Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

…eature/add_cylc_flow

.github/workflows/ubuntu-ci-x86_64.yaml

@@ -145,6 +145,7 @@ jobs:
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
           echo "Next steps ..."
+          ${SPACK_STACK_DIR}/util/ldd_check.py $SPACK_ENV 2>&1 | tee log.ldd_check
           spack clean -a
           spack module tcl refresh -y
           spack stack setup-meta-modules

configs/common/modules_lmod.yaml

@@ -129,20 +129,15 @@ modules:
             'MADIS_ROOT': '{prefix}'
       mapl:
         suffixes:
-          ^[email protected]~debug snapshot=none: 'esmf-8.2.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.2.0-debug'
-          ^[email protected]~debug snapshot=b09: 'esmf-8.3.0b09'
-          ^[email protected]+debug snapshot=b09: 'esmf-8.3.0b09-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.3.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.3.0-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.4.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.4.0-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.4.1'
-          ^[email protected]+debug snapshot=none: 'esmf-8.4.1-debug'
+          # Keeping this as a reminder how to do snapshots
+          #^[email protected]~debug snapshot=b09: 'esmf-8.3.0b09'
+          #^[email protected]+debug snapshot=b09: 'esmf-8.3.0b09-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.4.2'
           ^[email protected]+debug snapshot=none: 'esmf-8.4.2-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.5.0'
           ^[email protected]+debug snapshot=none: 'esmf-8.5.0-debug'
+          ^[email protected]~debug snapshot=none: 'esmf-8.6.0'
+          ^[email protected]+debug snapshot=none: 'esmf-8.6.0-debug'
       openmpi:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -131,20 +131,15 @@ modules:
             'MADIS_ROOT': '{prefix}'
       mapl:
         suffixes:
-          ^[email protected]~debug snapshot=none: 'esmf-8.2.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.2.0-debug'
-          ^[email protected]~debug snapshot=b09: 'esmf-8.3.0b09'
-          ^[email protected]+debug snapshot=b09: 'esmf-8.3.0b09-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.3.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.3.0-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.4.0'
-          ^[email protected]+debug snapshot=none: 'esmf-8.4.0-debug'
-          ^[email protected]~debug snapshot=none: 'esmf-8.4.1'
-          ^[email protected]+debug snapshot=none: 'esmf-8.4.1-debug'
+          # Keeping this as a reminder how to do snapshots
+          #^[email protected]~debug snapshot=b09: 'esmf-8.3.0b09'
+          #^[email protected]+debug snapshot=b09: 'esmf-8.3.0b09-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.4.2'
           ^[email protected]+debug snapshot=none: 'esmf-8.4.2-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.5.0'
           ^[email protected]+debug snapshot=none: 'esmf-8.5.0-debug'
+          ^[email protected]~debug snapshot=none: 'esmf-8.6.0'
+          ^[email protected]+debug snapshot=none: 'esmf-8.6.0-debug'
       openmpi:
         environment:
           set:

configs/common/packages.yaml

@@ -27,18 +27,15 @@
       variants: +python
     cairo:
       variants: +pic
-    # Newer versions of CDO require the C++-17 standard, which doesn't
-    # work with all compilers that are currently in use in spack-stack
-    # When making changes here, also check Hercules/Casper site configs
     cdo:
-      version: ['2.0.5']
+      version: ['2.2.0']
       variants: ~openmp
     cmake:
       version: ['3.23.1']
       variants: +ownlibs
     # Attention - when updating also check the various jcsda-emc-bundles env packages
     crtm:
-      version: ['2.4.0']
+      version: ['2.4.0.1']
       variants: +fix
     ecbuild:
       version: ['3.7.2']
@@ -49,10 +46,10 @@
       version: ['5.11.4']
       variants: +ui
     eckit:
-      version: ['1.24.4']
+      version: ['1.24.5']
       variants: linalg=eigen,lapack compression=lz4,bzip2
     ecmwf-atlas:
-      version: ['0.35.0']
+      version: ['0.35.1']
       variants: +fckit +trans +tesselation +fftw
     ectrans:
       version: ['1.2.0']
@@ -80,9 +77,7 @@
     fiat:
       version: ['1.2.0']
     fms:
-      #version: ['2023.01']
-      #variants: precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release
-      version: ['2023.02.01']
+      version: ['2023.04']
       variants: precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io
     fontconfig:
       variants: +pic
@@ -178,9 +173,8 @@
     netcdf-cxx4:
       version: ['4.3.1']
     netcdf-fortran:
-      version: ['4.6.0']
-    # ninja - when adding information here, also check Cheyenne
-    # and Discover site configs
+      version: ['4.6.1']
+    # ninja - when adding information here, also check Discover site config
     nlohmann-json:
       version: ['3.10.5']
     nlohmann-json-schema-validator:

configs/containers/specs/jedi-ci.yaml

@@ -1,14 +1,14 @@
-  ### spack-stack-1.5.1 / skylab-6.1.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
+  ### spack-stack-1.6.0 / skylab-7.0.0 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].4, [email protected].0 +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,
+    [email protected].5, [email protected].1 +fckit +trans +tesselation +fftw, [email protected], [email protected] +fftw,
     [email protected], [email protected], fms@release-jcsda, [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected],
-    [email protected].0, [email protected], [email protected],
+    [email protected].1, [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected],
-    [email protected], py-pip, py-pyyaml@5.4.1, [email protected], [email protected], py-xarray@2022.3.0,
+    [email protected], py-pip, py-pyyaml@6.0, [email protected], [email protected], py-xarray@2023.7.0,
     [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
     [email protected], [email protected]]
@@ -17,4 +17,3 @@
     # 2. Comment out for now until build problems are solved
     #    https://github.com/jcsda/spack-stack/issues/522
     #    [email protected]
-    # 3. Need to update [email protected] to 12.0.1!

