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Updating 219 from main. #426

Merged
merged 120 commits into from
Oct 18, 2024
Merged

Updating 219 from main. #426

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ff709c7
write review guidelines - Fixes #186
ccarouge Nov 28, 2023
8ff8a98
Remove 'Nonconforming tab character'
mcuntz Mar 12, 2024
77fa660
Remove 'Nonconforming tab character'
mcuntz Mar 12, 2024
563906f
Remove 'Nonconforming tab character' and 'continued character constant'
mcuntz Mar 12, 2024
ec74353
Remove 'Nonconforming tab character' and 'continued character constant'
mcuntz Mar 12, 2024
a30cbd3
Removed 'extra tokens at end of #ifndef directive'
mcuntz Mar 12, 2024
7b8d0e3
Name 'mland' was an ambiguous reference
mcuntz Mar 12, 2024
b174460
Use find_package to link against MPI libraries
SeanBryan51 Jan 23, 2024
c0ce0e4
List source files in alphabetical order
SeanBryan51 Feb 2, 2024
0369c4e
Portability fixes and improvements to build.bash
SeanBryan51 Mar 4, 2024
93ac165
Add --compiler flag and GNU compiler support
SeanBryan51 Mar 4, 2024
29d8b26
Add Matthias's configuration for example
SeanBryan51 Mar 12, 2024
dabb1c9
Additional CMake changes (#216)
SeanBryan51 Mar 15, 2024
ba007d5
Introduce SUBROUTINE GWspatialParameters
rkutteh Mar 17, 2024
281a621
Add model build CI for CABLE offline (#223)
SeanBryan51 Mar 19, 2024
fed2a4c
Introduce SUBROUTINE GWspatialParameters (#224)
rkutteh Apr 6, 2024
fba0e4a
Replace cable_gw_hydro.F90 with its new version
rkutteh Apr 7, 2024
46830b3
Compile with gfortran (#221)
ccarouge Apr 10, 2024
a6e0dcc
Add support for MPI builds with the GNU compiler (#241)
SeanBryan51 Apr 19, 2024
81b8795
(#285): run testcase from within src/offline/ for now.
May 7, 2024
45d1497
Fix testcase from Uber Quick guide. (#286)
ccarouge May 7, 2024
87c9592
(#186): additions to review guidelines
May 9, 2024
3ab8f45
(#186): formatting
May 10, 2024
5d7b808
(#186): revised text
May 10, 2024
8d73f90
(#186): few more edits
ccarouge May 15, 2024
d8b5538
(#186): simplify language (review)
May 16, 2024
38e2a64
Update content of pft_params.nml options under User Guide
rkutteh May 20, 2024
400f550
Auto refresh MathJax on page load
abhaasgoyal May 22, 2024
21195f6
(#303): increase max width.
ccarouge May 24, 2024
4d28958
(#303): reducing left and right margins (#305)
ccarouge May 24, 2024
0c4139f
Auto refresh MathJax on page load (#304)
abhaasgoyal May 24, 2024
63bd149
Defined ncid_mask for met data files with multiple sites. Fixes #306.
rml599gh May 30, 2024
d5acf42
Update documentation/docs/user_guide/inputs/pft_params_nml.md
rkutteh Jun 2, 2024
c2c0316
Update content of pft_params.nml options under User Guide (#299)
rkutteh Jun 3, 2024
cad3cc9
Update src/offline/cable_input.F90
rml599gh Jun 6, 2024
69331b6
Defined ncid_mask for met data files with multiple sites. Fixes #306.…
rml599gh Jun 6, 2024
43e6bcc
Update build-ci version (#271)
SeanBryan51 Jun 7, 2024
b70539d
Add missing ;; to case statement
SeanBryan51 May 17, 2024
e33ed3e
Specify CABLE_MPI option for non-MPI case
SeanBryan51 May 17, 2024
b4ace30
Remove all build artifacts and exit for --clean
SeanBryan51 May 17, 2024
39ae045
Rename -j option to --ncpus
SeanBryan51 May 17, 2024
42fb971
Add support for short command line options
SeanBryan51 Jun 14, 2024
3a1442e
Use curly braces everywhere instead of just in potentially ambiguous …
SeanBryan51 Jun 17, 2024
b17cbc0
build.bash improvements (#297)
SeanBryan51 Jun 17, 2024
16dbbe3
Add an "Input files" file to the User Guide
