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115 changes: 62 additions & 53 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# (C) Copyright 2017-2024 UCAR
# (C) Copyright 2017-2026 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.
Expand All @@ -25,59 +25,68 @@ include( ecbuild_bundle )
ecbuild_bundle_initialize()
# Use external jedi-cmake or build in bundle

if(DEFINED ENV{jedi_cmake_ROOT})
include( $ENV{jedi_cmake_ROOT}/share/jedicmake/Functions/git_functions.cmake )
list( APPEND CMAKE_MODULE_PATH $ENV{jedi_cmake_ROOT}/share/jedicmake/Modules )
message (INFO "CMAKE_MODULE_PATH")
# If the gpu toolchain is loaded, only configure MPAS-Model
if(CMAKE_Fortran_COMPILER_ID MATCHES NVHPC)
ecbuild_bundle( PROJECT MPAS GIT "https://github.com/MPAS-Dev/MPAS-Model.git" BRANCH develop UPDATE )
else()
ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/JCSDA/jedi-cmake.git" BRANCH develop UPDATE RECURSIVE )
include( jedicmake/cmake/Functions/git_functions.cmake )
list( APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/jedicmake/CMakeModules/Modules )
endif()

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 eckit 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
ecbuild_bundle( PROJECT eckit GIT "https://github.com/ecmwf/eckit.git" TAG 1.24.4 )
ecbuild_bundle( PROJECT fckit GIT "https://github.com/ecmwf/fckit.git" TAG 0.11.0 )
ecbuild_bundle( PROJECT atlas GIT "https://github.com/ecmwf/atlas.git" TAG 0.34.0 )

#TODO: When mpas-bundle becomes a public repo, consider changing the default value of BUNDLE_SKIP_ROPP-UFO to "ON"
option(BUNDLE_SKIP_ROPP-UFO "Don't build ROPP-UFO" "ON") # Build ropp-ufo unless user passes -DBUNDLE_SKIP_ROPP-UFO=ON
ecbuild_bundle( PROJECT ropp-ufo GIT "https://github.com/JCSDA-internal/ropp-test.git" BRANCH develop UPDATE )
option(BUNDLE_SKIP_RTTOV "Don't build rttov" "ON") # Skip rttov build unless user passes -DBUNDLE_SKIP_RTTOV=OFF
ecbuild_bundle( PROJECT rttov GIT "https://github.com/JCSDA-internal/rttov.git" BRANCH develop UPDATE )

ecbuild_bundle( PROJECT oops GIT "https://github.com/JCSDA/oops.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT vader GIT "https://github.com/JCSDA/vader.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT saber GIT "https://github.com/JCSDA/saber.git" BRANCH develop UPDATE)
ecbuild_bundle( PROJECT crtm GIT "https://github.com/JCSDA/CRTMv3.git" BRANCH develop UPDATE )

option(ENABLE_IODA_DATA "Obtain ioda test data from ioda-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT ioda GIT "https://github.com/JCSDA/ioda.git" BRANCH develop UPDATE )
option(ENABLE_UFO_DATA "Obtain ufo test data from ufo-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT ufo GIT "https://github.com/JCSDA/ufo.git" BRANCH develop UPDATE )


# Find external ESMF for mpas-model (optional)
find_package(ESMF 8.3.0 MODULE)

set(MPAS_DOUBLE_PRECISION "ON" CACHE STRING "MPAS-Model: Use double precision 64-bit Floating point.")
set(MPAS_CORES init_atmosphere atmosphere CACHE STRING "MPAS-Model: cores to build.")

ecbuild_bundle( PROJECT MPAS GIT "https://github.com/MPAS-Dev/MPAS-Model" BRANCH develop UPDATE )
option(ENABLE_MPAS_JEDI_DATA "Obtain mpas-jedi test data from mpas-jedi-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT mpas-jedi-data GIT "https://github.com/JCSDA-internal/mpas-jedi-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT mpas-jedi GIT "https://github.com/JCSDA/mpas-jedi" BRANCH develop UPDATE )

# Set GIT_BRANCH_FUNC to MPAS-JEDI's current branch so that it can be used for mpas-jedi-data
find_branch_name(REPO_DIR_NAME mpas-jedi)