configs/sites/casper/packages.yaml

@@ -17,9 +17,6 @@ packages:
       - cuda/12.2.1
 
 ### Modifications of common packages
-  # Version 2.0.5 doesn't compile on Casper with gcc
-  cdo:
-    version:: ['2.2.0']
 
 ### All other external packages listed alphabetically
   autoconf:

configs/sites/hercules/packages.yaml

@@ -22,12 +22,9 @@ packages:
       - mvapich2/2.3.7
 
 ### Modifications of common packages
-  # Version 2.0.5 doesn't compile on Hercules with gcc
-  cdo:
-    version:: ['2.2.0']
-  # Version 2.0.8 doesn't compile on Hercules
-  wgrib2:
-    version:: ['3.1.1']
+  # 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:

configs/sites/noaa-aws/README.md

@@ -1,6 +1,6 @@
 This README provides step by step instructions for installing the basic packages
 (OS packages, external packages) for spack-stack. Following these steps ensures
-that the site configuration files in `configs/sites/noaa-*` work out of the box.
+that the site configuration files in `configs/sites/noaa-aws` work out of the box.
 
 # Basic system packages (need to be installed each time a cluster is spun up)
 
@@ -124,3 +124,14 @@ make install 2>&1 | tee log.install
 cd /contrib/spack-stack/modulefiles
 mkdir 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 unuse /opt/cray/craype/default/modulefiles
+module unuse /opt/cray/modulefiles
+module use /contrib/spack-stack/modulefiles
+module load cmake/3.27.2
+module load ecflow/5.8.4
+module load mysql/8.0.31
+module load git-lfs/2.4.1
+

configs/sites/noaa-azure/README.md

@@ -0,0 +1,143 @@
+This README provides step by step instructions for installing the basic packages
+(OS packages, external packages) for spack-stack. Following these steps ensures
+that the site configuration files in `configs/sites/noaa-azure` work out of the box.
+
+# Basic system packages (need to be installed each time a cluster is spun up)
+
+sudo su
+chmod 777 /contrib
+yum install -y m4
+yum install -y qt5-qtbase-devel
+yum install -y qt5-qtsvg-devel
+yum install -y xorg-x11-xauth
+yum install -y xorg-x11-apps
+yum install -y perl-IPC-Cmd
+yum install -y gettext-devel
+yum install -y ncurses-devel
+yum install -y ncurses-static
+exit
+
+# Create a script that can be added to the cluster resource config so that these packages get installed automatically
+
+mkdir -p /contrib/admin
+cat <<EOF > /contrib/admin/basic_setup.sh
+#!/bin/bash
+
+chmod 777 /contrib
+yum install -y qt5-qtbase-devel
+yum install -y qt5-qtsvg-devel
+yum install -y xorg-x11-xauth
+yum install -y xorg-x11-apps
+yum install -y perl-IPC-Cmd
+yum install -y gettext-devel
+yum install -y ncurses-devel
+yum install -y ncurses-static
+yum install -y m4
+EOF
+
+chmod a+x /contrib/admin/basic_setup.sh
+
+# Create a mysql config for local R2D2 use (if applicable)
+
+sudo su
+cat <<EOF > /contrib/admin/my.cnf
+[mysqld]
+datadir=/mysql_local/data
+socket=/mysql_local/data/mysql.sock
+symbolic-links=0
+default-authentication-plugin=mysql_native_password
+
+[mysqld_safe]
+log-error=/mysql_local/log/mariadb.log
+pid-file=/mysql_local/run/mariadb.pid
+EOF
+chmod 644 /contrib/admin/my.cnf
+exit
+
+# Build external packages for spack-stack
+
+mkdir -p /contrib/spack-stack
+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/
+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/* ..
+rmdir mysql-8.0.31-linux-glibc2.17-x86_64-minimal
+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
+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
+
+# Build static boost (to not interfere with spack-stack boost)
+cd $BOOST_ROOT
+./bootstrap.sh 2>&1 | tee bootstrap.log
+$WK/build_scripts/boost_build.sh 2>&1 | tee boost_build.log
+
+# Build ecFlow
+cd $WK
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/contrib/spack-stack/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
+# 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 unuse /opt/cray/craype/default/modulefiles
+module unuse /opt/cray/modulefiles
+module use /contrib/spack-stack/modulefiles
+module load cmake/3.27.2
+module load ecflow/5.8.4
+module load mysql/8.0.31
+module load git-lfs/2.4.1
+#
+
+

configs/sites/noaa-azure/packages.yaml

@@ -134,6 +134,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /contrib/spack-stack/mysql-8.0.31
+  ncurses:
+    externals:
+    - spec: [email protected]+termlib abi=5
+      prefix: /usr
   openjdk:
     externals:
     - spec: [email protected]_322-b06