Add build script, bundle CMakeLists.txt and modify .gitignore files

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# bin directory
+bin/

modulefiles/GDAS/hera.lua

@@ -0,0 +1,24 @@
+-- NOAA RDHPCS Hera Modulefile for UFS-DA
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+local jedi_opt = '/scratch1/NCEPDEV/jcsda/jedipara/opt/modules'
+setenv('JEDI_OPT', jedi_opt)
+local jedi_core = pathJoin(jedi_opt, 'modulefiles/core')
+prepend_path("MODULEPATH", jedi_core)
+
+load('jedi/intel-impi/2020.2')
+
+local mpiexec = '/apps/slurm/default/bin/srun'
+local mpinproc = '-n'
+setenv('MPIEXEC_EXEC', mpiexec)
+setenv('MPIEXEC_NPROC', mpinproc)
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: UFS-DA")
+whatis("Description: Load JEDI-Stack for UFS-DA")

modulefiles/GDAS/orion.lua

@@ -0,0 +1,29 @@
+-- NOAA HPC Orion Modulefile for UFS-DA
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+local jedi_opt = '/work/noaa/da/jedipara/opt/modules'
+setenv('JEDI_OPT', jedi_opt)
+local jedi_core = pathJoin(jedi_opt, 'modulefiles/core')
+prepend_path("MODULEPATH", jedi_core)
+
+load('jedi/intel-impi')
+
+local mpiexec = '/opt/slurm/bin/srun'
+local mpinproc = '-n'
+setenv('MPIEXEC_EXEC', mpiexec)
+setenv('MPIEXEC_NPROC', mpinproc)
+
+-- add R2D2 and SOLO to PYTHONPATH
+prepend_path("PYTHONPATH", "/work2/noaa/da/cmartin/UFSDA/python/local/lib/python3.9/site-packages")
+-- add R2D2 to path
+prepend_path("PATH", "/work2/noaa/da/cmartin/UFSDA/python/local/bin")
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: UFS-DA")
+whatis("Description: Load JEDI-Stack for UFS-DA")

src/.gitignore

@@ -0,0 +1,24 @@
+atlas/
+crtm/
+eckit/
+fckit/
+femps/
+fms/
+fv3/
+fv3-jedi/
+fv3-jedi-data/
+fv3-jedi-lm/
+gsw/
+ioda/
+ioda-data/
+iodaconv/
+jedicmake/
+mom6/
+oops/
+saber/
+saber-data/
+soca/
+test-data-release/
+ufo/
+ufo-data/
+build/