# If mpas-jedi's current branch is available in mpas-jedi-data repo, that branch will be checked out
branch_checkout (REPO_DIR_NAME mpas-jedi-data
if(DEFINED ENV{jedi_cmake_ROOT})
include( $ENV{jedi_cmake_ROOT}/share/jedicmake/Functions/git_functions.cmake )
list( APPEND CMAKE_MODULE_PATH $ENV{jedi_cmake_ROOT}/share/jedicmake/Modules )
message (INFO "CMAKE_MODULE_PATH")
else()
ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/JCSDA/jedi-cmake.git" BRANCH develop UPDATE RECURSIVE )
include( jedicmake/cmake/Functions/git_functions.cmake )
list( APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/jedicmake/CMakeModules/Modules )
endif()

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 eckit 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
ecbuild_bundle( PROJECT eckit GIT "https://github.com/ecmwf/eckit.git" TAG 1.24.4 )
ecbuild_bundle( PROJECT fckit GIT "https://github.com/ecmwf/fckit.git" TAG 0.11.0 )
ecbuild_bundle( PROJECT atlas GIT "https://github.com/ecmwf/atlas.git" TAG 0.34.0 )

#TODO: When mpas-bundle becomes a public repo, consider changing the default value of BUNDLE_SKIP_ROPP-UFO to "ON"
option(BUNDLE_SKIP_ROPP-UFO "Don't build ROPP-UFO" "ON") # Build ropp-ufo unless user passes -DBUNDLE_SKIP_ROPP-UFO=ON
ecbuild_bundle( PROJECT ropp-ufo GIT "https://github.com/JCSDA-internal/ropp-test.git" BRANCH develop UPDATE )
option(BUNDLE_SKIP_RTTOV "Don't build rttov" "ON") # Skip rttov build unless user passes -DBUNDLE_SKIP_RTTOV=OFF
ecbuild_bundle( PROJECT rttov GIT "https://github.com/JCSDA-internal/rttov.git" BRANCH develop UPDATE )

ecbuild_bundle( PROJECT oops GIT "https://github.com/JCSDA/oops.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT vader GIT "https://github.com/JCSDA/vader.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT saber GIT "https://github.com/JCSDA/saber.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT crtm GIT "https://github.com/JCSDA/CRTMv3.git" BRANCH develop UPDATE )

option(ENABLE_IODA_DATA "Obtain ioda test data from ioda-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT ioda GIT "https://github.com/JCSDA/ioda.git" BRANCH develop UPDATE )
option(ENABLE_UFO_DATA "Obtain ufo test data from ufo-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT ufo GIT "https://github.com/JCSDA/ufo.git" BRANCH develop UPDATE )

# Build IODA converters if requested
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()

# Find external ESMF for mpas-model (optional)
find_package(ESMF 8.3.0 MODULE)

set(MPAS_DOUBLE_PRECISION "ON" CACHE STRING "MPAS-Model: Use double precision 64-bit Floating point.")
set(MPAS_CORES init_atmosphere atmosphere CACHE STRING "MPAS-Model: cores to build.")

ecbuild_bundle( PROJECT MPAS GIT "https://github.com/MPAS-Dev/MPAS-Model" BRANCH develop UPDATE )
option(ENABLE_MPAS_JEDI_DATA "Obtain mpas-jedi test data from mpas-jedi-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT mpas-jedi-data GIT "https://github.com/JCSDA-internal/mpas-jedi-data.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT mpas-jedi GIT "https://github.com/JCSDA/mpas-jedi" BRANCH develop UPDATE )

# Set GIT_BRANCH_FUNC to MPAS-JEDI's current branch so that it can be used for mpas-jedi-data
find_branch_name(REPO_DIR_NAME mpas-jedi)

# If mpas-jedi's current branch is available in mpas-jedi-data repo, that branch will be checked out
branch_checkout (REPO_DIR_NAME mpas-jedi-data
BRANCH ${GIT_BRANCH_FUNC} )

endif()

ecbuild_bundle_finalize()
6 changes: 6 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,8 @@ _**For performance and memory reasons, it is recommended to compile ```mpas-bund

```bash
git clone https://github.com/JCSDA/mpas-bundle.git
```
```bash
cd mpas-bundle
```

