_INSTALL_PREFIX=/contrib/spack-stack-rocky8/ecflow-5.8.4 2>&1 | tee log.cmake
 make -j4 2>&1 | tee log.make
 make install 2>&1 | tee log.install
 
-cd /contrib/spack-stack/modulefiles
-mkdir ecflow
+cd /contrib/spack-stack-rocky8/
+mkdir -p ./modulefiles/ecflow
 # Create the modulefile from the template in doc/modulefile_templates
 
+
 ############## Steps to perform when starting a new cluster ##############
 source /contrib/admin/basic_setup.sh  # sudo privileges requred to install packages
+module purge
 module unuse /opt/cray/craype/default/modulefiles
 module unuse /opt/cray/modulefiles
-module use /contrib/spack-stack/modulefiles
-module load cmake/3.27.2
+
+# For noaa-aws, run the line below as well:
+module unuse /opt/intel/impi/2019.5.281/intel64/modulefiles
+module use /contrib/spack-stack-rocky8/modulefiles
+
+# Loading modules
+# 
 module load ecflow/5.8.4
 module load mysql/8.0.31
-module load git-lfs/2.4.1
 
+module load gnu
+module load intel/2023.2.0
+module load impi/2023.2.0 
+module unload gnu
+
+cd /contrib/spack-stack-rocky8/spack-stack-1.6.0
+source setup.sh
+## Create spack-stack environment, use the CSP name as needed:
+## set CLOUD variable to noaa-aws, noaa-gcloud, or noaa-azure
+CLOUD=noaa-aws
+spack stack create env --site $CLOUD --template unified-dev --name ue-intel
+cd envs/ue-intel
+spack env activate .
+
+############## spack.yaml edits:
+edit spack.yaml:
+#  1) leave only "%intel" in "compilers" definitions
+#  2) replace ^[email protected]  by ^[email protected] under definitions,
+#       except for the Various esmf/mapl tags section
+
+spack concretize 2>&1 | tee log.concretize
+spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install
+spack module lmod refresh
+spack stack setup-meta-modules

configs/sites/noaa-aws/compilers.yaml

@@ -1,32 +1,17 @@
 compilers:
 - compiler:
-    spec: intel@2021.3.0
+    spec: intel@2021.10.0
     paths:
-      cc: /apps/oneapi/compiler/2021.3.0/linux/bin/intel64/icc
-      cxx: /apps/oneapi/compiler/2021.3.0/linux/bin/intel64/icpc
-      f77: /apps/oneapi/compiler/2021.3.0/linux/bin/intel64/ifort
-      fc: /apps/oneapi/compiler/2021.3.0/linux/bin/intel64/ifort
-    flags: {}
-    operating_system: centos7
+      cc: /apps/oneapi/compiler/2023.2.0/linux/bin/intel64/icc
+      cxx: /apps/oneapi/compiler/2023.2.0/linux/bin/intel64/icpc
+      f77: /apps/oneapi/compiler/2023.2.0/linux/bin/intel64/ifort
+      fc: /apps/oneapi/compiler/2023.2.0/linux/bin/intel64/ifort
+    operating_system: rocky8
     target: x86_64
     modules:
-    - intel/2021.3.0
+    - intel/2023.2.0
     environment:
       prepend_path:
-        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/gnu/gcc-9.2.0/bin/gcc
-      cxx: /apps/gnu/gcc-9.2.0/bin/g++
-      f77: /apps/gnu/gcc-9.2.0/bin/gfortran
-      fc: /apps/gnu/gcc-9.2.0/bin/gfortran
+        LD_LIBRARY_PATH: '/apps/oneapi/compiler/2023.2.0/linux/compiler/lib/intel64_lin:/apps/gnu/gcc-13.2.0/lib64'
     flags: {}
-    operating_system: centos7
-    target: x86_64
-    modules:
-    - gnu/9.2.0
-    environment: {}
     extra_rpaths: []