Update config files for NOAA cloud

JCSDA · Oct 2, 2024 · 642ee98 · 642ee98
1 parent ff269c0
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Showing 7 changed files with 51 additions and 152 deletions.
diff --git a/configs/sites/tier1/noaa-aws/README.md b/configs/sites/tier1/noaa-aws/README.md
@@ -44,37 +44,8 @@ cd /contrib/spack-stack-rocky8/spack-stack-1.8.0
 . setup.sh
 spack stack create env --name gsi-intel-2021.10.0 --template gsi-addon-dev --site noaa-aws --upstream /contrib/spack-stack-rocky8/spack-stack-1.8.0/envs/ue-intel-2021.10.0/install --compiler intel
 cd envs/gsi-intel-2021.10.0
+spack env activate .
 spack concretize 2>&1 | tee log.concretize
 spack install --verbose 2>&1 | tee log.install
 spack module lmod refresh --upstream-modules
 spack stack setup-meta-modules
-
-## Steps to install external applications (MySQL, ecFlow)
-
- MySQL:
-mkdir -p /contrib/spack-stack-rocky8/mysql-8.0.31/src
-cd /contrib/spack-stack-rocky8/mysql-8.0.31/src
-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/* ..
-rmdir mysql-8.0.31-linux-glibc2.17-x86_64-minimal
-
- ecFlow:
-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-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
-cd $BOOST_ROOT
-./bootstrap.sh 2>&1 | tee bootstrap.log
-$WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log
-cd $WK
-mkdir build
-cd build
-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
diff --git a/configs/sites/tier1/noaa-aws/packages.yaml b/configs/sites/tier1/noaa-aws/packages.yaml
@@ -65,7 +65,7 @@ packages:
   mysql:
     externals:
     - spec: [email protected]
-      prefix: /contrib/spack-stack/mysql-8.0.31
+      prefix: /contrib/spack-stack-rocky8/mysql-8.0.31
   ncurses:
     externals:
     - spec: [email protected]+termlib abi=5
@@ -111,4 +111,4 @@ packages:
     - spec: [email protected]
       prefix: /usr
   zlib:
-     require: ["~shared"]
+     require: [~shared]
diff --git a/configs/sites/tier1/noaa-azure/compilers.yaml b/configs/sites/tier1/noaa-azure/compilers.yaml
@@ -1,20 +1,19 @@
 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'
+        LD_LIBRARY_PATH: '/apps/oneapi/compiler/2023.2.0/linux/compiler/lib/intel64_lin:/apps/gnu/gcc-13.2.0/lib64'
+    flags: {}
     extra_rpaths: []
 - compiler:
     spec: [email protected]
@@ -24,8 +23,7 @@ compilers:
       f77: /apps/gnu/gcc-9.2.0/bin/gfortran
       fc: /apps/gnu/gcc-9.2.0/bin/gfortran
     flags: {}
-    operating_system: centos7
-    target: x86_64
+    operating_system: rocky8
     modules:
     - gnu/9.2.0
     environment: {}

