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Update CMakeLists.txt for new data download logic, update fv3-jedi/fv…
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…3-jedi-data branches from develop (#41)

* Update fv3-jedi/fv3-jedi-data branches for merge from develop, update CMakeLists.txt for new cmake data download logic

* Update README.md

* Replace ecbuild with cmake

* Revert fv3-jedi and fv3-jedi-data branch names
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@climbfuji
climbfuji authored Oct 20, 2023
1 parent c866144 commit 8584482
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Showing 3 changed files with 29 additions and 52 deletions.
8 changes: 4 additions & 4 deletions .github/workflows/run_ec2_pcluster.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ jobs:
cd ${JEDI_ENV}
mkdir -p build-atm
cd build-atm
ecbuild -DUFS_APP=ATM ../ufs-bundle
cmake -DUFS_APP=ATM ../ufs-bundle
make update
make -j8
Expand All @@ -147,7 +147,7 @@ jobs:
cd ${JEDI_ENV}
mkdir -p build-atmaero
cd build-atmaero
ecbuild -DUFS_APP=ATMAERO ../ufs-bundle
cmake -DUFS_APP=ATMAERO ../ufs-bundle
make update
make -j8
Expand All @@ -156,15 +156,15 @@ jobs:
#cd ${JEDI_ENV}
#mkdir -p build-ng-godas
#cd build-ng-godas
#ecbuild -DUFS_APP=NG-GODAS ../ufs-bundle
#cmake -DUFS_APP=NG-GODAS ../ufs-bundle
#make update
#make -j8
#
## UFS_APP=S2S
#cd ${JEDI_ENV}
#mkdir -p build-s2s
#cd build-s2s
#ecbuild -DUFS_APP=S2S ../ufs-bundle
#cmake -DUFS_APP=S2S ../ufs-bundle
#make update
#make -j8
Expand Down
57 changes: 17 additions & 40 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,7 @@ set( ENABLE_MPI ON CACHE BOOL "Compile with MPI")
set( ENABLE_OMP ON CACHE BOOL "Compile with OpenMP")

# 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 )
else()
ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda-internal/jedi-cmake.git" TAG 1.4.0 UPDATE RECURSIVE )
include( jedicmake/cmake/Functions/git_functions.cmake )
endif()
include( $ENV{jedi_cmake_ROOT}/share/jedicmake/Functions/git_functions.cmake )

# ECMWF libs
# ----------
Expand All @@ -57,8 +52,13 @@ endif()

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

ecbuild_bundle( PROJECT ioda GIT "https://github.com/jcsda-internal/ioda.git" BRANCH develop UPDATE )
ecbuild_bundle( PROJECT ufo GIT "https://github.com/jcsda-internal/ufo.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-internal/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-internal/ufo.git" BRANCH develop UPDATE )

# Options for building with certain models
# ----------------------------------------
Expand Down Expand Up @@ -152,45 +152,22 @@ set_target_properties(fv3atm PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/${C
set_target_properties(ccppphys PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/${CMAKE_INSTALL_LIBDIR}/libccpp_physics.a)
set_target_properties(mom6 PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/${CMAKE_INSTALL_LIBDIR}/libmom6.a)

if(UFS_APP MATCHES "^(S2S)$")
# fv3-jedi and associated repositories
# ------------------------------------
ecbuild_bundle( PROJECT femps GIT "https://github.com/jcsda-internal/femps.git" TAG 1.2.0 )
ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs_dom UPDATE ) # updated from develop Aug 30 2023
ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_dom UPDATE ) # note this has not been updated in a while, there are many merge conflicts that need to be resolved
add_dependencies(soca ufs-weather-model)
if(UFS_APP MATCHES "^(ATM)$" OR UFS_APP MATCHES "^(ATMAERO)$" OR UFS_APP MATCHES "^(S2S)$")
ecbuild_bundle( PROJECT femps GIT "https://github.com/jcsda-internal/femps.git" TAG 1.2.0 )
option(ENABLE_FV3_JEDI_DATA "Obtain fv3-jedi test data from fv3-jedi-data repository (vs tarball)" ON)
ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH feature/ufs_dom UPDATE ) # updated from develop Oct 20 2023
ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs_dom UPDATE ) # updated from develop Oct 20 2023
if(UFS_APP MATCHES "^(S2S)$")
ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_dom UPDATE ) # note this has not been updated in a while, there are many merge conflicts that need to be resolved
add_dependencies(soca ufs-weather-model)
endif()
elseif(UFS_APP MATCHES "^(NG-GODAS)$")
ecbuild_bundle( PROJECT soca GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_dom UPDATE ) # note this has not been updated in a while, there are many merge conflicts that need to be resolved
add_dependencies(soca ufs-weather-model)
elseif(UFS_APP MATCHES "^(ATM)$" OR UFS_APP MATCHES "^(ATMAERO)$")
ecbuild_bundle( PROJECT femps GIT "https://github.com/jcsda-internal/femps.git" TAG 1.2.0 )
ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs_dom UPDATE ) # updated from develop Aug 30 2023
else()
message(FATAL_ERROR "ufs-bundle unknown UFS_APP ${UFS_APP}")
endif()