Expand All @@ -60,8 +62,12 @@ _**For performance and memory reasons, it is recommended to compile ```mpas-bund
| __csh/tcsh__ | `source <mpas_bundle_dir>/env-setup/gnu-derecho.csh` | `source <mpas_bundle_dir>/env-setup/intel-derecho.csh` |
* Create and navigate into the build directory.

```bash
mkdir -p <mpas-bundle_build_dir>
```
```bash
cd <mpas-bundle_build_dir>
```
* To configure the build using CMake, set the `MPAS_DOUBLE_PRECISION` flag according to your usage needs:
enable it (`-DMPAS_DOUBLE_PRECISION=ON`) for running the `mpas-jedi` test suite, or
disable it for `MPAS-Workflow` calculations when using the `mpas-bundle` build.
Expand Down
58 changes: 38 additions & 20 deletions env-setup/crontab.sh
Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,27 @@
# run scripts to build mpas-bundle and run ctest
# to use this,
# 1. log on to cron.hpc.ucar.edu
# 2. run: crontab bundle-crontab
# 2. run: crontab crontab.sh

# set this to the directory the mpas-bundle repository has been cloned to
bundle_dir=/glade/work/jwittig/repos1/mpas-bundle-cron/mpas-bundle/
# don't put it on scratch or it will get corrupted due to scratch retention policy
bundle_dir=/glade/work/jwittig/repos1/mpas-bundle-cron-src/mpas-bundle
# set this to where the builds are - we want them on scratch so they get cleaned up
builds_dir=/glade/derecho/scratch/jwittig/repos-s/mpas-bundle-cron/
# the directory where the single precision bundle build is
bundle_build_dir=/glade/work/jwittig/repos1/mpas-bundle-cron/build-gnu-1p/
bundle_build_dir="'/glade/derecho/scratch/jwittig/repos-s/mpas-bundle-cron/build-gnu-1p_[01]'"
# this is the build script to execute, relative to the mpas-bundle source directory
build_script=env-setup/mpas-bundle-cron.sh

# the workflow directory with the develop branch, used when running the cylc workflow
workflow_dev_dir=/glade/derecho/scratch/jwittig/repos-s/MPAS-Workflow-develop
# the workflow directory with the script to run a workflow and make graphs
workflow_dir=/glade/derecho/scratch/jwittig/repos-s/MPAS-Workflow-cron
# the script to run a cylc job and to create graphs, relative to the workflow directory
workflow_script=env-setup/run_cylc.sh
# the workflow scenario to run, relative to the workflow directory
workflow_scenario=scenarios/3denvar_OIE120km_WarmStart_VarBC_cron.yaml
workflow_scenario2=scenarios/3dhybrid_OIE120km_WarmStart_cron.yaml

# the directory with the graphics scripts
graphs_dir=/glade/derecho/scratch/jwittig/repos-s/mpas-jedi-cron/graphics
Expand All @@ -26,36 +32,48 @@ graphs_out_dir=/glade/derecho/scratch/jwittig/graphs/data/
# derecho hpc
derecho=derecho.hpc.ucar.edu
# mmm web server
webserver=whitedwarf.mmm.ucar.edu
webserver=eris.mmm.ucar.edu
# destination for graphs
web_graphs_dir=/web/htdocs/projects/mpas-jedi/weekly-cycling/cylc_graphs

# start at 11:05 PM and clean up log files
05 23 * * * ssh $derecho "cd ~/my_cron_logs && (gunzip mpas-bundle-cron.log.tar.gz ; tar --remove-files -uf mpas-bundle-cron.log.tar mpas-bundle-cron.log.2* ; tar --remove-files -uf mpas-bundle-cron.log.tar git_shas* ; gzip mpas-bundle-cron.log.tar)"
05 23 * * 7 ssh $derecho "cd ~/my_cron_logs && (gunzip mpas-bundle-cron.log.tar.gz ; tar --remove-files -uf mpas-bundle-cron.log.tar mpas-bundle-cron.log.2* ; tar --remove-files -uf mpas-bundle-cron.log.tar git_shas* ; gzip mpas-bundle-cron.log.tar)"