diff --git a/configs/sites/tier1/noaa-azure/packages.yaml b/configs/sites/tier1/noaa-azure/packages.yaml
@@ -1,146 +1,110 @@
 packages:
-### Modifications of common packages
-  # Pin flex to avoid duplicate packages
-  flex:
-    version: ['2.6.4']
-### All other external packages listed alphabetically
-  autoconf:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  automake:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   bash:
     externals:
-    - spec: bash@4.2.46
+    - spec: bash@4.4.20
       prefix: /usr
   berkeley-db:
     externals:
-    - spec: [email protected].21
+    - spec: [email protected].28
       prefix: /usr
   cpio:
     externals:
-    - spec: cpio@2.11
+    - spec: cpio@2.12
       prefix: /usr
   diffutils:
     externals:
-    - spec: [email protected]
-      prefix: /usr
-  doxygen:
-    externals:
-    - spec: [email protected]~graphviz~mscgen
+    - spec: [email protected]
       prefix: /usr
   ecflow::
     buildable: False
     externals:
     - spec: [email protected]+ui+static_boost
-      prefix: /contrib/spack-stack/ecflow-5.8.4
+      prefix: /contrib/spack-stack-rocky8/ecflow-5.8.4
+      modules:
+      - ecflow/5.8.4
   file:
     externals:
-    - spec: file@5.11
+    - spec: file@5.33
       prefix: /usr
   findutils:
     externals:
-    - spec: findutils@4.5.11
+    - spec: findutils@4.6.0
       prefix: /usr
-  gawk:
+  flex:
     externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
-  gettext:
+  gawk:
     externals:
-    - spec: [email protected].1
+    - spec: [email protected].1
       prefix: /usr
   git:
     externals:
-    - spec: git@1.8.3.1~tcltk
+    - spec: git@2.39.3~tcltk
       prefix: /usr
   git-lfs:
     externals:
-    - spec: [email protected]
-      prefix: /contrib/spack-stack/git-lfs-2.4.1
-  gmake:
-    externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
-  groff:
+  gmake:
     externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
   hwloc:
     externals:
-    - spec: hwloc@1.11.8
+    - spec: hwloc@2.2.0
       prefix: /usr
   krb5:
     externals:
-    - spec: [email protected]
-      prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  # Problem untarring libxml2 on the Azure filesystem
-  # so mark it as external
-  libxml2:
-    buildable: False
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  lustre:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  m4:
-    externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
   mysql:
     externals:
     - spec: [email protected]
-      prefix: /contrib/spack-stack/mysql-8.0.31
+      prefix: /contrib/spack-stack-rocky8/mysql-8.0.31
   ncurses:
     externals:
-    - spec: ncurses@5.9-14.20130511+termlib abi=5
+    - spec: ncurses@6.1-10.20180224+termlib abi=5
       prefix: /usr
   openjdk:
     externals:
-    - spec: [email protected].0_322-b06
+    - spec: [email protected].0_402-b06
       prefix: /usr
   perl:
     externals:
-    - spec: perl@5.16.3~cpanm+shared+threads
+    - spec: perl@5.26.3~cpanm+shared+threads
       prefix: /usr
   pkg-config:
     externals:
-    - spec: pkg-config@0.27.1
+    - spec: pkg-config@1.4.2
       prefix: /usr
   rsync:
     externals:
-    - spec: [email protected].2
+    - spec: [email protected].3
       prefix: /usr
   ruby:
     externals:
-    - spec: ruby@2.0.0
+    - spec: ruby@2.5.9p229
       prefix: /usr
   sed:
     externals:
-    - spec: sed@4.2.2
+    - spec: sed@4.5
       prefix: /usr
   tar:
     externals:
-    - spec: tar@1.26
+    - spec: tar@1.30
       prefix: /usr
   texinfo:
     externals:
-    - spec: texinfo@5.1
+    - spec: texinfo@6.5-7
       prefix: /usr
   wget:
     externals:
-    - spec: wget@1.14
+    - spec: wget@1.19.5
       prefix: /usr
   zip:
     externals:
     - spec: [email protected]
       prefix: /usr
+  zlib:
+     require: [~shared]
diff --git a/configs/sites/tier1/noaa-azure/packages_intel.yaml b/configs/sites/tier1/noaa-azure/packages_intel.yaml
@@ -1,8 +1,8 @@
 packages:
   all:
-    compiler:: [intel@2021.3.0,[email protected].0]
+    compiler:: [intel@2021.10.0]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.3.0]
+      mpi:: [intel-oneapi-mpi@2021.10.0]
       # Remove the next three lines to switch to intel-oneapi-mkl
       blas:: [openblas]
       fftw-api:: [fftw]
@@ -11,10 +11,10 @@ packages:
     buildable: False
   intel-oneapi-mpi:
     externals:
-    - spec: intel-oneapi-mpi@2021.3.0%intel@2021.3.0
+    - spec: intel-oneapi-mpi@2021.10.0%intel@2021.10.0
       prefix: /apps/oneapi
       modules:
-      - impi/2021.3.0
+      - impi/2023.2.0
   intel-oneapi-mkl:
     # Remove buildable: False and configure+uncomment externals section below to use intel-oneapi-mkl
     buildable: False

diff --git a/configs/sites/tier1/noaa-gcloud/README.md b/configs/sites/tier1/noaa-gcloud/README.md
@@ -46,33 +46,3 @@ spack concretize 2>&1 | tee log.concretize
 spack install --verbose 2>&1 | tee log.install
 spack module lmod refresh --upstream-modules
 spack stack setup-meta-modules
-
-## Steps to install external applications (MySQL, ecFlow)
-
- MySQL:
-mkdir -p /contrib/spack-stack-rocky8/mysql-8.0.31/src
-cd /contrib/spack-stack-rocky8/mysql-8.0.31/src
-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/* ..
-rmdir mysql-8.0.31-linux-glibc2.17-x86_64-minimal
-
- ecFlow:
-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-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
-cd $BOOST_ROOT
-./bootstrap.sh 2>&1 | tee bootstrap.log
-$WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log
-cd $WK
-mkdir build
-cd build
-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
diff --git a/configs/sites/tier1/noaa-gcloud/packages.yaml b/configs/sites/tier1/noaa-gcloud/packages.yaml
@@ -50,10 +50,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  groff:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   hwloc:
     externals:
     - spec: [email protected]
@@ -65,7 +61,7 @@ packages:
   mysql:
     externals:
     - spec: [email protected]
-      prefix: /contrib/spack-stack/mysql-8.0.31
+      prefix: /contrib/spack-stack-rocky8/mysql-8.0.31
   ncurses:
     externals:
     - spec: [email protected]+termlib abi=5
@@ -111,4 +107,4 @@ packages:
     - spec: [email protected]
       prefix: /usr
   zlib:
-     require: ["~shared"]
+     require: [~shared]