# ioda, ufo and fv3-jedi test data
#----------------------------------------

# 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} )
ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
endif()

# same procedure for ufo-data
if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} )
ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
endif()

# same procedure for fv3-jedi-data
if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} )
# DH* 20230718 revert this to feature/ufs_dom once https://github.com/JCSDA-internal/fv3-jedi-data/pull/78 is merged
ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH feature/ufs_dom_update_ufswm_20230717 ) # updated from develop Aug 30 2023
# *DH 20230718
endif()

# Build Doxygen documentation
# ---------------------------
option(BUILD_UFSJEDI_BUNDLE_DOC "Build documentation" OFF)
Expand Down
16 changes: 8 additions & 8 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -51,14 +51,14 @@ The bundle can be built in three different configuragions: with fv3-jedi and the
with soca and the UFS configured with a data-atmosphere using NG-GODAS, or with fv3-jedi and soca and the UFS
configured with S2S coupling. Only the first two configurations have test cases and are known to work, but all will build.

The parameter for specifying the configuration type is `-DAPP=[ATM|NG-GODAS|S2S]` on the ecbuild configuration line. Create a build directory under/outside `ufs-bundle` and `cd` to it. Then run one of the following `ecbuild` commands:
The parameter for specifying the configuration type is `-DAPP=[ATM|NG-GODAS|S2S]` on the cmake configuration line. Create a build directory under/outside `ufs-bundle` and `cd` to it. Then run one of the following `cmake` commands:
```
ecbuild --build=debug -DUFS_APP=ATM .. 2>&1 | tee log.ecbuild
ecbuild --build=debug -DUFS_APP=ATMAERO .. 2>&1 | tee log.ecbuild
ecbuild --build=debug -DUFS_APP=NG-GODAS .. 2>&1 | tee log.ecbuild
ecbuild --build=debug -DUFS_APP=S2S .. 2>&1 | tee log.ecbuild
cmake -DCMAKE_BUILD_TYPE=Debug -DUFS_APP=ATM .. 2>&1 | tee log.cmake
cmake -DCMAKE_BUILD_TYPE=Debug -DUFS_APP=ATMAERO .. 2>&1 | tee log.cmake
cmake -DCMAKE_BUILD_TYPE=Debug -DUFS_APP=NG-GODAS .. 2>&1 | tee log.cmake
cmake -DCMAKE_BUILD_TYPE=Debug -DUFS_APP=S2S .. 2>&1 | tee log.cmake
```
When using the native Apple `clang` compiler on macOS with `llvm-openmp` installed via homebrew or spack, it may be necessary to add `-DCMAKE_SHARED_LINKER_FLAGS="${llvm_openmp_ROOT}/lib/libomp.dylib"` to the ecbuild command.
When using the native Apple `clang` compiler on macOS with `llvm-openmp` installed via homebrew or spack, it may be necessary to add `-DCMAKE_SHARED_LINKER_FLAGS="${llvm_openmp_ROOT}/lib/libomp.dylib"` to the `cmake` command.

macOS users may also encounter this error during the linker phase:
```
Expand Down Expand Up @@ -86,7 +86,7 @@ install_name_tool -id ${parallelio_ROOT}/lib/libpiof.dylib ${parallelio_ROOT}/li
install_name_tool -change libpioc.dylib ${parallelio_ROOT}/lib/libpioc.dylib ${parallelio_ROOT}/lib/libpiof.dylib
```

While building with soca (NG-GODAS or S2S), there will be a long pause during configuration when `ecbuild` is downloading the input files for the test to be run.
While building with soca (NG-GODAS or S2S), there will be a long pause during configuration when `cmake` is downloading the input files for the test to be run.

After configuration, run `make -j 8` to build.

Expand Down Expand Up @@ -133,4 +133,4 @@ Errors while running CTest

At this point, there are no ctests for ATMAERO or S2S.

Note for later for running on Hera: need to add `-DMPIEXEC_EXECUTABLE="/apps/slurm/default/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n"` to `ecbuild` command, then run `ctest -R get_` on login node, then acquire a compute node, for example via `salloc -N 1 -n 24 --time=480 --qos=batch -A da-cpu -I`, then run the actual `ctests` on the compute node.
Note for later for running on Hera: need to add `-DMPIEXEC_EXECUTABLE="/apps/slurm/default/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n"` to `cmake` command, then run `ctest -R get_` on login node, then acquire a compute node, for example via `salloc -N 1 -n 24 --time=480 --qos=batch -A da-cpu -I`, then run the actual `ctests` on the compute node.

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