Merge pull request #98 from JCSDA-internal/release/1.1.0

Release/1.1.0

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Use this template to report bugs
+title: "[Bug]"
+labels: 'bug'
+assignees: ''
+
+---
+
+## Current behavior (describe the bug)
+>[Be sure to add a Pipeline, Label, Estimate, Assignees, and Epic](https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/inside/practices/issues.html)
+
+## To Reproduce
+
+> What computer are you running on?
+
+> What compilers/modules are you using?
+
+> Steps to reproduce the behavior
+
+1.
+2.
+3.
+...
+
+## Expected behavior
+
+## Additional information (optional)

.github/ISSUE_TEMPLATE/config.yaml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: JCSDA
+    url: https://jcsda.org/
+    about: JCSDA web site
+  - name: Forums
+    url: https://forums.jcsda.org/
+    about: JCSDA user/developer forums

.github/ISSUE_TEMPLATE/general-issue.md

@@ -0,0 +1,26 @@
+---
+name: General issue template
+about: Use this template for general issues
+title: "[New issue]"
+labels: ''
+assignees: ''
+
+---
+
+## Description
+>Provide a detailed description of this issue.
+>What problem needs to be fixed? What new capability needs to be added?
+>If this is a bug, describe the current behavior (or use the bug template).
+>[Be sure to add a Pipeline, Label, Estimate, Assignees, and Epic](https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/inside/practices/issues.html)
+
+## Requirements
+
+>If this is a new feature: What does the new code need to accomplish? Does it require new software dependencies (e.g. new jedi-stack components or new python modules?)
+>If this is a bugfix: What is the expected behavior?
+
+## Acceptance Criteria (Definition of Done)
+>What does it mean for this to be finished?
+
+## Dependencies
+>What must be done before this can be done? Add issue dependencies in ZenHub as appropriate
+>Does this block progress on other issues? Add this issue as a dependency to other ZenHub issues as appropriate

buildscripts/Mac/README.md

@@ -0,0 +1,16 @@
+# Notes on building the Software Stack for JEDI applications on Mac OS
+
+Installing a minimal JEDI software stack on Mac OS (*catalina 10.15.7* and newer) is described in some detail elsewhere, in particular:
+
+[Minimum steps for working with JEDI natively on Mac OS](https://github.com/JCSDA-internal/jedi-docs/blob/develop/howto/macos/minimum.md)
+
+The [brew](https://brew.sh) package manager installs packages to their own directory (`/usr/local/Cellar/<package>)` and then symlinks their files into the system location `/usr/local`. There are exceptions: Sometimes, brew cannot symlink to header files or libraries in `/usr/local`, and for some packages that have multiple related components, they are not installed in a common root location in `/usr/local/Cellar`.
+
+If you are building the optional jedi-stack component [ecFlow](https://confluence.ecmwf.int/display/ECFLOW/ecflow+home), two scripts are provided to properly symlink software packages that ecFlow requires:
+
+| software  | helper script | Notes |
+| -------   | --------------- | ----- |
+| openssl   | linkOpenSSLmacOS.sh | backs up deprecated versions of system libraries and symlinks to brew's version |
+| boost / boost-python3 | linkBoostPythonLibsmacOS.sh | co-locates boost and boost-python libraries, allowing you to set the build config variable `BOOST_ROOT` |
+
+Running these scripts after installing openssl and boost / boost-python3 will properly set up symlinks for jedi-stack components that depend on them to build correctly.