src/CMakeLists.txt

@@ -0,0 +1,130 @@
+# # ------------------------------------------------------------------------- #
+# # ufs-da-bundle for building all the components needed for the UFS-DA system #
+# # ------------------------------------------------------------------------- #
+
+
+# Preamble
+# --------
+
+# Check for minimim cmake requirement
+cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
+
+# Create project
+project( ufsda-bundle VERSION 1.0.0 LANGUAGES C CXX Fortran )
+
+# Include ecbuild_bundle macro
+include( ecbuild_bundle )
+
+# Default build mode, change with --build=[release]|debug|bit
+set( ECBUILD_DEFAULT_BUILD_TYPE Release )
+
+# Enable MPI
+set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
+
+
+# Initialize bundle
+# -----------------
+ecbuild_bundle_initialize()
+
+
+# Add packages to the bundle
+# --------------------------
+
+# jedi-cmake
+ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda/jedi-cmake.git" BRANCH develop UPDATE )
+
+# ECMWF libraries
+option("BUNDLE_SKIP_ECKIT" "Don't build eckit" "ON" ) # Skip eckit build unless user passes -DBUNDLE_SKIP_ECKIT=OFF
+option("BUNDLE_SKIP_FCKIT" "Don't build fckit" "ON") # Skip fckit build unless user passes -DBUNDLE_SKIP_FCKIT=OFF
+option("BUNDLE_SKIP_ATLAS" "Don't build atlas" "ON") # Skip atlas build unless user passes -DBUNDLE_SKIP_ATLAS=OFF
+
+# turn off optional OOPS toy models
+option( ENABLE_LORENZ95_MODEL "Build LORENZ95 toy model" OFF )
+option( ENABLE_QG_MODEL "Build QG toy model" OFF )
+
+ecbuild_bundle( PROJECT eckit GIT "https://github.com/ecmwf/eckit.git" TAG 1.16.0 )
+ecbuild_bundle( PROJECT fckit GIT "https://github.com/ecmwf/fckit.git" TAG 0.9.2 )
+ecbuild_bundle( PROJECT atlas GIT "https://github.com/ecmwf/atlas.git" TAG 0.24.1 )
+
+# External (required) observation operators
+ecbuild_bundle( PROJECT crtm GIT "https://github.com/jcsda/crtm.git"   TAG v2.3-jedi.3 )
+
+# Core JEDI repositories
+ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda/oops.git"  BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda/saber.git" BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda/ioda.git"  BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT ufo   GIT "https://github.com/noaa-emc/ufo.git"   BRANCH feature/ufsda UPDATE )
+
+# FMS and FV3 dynamical core
+ecbuild_bundle( PROJECT fms GIT "https://github.com/jcsda/FMS.git" BRANCH release-stable UPDATE )
+ecbuild_bundle( PROJECT fv3 GIT "https://github.com/jcsda/GFDL_atmos_cubed_sphere.git" BRANCH release-stable UPDATE )
+
+# fv3-jedi and associated repositories
+ecbuild_bundle( PROJECT femps       GIT "https://github.com/jcsda/femps.git"                BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT fv3-jedi-lm GIT "https://github.com/jcsda/fv3-jedi-linearmodel.git" BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT fv3-jedi    GIT "https://github.com/jcsda/fv3-jedi.git"             BRANCH develop UPDATE )
+
+# SOCA associated repositories
+ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git" UPDATE BRANCH develop )
+ecbuild_bundle( PROJECT mom6 GIT "https://github.com/jcsda-internal/MOM6.git" UPDATE BRANCH main-ecbuild RECURSIVE )
+ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" UPDATE BRANCH develop )
+
+# Build IODA converters
+option(BUILD_IODA_CONVERTERS "Build IODA Converters" OFF)
+if(BUILD_IODA_CONVERTERS)
+  ecbuild_bundle( PROJECT iodaconv GIT "https://github.com/JCSDA-internal/ioda-converters.git" BRANCH develop UPDATE )
+endif()
+
+# ioda, ufo, fv3-jedi, and saber test data
+#---------------------------------
+
+# If IODA branch is being built set GIT_BRANCH_FUNC to IODA's current branch.
+# If a tagged version of IODA is being built set GIT_TAG_FUNC to ioda's current tag. In this case,
+# IODA test files will be download from UCAR DASH and ioda-data repo will not be cloned.
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+
+find_branch_name(REPO_DIR_NAME ioda)
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
+  ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
+
+  # If IODA's current branch is available in ioda-data repo, that branch will be checked out
+  branch_checkout (REPO_DIR_NAME ioda-data
+                   BRANCH ${GIT_BRANCH_FUNC} )
+endif()
+
+# same procedure for ufo-data
+find_branch_name(REPO_DIR_NAME ufo)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
+  ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
+
+  # If UFO's current branch is available in ioda-data repo, that branch will be checked out
+  branch_checkout (REPO_DIR_NAME ufo-data
+                   BRANCH ${GIT_BRANCH_FUNC} )
+endif()
+
+# same procedure for fv3-jedi-data
+find_branch_name(REPO_DIR_NAME fv3-jedi)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
+  ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH develop UPDATE )
+
+  # If fv3-jedi's current branch is available in ioda-data repo, that branch will be checked out
+  branch_checkout (REPO_DIR_NAME fv3-jedi-data
+                   BRANCH ${GIT_BRANCH_FUNC} )
+endif()
+
+# same procedure for saber-data
+find_branch_name(REPO_DIR_NAME saber)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED GIT_TAG_FUNC )
+  ecbuild_bundle( PROJECT saber-data GIT "https://github.com/JCSDA-internal/saber-data.git" BRANCH develop UPDATE )
+
+  # If saber's current branch is available in saber-data repo, that branch will be checked out
+  branch_checkout (REPO_DIR_NAME saber-data
+                   BRANCH ${GIT_BRANCH_FUNC} )
+endif()
+
+# Finalize bundle
+# ---------------
+ecbuild_bundle_finalize()

ush/build_GDASApp.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+# build_GDASApp.sh
+# 1 - determine if on supported host, load modules if so
+# 2 - run ecbuild
+# 3 - build
+# 4 - optional, run unit tests
+
+set -eux
+
+dir_root="$( cd "$( dirname "${BASH_SOURCE[0]}" )/.." >/dev/null 2>&1 && pwd )"
+
+dir_modules=$dir_root/modulefiles
+
+if [ ${BUILD_TARGET:-} = "orion" -o ${BUILD_TARGET:-} = "hera" ]; then
+    set +x
+    source $MODULESHOME/init/sh
+    module purge
+    module use $dir_modules
+    module load GDAS/${BUILD_TARGET}
+    module list
+    set -x
+fi
+
+# remove/create directories
+[ -d $dir_root/bin ] || mkdir -p $dir_root/bin
+
+rm -rf $dir_root/src/build
+mkdir -p $dir_root/src/build
+cd $dir_root/src/build
+
+# run ecbuild
+ecbuild -DMPIEXEC_EXECUTABLE=$MPIEXEC_EXEC -DMPIEXEC_NUMPROC_FLAG=$MPIEXEC_NPROC ../
+
+# run make
+make -j ${BUILD_JOBS:-8} VERBOSE=${BUILD_VERBOSE:-}
+
+# link executables to exec dir
+ln -sf $dir_root/src/build/bin/fv3jedi* $dir_root/bin/.
+ln -sf $dir_root/src/build/bin/soca* $dir_root/bin/.
+
+exit 0