# start at 12:05 AM Sun through Fri
# change 'gnu' to 'intel' to use the intel build toolchain, or 'both' to build both
# double precision (-p 2), to be used for ctests.
# don't do anything if no source code changed from previous run (don't provide -f)
#05 00 * * 0-5 $bundle_dir/$build_script -d $bundle_dir -q main@desched1 -c gnu -p 2
#05 00 * * 0-5 $bundle_dir/$build_script -d $bundle_dir -q develop@desched1 -c gnu -p 2 -l $bundle_dir/$build_script.lock
# at 7:30 AM on 7th day of the month clean up last months cylc log files
lastmon=$(date --date='-1 month' +%Y-%m)
30 7 7 * * ssh $derecho "cd ~/my_cron_logs/cylc/logs && tar --remove-files -czf run_cylc.cron.$lastmon.tgz *.$lastmon*.log"

bld_suffix=date +%0m_%0d_%y

# start at 12:05 AM on Mon-Fri
# make a double precision build of mpas-bundle and run ctest
# the build script won't do anything if there have been no changes to the
# modules used to create mpas-bundle (unless the '-f' parameter is provided).
05 00 * * 1-5 ssh $derecho "echo ${bld_suffix} ${bundle_dir} 'make 2p' >> ~/my_cron_logs/cron.log && cd $bundle_dir && git fetch -p >> ~/my_cron_logs/cron.log ; git status >> ~/my_cron_logs/cron.log ; git pull >> ~/my_cron_logs/cron.log" ;$bundle_dir/$build_script -d $bundle_dir -b $builds_dir -q develop@desched1 -c gnu -p 2 -a nmmm0015

# start at 12:05 AM on Sat
# always build, even if no source change from previous run (-f)
05 00 * * 6 $bundle_dir/$build_script -d $bundle_dir -q develop@desched1 -c gnu -p 2 -f
05 00 * * 6 $bundle_dir/$build_script -d $bundle_dir -b $builds_dir -q develop@desched1 -c gnu -p 2 -f -a nmmm0015

# start at 1:05 AM on Sat
# always build, even if no source change from previous run (-f)
# single precision (-p 1), to be used for cylc experiment.
05 01 * * 6 $bundle_dir/$build_script -d $bundle_dir -q develop@desched1 -c gnu -p 1 -f -l $bundle_dir/$build_script.lock
# use the date as part of the build directory name, so each week's build is unique.
05 01 * * 6 $bundle_dir/$build_script -d $bundle_dir -b $builds_dir -q develop@desched1 -c gnu -p 1 -f -l $bundle_dir/$build_script.lock -x $(${bld_suffix}) -a nmmm0015
# build gpu enabled MPAS-Model
#20 12 * * 1 $bundle_dir/$build_script -d $bundle_dir -b $builds_dir -q develop@desched1 -c nvhpc -p 1 -f -l $bundle_dir/$build_script.lock -x $(${bld_suffix}) -a nmmm0015

# at 12:05 am on Sun run the workflow
# at 12:05 am on Sun update the develop branch of MPAS-Workflow repo and run the workflow
suffix=$(date +%F)
05 00 * * 7 ssh $derecho $workflow_dir/$workflow_script -w $workflow_dir -d $bundle_build_dir -k $bundle_dir/$build_script.lock -s $workflow_scenario -x $suffix

# at 12:05 am Mon-Fri try to graph results from the completed workflow runs
05 00 * * 1-5 ssh $derecho $workflow_dir/$workflow_script -w $workflow_dir -g $graphs_dir -o $graphs_out_dir
05 00 * * 7 ssh $derecho "echo $suffix 'run workflow in ' $workflow_dir >> ~/my_cron_logs/cron.log && cd $workflow_dir && git fetch -p >> ~/my_cron_logs/cron.log 2>&1 && git co develop >> ~/my_cron_logs/cron.log 2>&1 && git pull >> ~/my_cron_logs/cron.log 2>&1 && $workflow_dir/$workflow_script -w $workflow_dir -d $bundle_build_dir -k $bundle_dir/$build_script.lock -s $workflow_scenario -x $suffix"
# at 1:05 am on Sun run the 3dhybrid workflow
05 01 * * 7 ssh $derecho "echo $suffix 'run workflow in ' $workflow_dir >> ~/my_cron_logs/cron.log && cd $workflow_dir && $workflow_dir/$workflow_script -w $workflow_dir -d $bundle_build_dir -k $bundle_dir/$build_script.lock -s $workflow_scenario2 -x $suffix"