buildscripts/Mac/linkBoostPythonLibsmacOS.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Co-locate (via symlink) brew-installed boost / boost-python libraries and headers
+#   brew installs these packages in different locations; a typical build from source
+#   code would co-locate them, so that setting BOOST_ROOT for use in building other
+#   software is made easier.
+# Steps:
+#   brew install boost boost-python3
+#   run this script
+
+# Boost libraries and headers: version and location
+boostLib_version=`brew list --versions | grep "boost " | cut -d ' ' -f 2`
+boostLib_cellar=`brew --cellar boost`
+
+# Boost python libraries: version and location
+boostPython_version=`brew list --versions | grep boost-python3 | cut -d ' ' -f 2`
+boostPython_cellar=`brew --cellar boost-python3`
+
+echo 'Linking boost-python3 libraries into boost installation location'
+for lib in `ls $boostPython_cellar/$boostPython_version/lib/lib*`; do
+    echo "Linking $lib  into  $boostLib_cellar/$boostLib_version/lib"
+    sudo ln -s $lib $boostLib_cellar/$boostLib_version/lib
+done
+

buildscripts/Mac/linkOpenSSLmacOS.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+# Replace macOS-supplied openssl libraries; macOS SIP often prevents proper linking
+# Steps:
+#   brew install [email protected]
+#   run this script
+
+version=`brew list --versions | grep openssl | cut -d ' ' -f 2`
+cellar=`brew --cellar openssl`
+
+echo 'Linking [email protected] v$version libraries and pkgconfig files'
+
+if [ -f /usr/local/lib/libssl.dylib ]; then
+    echo 'backing up existing libssl.dylib'
+    mv /usr/local/lib/libssl.dylib /usr/local/lib/libssl_bak.dylib
+fi
+
+if [ -f /usr/local/lib/libcrypto.dylib ]; then
+    echo 'backing up existing libcrypto.dylib'
+    mv /usr/local/lib/libcrypto.dylib /usr/local/lib/libcrypto_bak.dylib
+fi
+
+echo 'add symlink for openssl libs'
+
+if [ -f $cellar/$version/lib/libssl.1.1.dylib ]; then
+    sudo ln -s $cellar/$version/lib/libssl.1.1.dylib /usr/local/lib/libssl.dylib
+fi
+
+if [ -f $cellar/$version/lib/libcrypto.1.1.dylib ]; then
+    sudo ln -s $cellar$version/lib/libcrypto.1.1.dylib /usr/local/lib/libcrypto.dylib
+fi
+
+echo 'add symlink for openssl pkgconfig files'
+
+if [ -f $cellar/$version/lib/pkgconfig/openssl.pc ]; then
+    sudo ln -s $cellar/$version/lib/pkgconfig/openssl.pc /usr/local/lib/pkgconfig/openssl.pc
+fi
+
+if [ -f $cellar/$version/lib/pkgconfig/libssl.pc ]; then
+    sudo ln -s $cellar/$version/lib/pkgconfig/libssl.pc /usr/local/lib/pkgconfig/libssl.pc
+fi
+
+if [ -f $cellar/$version/lib/pkgconfig/libcrypto.pc ]; then
+    sudo ln -s $cellar/$version/lib/pkgconfig/libcrypto.pc /usr/local/lib/pkgconfig/libcrypto.pc
+fi

buildscripts/build_stack.sh

@@ -77,18 +77,18 @@ $MODULES && (set +x;  source $MODULESHOME/init/bash; module purge; set -x)
 # - should add a check at some point to see if they are already there.
 # this can be done in each script individually
 # it might warrant a --force flag to force rebuild when desired
-build_lib CMAKE cmake 3.17.2
-build_lib UDUNITS udunits 2.2.26
+build_lib CMAKE cmake 3.20.0
+build_lib UDUNITS udunits 2.2.28
 build_lib JPEG jpeg 9.1.0
 build_lib ZLIB zlib 1.2.11
 build_lib PNG png 1.6.35
 build_lib SZIP szip 2.1.1
 build_lib LAPACK lapack 3.8.0
 build_lib BOOST_HDRS boost 1.68.0 headers-only
 build_lib EIGEN3 eigen 3.3.7
-build_lib BUFRLIB bufrlib 11.3.2
-build_lib ECBUILD ecbuild jcsda 3.3.2.jcsda3
-build_lib CGAL cgal 5.0.2
+build_lib BUFR bufr noaa-emc 11.5.0
+build_lib ECBUILD ecbuild ecmwf 3.6.1
+build_lib CGAL cgal 5.0.4
 build_lib GITLFS git-lfs 2.11.0
 
