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Update to use FMS 2023.04 #1043

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Update to use FMS 2023.04 #1043

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cd4a0eb
switch fms mom6 versions
travissluka Apr 16, 2024
f58b804
fix ctest
travissluka Apr 16, 2024
47c490a
Merge develop into feature/mom6_fms_update, temporarily name as featu…
climbfuji May 9, 2024
2614968
Bug fix in src/soca/Geometry/soca_geom_mod.F90
climbfuji May 9, 2024
be6a330
Merge remote-tracking branch 'origin/develop' into feature/mom6_fms_u…
travissluka May 14, 2024
41ddfa8
mom6.x -> mom6solo
travissluka May 14, 2024
bae49b1
Add explicit dependency on FMS to work around fms openmp dependency bug
climbfuji May 15, 2024
ab42379
Merge branch 'develop' into feature/mom6_fms_update_dom_20240509
shlyaeva Jun 10, 2024
0e4c70c
trigger CI
Jun 11, 2024
dc4eb54
trigger CI with mom6 removed from CI
eap Jun 11, 2024
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10 changes: 4 additions & 6 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,9 @@ find_package( vader 1.7.0 REQUIRED)
find_package( saber 1.10.0 REQUIRED)
find_package( ioda 2.9.0 REQUIRED)
find_package( ufo 1.10.0 REQUIRED)
find_package( fms 2020.4.0 REQUIRED) # NOTE: remove this when we update to latest MOM6
find_package( mom6 2020.4.0 REQUIRED) # NOTE: remove this when we update to latest MOM6
find_package( fms 2023.3.0 REQUIRED COMPONENTS R4 R8)
add_library( fms ALIAS FMS::fms_r8)
find_package( OpenMP COMPONENTS C Fortran REQUIRED)

# Optionally look for Torch and daml
find_package(Torch QUIET)
Expand All @@ -47,10 +48,7 @@ include_directories( ${NETCDF_INCLUDE_DIRS} )
# Model
# TODO update to allow switching between mom6solo (here) and UFS (external)
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note to self, or anyone else that cares, this is fine for now but I'm assuming we're building MOM6 twice when soca is built as part of the ufs-bundle. No real harm, but wasteful. At some point special logic should be added to use a prebuilt mom6 lib if it exists.

################################################################################
# # NOTE enable these when we're ready to update to latest MOM6
# find_package( fms 2023.3.0 REQUIRED COMPONENTS R4 R8)
# add_library( fms ALIAS FMS::fms_r8)
# add_subdirectory(mom6)
add_subdirectory(mom6)

################################################################################
# Sources
Expand Down
1 change: 0 additions & 1 deletion bundle/CMakeLists.txt
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Expand Up @@ -45,7 +45,6 @@ ecbuild_bundle( PROJECT vader GIT "https://github.com/jcsda-internal/v
ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda-internal/saber.git" UPDATE BRANCH develop )
ecbuild_bundle( PROJECT ioda GIT "https://github.com/jcsda-internal/ioda.git" UPDATE BRANCH develop )
ecbuild_bundle( PROJECT ufo GIT "https://github.com/jcsda-internal/ufo.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 SOURCE "../" )

#===================================================================================================
Expand Down
7 changes: 5 additions & 2 deletions mom6/CMakeLists.txt
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Expand Up @@ -36,7 +36,9 @@ target_include_directories(mom6 PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/config_src/memory/dynamic_nonsymmetric>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
# TODO use symmetric memory above if doing regional MOM6
target_link_libraries(mom6 PUBLIC NetCDF::NetCDF_C NetCDF::NetCDF_Fortran fms )
# Note that the explicit dependency on OpenMP is only because FMS is not declaring its OpenMP dependency correctly
# This will be fixed with fms version 2024.01
target_link_libraries(mom6 PUBLIC NetCDF::NetCDF_C NetCDF::NetCDF_Fortran fms OpenMP::OpenMP_Fortran OpenMP::OpenMP_C)

####################################################
### Create standalone MOM6 executable
Expand Down Expand Up @@ -71,4 +73,5 @@ install (
COMPONENT Library)
install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod DESTINATION ${CMAKE_INSTALL_PREFIX}/MOM6)
install(EXPORT mom6-config
DESTINATION lib/cmake)
DESTINATION lib/cmake)

2 changes: 2 additions & 0 deletions src/soca/Geometry/Geometry.cc
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Expand Up @@ -172,4 +172,6 @@ namespace soca {
}
// -----------------------------------------------------------------------------

// -----------------------------------------------------------------------------

} // namespace soca
4 changes: 1 addition & 3 deletions src/soca/Geometry/soca_geom_mod.F90
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Expand Up @@ -175,7 +175,6 @@ subroutine soca_geom_init(self, f_conf, f_comm, gen)
type(time_type) :: Start_time
type(ocean_grid_type), pointer :: grid !< Grid metrics
type(MOM_control_struct) :: CSp
type(MOM_restart_CS), pointer :: restart_CSp !< NOTE remove this when updating MOM6