# at 6:05 am weekdays tar any graphics files and copy them to an mmm web server
05 06 * * 1-5 echo "`date` checking $graphs_out_dir" >> ~/my_cron_logs/cp_graphs.log && for dir in $(/bin/ls $graphs_out_dir); do echo "`date` dir to copy:$dir" >> ~/my_cron_logs/cp_graphs.log; echo "ssh $derecho cd $graphs_out_dir && tar --remove-files -czf $dir.tgz $dir" >> ~/my_cron_logs/cp_graphs.log; ssh $derecho "cd $graphs_out_dir && tar --remove-files -czf $dir.tgz $dir"; echo "scp $graphs_out_dir/$dir.tgz $webserver:$web_graphs_dir/" >> ~/my_cron_logs/cp_graphs.log; scp $graphs_out_dir/$dir.tgz $webserver:$web_graphs_dir/; echo "ssh $webserver cd $web_graphs_dir/ && tar -xzf $dir.tgz" >> ~/my_cron_logs/cp_graphs.log; ssh $webserver "cd $web_graphs_dir/ && tar -xzf $dir.tgz"; mv $graphs_out_dir/$dir.tgz $graphs_out_dir/../copied; echo "finished $dir" >> ~/my_cron_logs/cp_graphs.log; done
# run the weekly cylc scenario using a gpu build of MPAS-Model
suffix_gpu=2025-05-30_new
workflow_scenario_gpu=scenarios/3denvar_OIE120km_WarmStart_VarBC_gpu_cron.yaml
#55 15 * * * ssh $derecho "echo $suffix >> ~/my_cron_logs/cron.log 2>&1 && cd $workflow_dev_dir && git fetch -p >> ~/my_cron_logs/cron.log 2>&1 && git co develop >> ~/my_cron_logs/cron.log 2>&1 && git pull >> ~/my_cron_logs/cron.log && $workflow_dir/$workflow_script -w $workflow_dir -d $bundle_build_dir -k $bundle_dir/$build_script.lock -s $workflow_scenario_gpu -x ${suffix}_gpu"

# at 2:05 am Mon-Fri try to graph results from the completed workflow runs
casper=casper.hpc.ucar.edu
05 02 * * 1-5 ssh $casper "$workflow_dir/$workflow_script -w $workflow_dir -g $graphs_dir -o $graphs_out_dir -m $webserver -c $web_graphs_dir/"
29 changes: 23 additions & 6 deletions env-setup/gnu-derecho.csh
Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,33 @@ endif

module purge
# ignore that the sticky module ncarenv/... is not unloaded
module load ncarenv/23.09
module load ncarenv/24.12
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/modulefiles
module load ecflow/5.8.4
module load mysql/8.0.33

module use /glade/work/epicufsrt/contrib/spack-stack/derecho/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
module load stack-gcc/12.2.0
module load stack-cray-mpich/8.1.25
module load stack-python/3.10.13
module load jedi-mpas-env
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/spack-stack-1.9.3/envs/ue-gcc-12.4.0/install/modulefiles/Core

module load stack-gcc/12.4.0
module load stack-cray-mpich/8.1.29
module load stack-python/3.11.7
module load py-pycodestyle/2.11.0
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This file seems to be the same as the file from "internal". It might be okay, but I wonder if we need this module (py-pycodestyle).

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This file seems to be the same as the file from "internal". It might be okay, but I wonder if we need this module (py-pycodestyle).
@byoung-joo I'll take a look.

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Sorry, I though that this was only loaded with csh. Please disregard my comment!

# module load jedi-mpas-env is commented out because it loads many modules not needed for
# building and running mpas-bundle on derecho.
# To load all of the modules which were loaded prior to 01/15/2026,
# uncomment out "module load jedi-mpas-env"
# module load jedi-mpas-env
module load atlas/0.40.0
module load ecbuild/3.7.2
module load netcdf-cxx4/4.3.1
module load parallelio/2.6.2
module load gsl-lite/0.37.0
module load nccmp/1.9.0.1
module load udunits/2.2.28
# Following modules are required for ioda-converters build
module load bufr/12.1.0
module load py-pybind11/2.13.5
module list

limit stacksize unlimited
setenv F_UFMTENDIAN 'big_endian:101-200'
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