 #----------------------
@@ -97,11 +97,11 @@ build_lib HDF5 hdf5 1.12.0
 build_lib PNETCDF pnetcdf 1.12.1
 build_lib NETCDF netcdf 4.7.4 4.5.3 4.3.0
 build_lib NCCMP nccmp 1.8.7.0
-build_lib ECKIT eckit jcsda 1.11.6.jcsda2
-build_lib FCKIT fckit jcsda 0.7.0.jcsda1
-build_lib ATLAS atlas jcsda 0.20.2.jcsda1
+build_lib ECKIT eckit ecmwf 1.16.0
+build_lib FCKIT fckit ecmwf 0.9.2
+build_lib ATLAS atlas ecmwf 0.24.1
 build_lib ODB odb 0.18.1.r2
-build_lib ODC odc jcsda 1.0.3
+build_lib ODC odc ecmwf 2021.03.0
 
 # ===============================================================================
 # Optional Extensions to the JEDI Stack
@@ -115,17 +115,18 @@ build_lib NCEPLIBS nceplibs fv3
 build_lib TKDIFF tkdiff 4.3.5
 build_lib PYJEDI pyjedi
 build_lib PYBIND11 pybind11 2.5.0
-build_lib GSL_LITE gsl_lite 0.34.0
+build_lib GSL_LITE gsl_lite 0.37.0
 build_lib GEOS geos 3.8.1
 build_lib SQLITE sqlite 3.32.3
 build_lib PROJ proj 7.1.0
 build_lib JSON json 3.9.1
 build_lib JSON_SCHEMA_VALIDATOR json-schema-validator 2.1.0
+build_lib ECFLOW ecflow ecmwf 5.5.3 boost 1.68.0
 
 #----------------------
 # These must be rebuilt for each MPI implementation
 build_lib GPTL gptl 8.0.3
-build_lib NCO nco 4.7.9
+build_lib NCO nco 4.9.9
 build_lib PIO pio 2.5.1
 build_lib FFTW fftw 3.3.8
 build_lib BOOST_FULL boost 1.68.0

buildscripts/config/choose_modules.sh

@@ -4,32 +4,32 @@
 # http://www.apache.org/licenses/LICENSE-2.0.
 
 # Minimal JEDI Stack
-export      STACK_BUILD_CMAKE=N
+export      STACK_BUILD_CMAKE=Y
 export     STACK_BUILD_GITLFS=N
 export       STACK_BUILD_SZIP=Y
 export    STACK_BUILD_UDUNITS=Y
 export       STACK_BUILD_ZLIB=Y
-export     STACK_BUILD_LAPACK=N
+export     STACK_BUILD_LAPACK=Y
 export STACK_BUILD_BOOST_HDRS=Y
-export    STACK_BUILD_BUFRLIB=Y
+export       STACK_BUILD_BUFR=Y
 export     STACK_BUILD_EIGEN3=Y
 export       STACK_BUILD_HDF5=Y
 export    STACK_BUILD_PNETCDF=Y
 export     STACK_BUILD_NETCDF=Y
 export      STACK_BUILD_NCCMP=Y
 export    STACK_BUILD_ECBUILD=Y
 export      STACK_BUILD_ECKIT=Y
-export      STACK_BUILD_FCKIT=N
-export      STACK_BUILD_ATLAS=N
+export      STACK_BUILD_FCKIT=Y
+export      STACK_BUILD_ATLAS=Y
 export   STACK_BUILD_GSL_LITE=Y
+export   STACK_BUILD_PYBIND11=Y
 