! variables needed for reading gridspec file
integer :: r
Expand Down Expand Up @@ -205,8 +204,7 @@ subroutine soca_geom_init(self, f_conf, f_comm, gen)
call io_infra_init()
call set_calendar_type(JULIAN)
call time_interp_external_init
restart_CSp => NULL()
call initialize_MOM( Start_time, Start_time, param_file, dirs, CSp, restart_CSp )
call initialize_MOM( Start_time, Start_time, param_file, dirs, CSp )
call get_MOM_state_elements(CSp, G=grid)

! grab the grid properties that we need
Expand Down
4 changes: 2 additions & 2 deletions test/CMakeLists.txt
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Expand Up @@ -308,12 +308,12 @@ function(soca_add_test)
DEPENDS ${ARG_EXE}
TEST_DEPENDS ${ARG_TEST_DEPENDS})
elseif ( ARG_SCRIPT )
# running a test specific script, right now this is only for the mom6.x forecast
# running a test specific script, right now this is only for the mom6solo forecast
ecbuild_add_test( TARGET test_soca_${ARG_NAME}
COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/${ARG_SCRIPT}
WORKING_DIRECTORY ${WORKDIR}
ARGS ${CONFIG_FILE}
DEPENDS mom6.x
DEPENDS mom6solo
ENVIRONMENT "BIN_DIR=${CMAKE_BINARY_DIR}/bin"
"MPIEXE=${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPI}"
TEST_DEPENDS ${ARG_TEST_DEPENDS}
Expand Down
20 changes: 9 additions & 11 deletions test/mom6solo.py
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Expand Up @@ -8,9 +8,7 @@
import pandas as pd
from datetime import datetime, timedelta

# TODO put this back when updating MOM6
MOM6EXE = 'mom6.x'
#MOM6EXE = 'mom6solo'
MOM6EXE = 'mom6solo'

# get input parameters
binDir = os.environ['BIN_DIR']
Expand Down Expand Up @@ -44,7 +42,7 @@ def replace_config_content(content, replacements):
for key, value in changes.items():
def replacement_function(match):
start, end = match.group(1), match.group(3)
return f"{start}{value}{end}"
return f"{start}{value}{end}"
key_pattern = rf"(\b{key}\s*=\s*)([^,\n]*)(,|/|\n)"
section_content = re.sub(key_pattern, replacement_function, section_content, flags=re.MULTILINE)
# Replace the old section content with the new one
Expand Down Expand Up @@ -73,10 +71,10 @@ def replacement_function(match):
# link input restart files
#----------------------------------------------------------------------------------------
if os.path.exists ('RESTART'):
shutil.rmtree('RESTART')
shutil.rmtree('RESTART')
os.makedirs('RESTART')
if os.path.exists ('RESTART_IN'):
shutil.rmtree('RESTART_IN')
shutil.rmtree('RESTART_IN')
os.makedirs('RESTART_IN')
os.symlink("../"+config['initial condition']['ocn_filename'], 'RESTART_IN/MOM.res.nc')

Expand All @@ -89,7 +87,7 @@ def replacement_function(match):
file.write(" 4 (Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)\n")
file.write(f" {init_date.year:4d} {init_date.month:2d} {init_date.day:2d} {init_date.hour:2d} {init_date.minute:2d} {init_date.second:2d} Model start time: year, month, day, hour, minute, second\n")
file.write(f" {init_date.year:4d} {init_date.month:2d} {init_date.day:2d} {init_date.hour:2d} {init_date.minute:2d} {init_date.second:2d} Current model time: year, month, day, hour, minute, second\n")


#----------------------------------------------------------------------------------------
# run executable
Expand All @@ -111,15 +109,15 @@ def replacement_function(match):
#----------------------------------------------------------------------------------------
for fcstHr in range(restartFrequency, fcst_len+1, restartFrequency):
rstDate = init_date + timedelta(hours=fcstHr)

# get rstDate in format such as MOM.res_Y2018_D105_S03600.nc
rst_day = rstDate.timetuple().tm_yday
rst_day = rstDate.timetuple().tm_yday
rst_seconds = rstDate.hour * 3600
rst_src = f"MOM.res_Y{rstDate.year}_D{rst_day:03}_S{rst_seconds:05}.nc"

# get init_date / fcstHr in a format such as ocn.forecast_mom6.fc.2018-04-15T00:00:00Z.PT1H.nc
forecast_date = init_date + timedelta(hours=fcstHr)
forecast_date_str = init_date.strftime("%Y-%m-%dT%H:%M:%SZ")
rst_dst = f"ocn.{config['output']['exp']}.fc.{forecast_date_str}.PT{fcstHr}H.nc"

shutil.move('RESTART/'+rst_src, config['output']['datadir']+'/'+rst_dst)