 # Optional Additions
 export           STACK_BUILD_ODC=N
-export           STACK_BUILD_PIO=Y
+export           STACK_BUILD_PIO=N
 export          STACK_BUILD_GPTL=N
 export           STACK_BUILD_NCO=N
 export        STACK_BUILD_PYJEDI=N
-export      STACK_BUILD_PYBIND11=N
 export      STACK_BUILD_NCEPLIBS=N
 export          STACK_BUILD_JPEG=N
 export           STACK_BUILD_PNG=N
@@ -47,5 +47,6 @@ export          STACK_BUILD_GEOS=N
 export        STACK_BUILD_SQLITE=N
 export          STACK_BUILD_PROJ=N
 export           STACK_BUILD_FMS=N
-export          STACK_BUILD_JSON=N
-export STACK_BUILD_JSON_SCHEMA_VALIDATOR=N
+export          STACK_BUILD_JSON=Y
+export STACK_BUILD_JSON_SCHEMA_VALIDATOR=Y
+export        STACK_BUILD_ECFLOW=N

buildscripts/config/config_ami-gnu-openmpi-dev.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+# © Copyright 2020 UCAR
+# This software is licensed under the terms of the Apache Licence Version 2.0 which can be obtained at
+# http://www.apache.org/licenses/LICENSE-2.0.
+
+
+# Compiler/MPI combination
+export JEDI_COMPILER="gnu/9.3.0"
+export JEDI_MPI="openmpi/4.1.0"
+
+# This tells jedi-stack how you want to build the compiler and mpi modules
+# valid options include:
+# native-module: load a pre-existing module (common for HPC systems)
+# native-pkg: use pre-installed executables located in /usr/bin or /usr/local/bin,
+#             as installed by package managers like apt-get or hombrewo.
+#             This is a common option for, e.g., gcc/g++/gfortrant
+# from-source: This is to build from source
+export COMPILER_BUILD="native-pkg"
+export MPI_BUILD="from-source"
+
+# Build options
+export PREFIX=/optjedi/modules
+export USE_SUDO=Y
+export PKGDIR=pkg
+export LOGDIR=buildscripts/log
+export OVERWRITE=N
+export NTHREADS=4
+export   MAKE_CHECK=N
+export MAKE_VERBOSE=N
+export   MAKE_CLEAN=N
+export DOWNLOAD_ONLY=F
+export STACK_EXIT_ON_FAIL=T
+export WGET="wget -nv"
+#Global compiler flags
+export FFLAGS=""
+export CFLAGS=""
+export CXXFLAGS=""
+export LDFLAGS=""
+

buildscripts/config/config_ami-intel-impi-dev.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+# © Copyright 2020 UCAR
+# This software is licensed under the terms of the Apache Licence Version 2.0 which can be obtained at
+# http://www.apache.org/licenses/LICENSE-2.0.
+
+
+# Compiler/MPI combination
+export JEDI_COMPILER="intel/2021.2"
+export JEDI_MPI="impi/2021.2"
+export PATH=/usr/local/bin:$PATH
+export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+export LIBRARY_PATH=/usr/local/lib:$LIBRARY_PATH
+export CPATH=/usr/local/include:$CPATH
+
+# This tells jedi-stack how you want to build the compiler and mpi modules
+# valid options include:
+# native-module: load a pre-existing module (common for HPC systems)
+# native-pkg: use pre-installed executables located in /usr/bin or /usr/local/bin,
+#             as installed by package managers like apt-get or hombrewo.
+#             This is a common option for, e.g., gcc/g++/gfortran
+# from-source: This is to build from source
+export COMPILER_BUILD="native-pkg"
+export MPI_BUILD="native-pkg"
+
+# Build options
+export PREFIX=/optjedi/modules
+export USE_SUDO=Y
+export PKGDIR=pkg
+export LOGDIR=buildscripts/log
+export OVERWRITE=N
+export NTHREADS=4
+export   MAKE_CHECK=N
+export MAKE_VERBOSE=N
+export   MAKE_CLEAN=N
+export DOWNLOAD_ONLY=F
+export STACK_EXIT_ON_FAIL=T
+export WGET="wget -nv"
+
+#Global compiler flags
+export FFLAGS=""
+export CFLAGS=""
+export CXXFLAGS=""
+export LDFLAGS=""
+