rkutteh Jun 17, 2024
29fe6cd
Update documentation/docs/user_guide/inputs/index.md
rkutteh Jun 18, 2024
b22a3e7
Update documentation/docs/user_guide/inputs/index.md
rkutteh Jun 18, 2024
70176c0
Add an "Input files" file to the User Guide (#315)
rkutteh Jun 18, 2024
2428535
one line bug fix to address screen level temperatures #313
Jun 21, 2024
1872ea5
Add a table of physical constants to the user guide
rkutteh Jun 27, 2024
e273737
Flags for range checks in CABLE vars (#225)
abhaasgoyal Apr 12, 2024
3084239
Merge remote-tracking branch 'origin/main' into 225-range-checks-cabl…
abhaasgoyal Jul 2, 2024
efe332b
Range checks cable parameters (#287)
abhaasgoyal Jul 2, 2024
5553fc6
Update documentation/docs/user_guide/constants/index.md
rkutteh Jul 2, 2024
a2e177b
Set ice density to 917 kg/m3
rkutteh Jul 3, 2024
86b086e
Review process for new contributions (#289)
ccarouge Jul 3, 2024
7b7dcc3
Reconcile versions of rplant (#274)
JhanSrbinovsky Jul 11, 2024
e521096
bug fix rm USE rplant1 and CALL rplant1 (#340)
JhanSrbinovsky Jul 12, 2024
44ce20e
(#344) - update value for checks%range
Jul 15, 2024
860094b
added potential evaporation to offline output, changed checks range, …
Jul 15, 2024
b8e24fe
(#344) - Changes for compatibility with GNU compiler
Jul 15, 2024
fa555ba
(#344) - Use enumerator values for conditions on check%ranges
Jul 15, 2024
4aaccb5
removes hard-wired lake index from code, part of #335 and #347
Jul 16, 2024
5cc5ba4
(#344) - Remove references to check%ranges as LOGICAL in documentation
Jul 16, 2024
b326199
enforcing lakes at saturation. fixes #335
Jul 16, 2024
c2a54da
Update value for checks%range (#345)
ccarouge Jul 16, 2024
b7068d4
consistency_ice_veg_soil
rkutteh Jul 16, 2024
0a69346
reversion of original %epot for connection to ACCESS; new %epot for o…
Jul 17, 2024
e53699f
Merge branch 'main' into 335-facilitate-output-of-potential-evaporati…
har917 Jul 18, 2024
a0d4fe2
(#351) - define sum_rad_gradis and sum_rad_rniso before wetLeaf call.
Jul 25, 2024
a9db7aa
reverting lake fix to use field capacity sfc not saturation ssat
Jul 25, 2024
45bec15
Merge branch 'main' into 341-lake-tiles-in-offline-appear-broken
har917 Jul 25, 2024
315b899
Update src/science/gw_hydro/cable_gw_hydro.F90
rkutteh Jul 25, 2024
f430650
Update src/science/gw_hydro/cable_gw_hydro.F90
rkutteh Jul 25, 2024
1c44581
Update src/science/gw_hydro/cable_gw_hydro.F90
rkutteh Jul 25, 2024
6fac982
Update src/science/gw_hydro/cable_gw_hydro.F90
rkutteh Jul 25, 2024
45251dd
Update src/offline/cable_parameters.F90
rkutteh Jul 25, 2024
7fdcd11
Update src/offline/cable_parameters.F90
rkutteh Jul 25, 2024
d8857aa
(#351) - Consistent use of sum_rad_gradis and sum_rad_rniso
Jul 25, 2024
fb4cc3b
Update src/offline/cable_parameters.F90
rkutteh Jul 25, 2024
b7b5850
Set ice density to 917 kg/m3 (#332)
rkutteh Jul 26, 2024
f6a95b2
fix bug in spitter call, use total SW down and apply equally to VIS&N…
Jul 30, 2024
00c70ec
(#359) - Bug fix: outputs broken in MPI implementation
Aug 2, 2024
93b16a1
(#359) - Set logn for workers
Aug 5, 2024
335aa6f
(#359) - Removing wlogn, using logn instead for workers and master
Aug 6, 2024
da63a72
Bug fix: outputs broken in MPI implementation (#360)
ccarouge Aug 6, 2024
c47f09d
one line bug fix to address screen level temperatures #313 (#316)
ccarouge Aug 6, 2024
e6be17c
added potential evaporation to offline output, changed checks range, …
ccarouge Aug 6, 2024
6311935
Merge branch 'main' into 338-consistency_ice_veg_soil
Aug 7, 2024
32ad6b7
fixing broken lake tiles in offline #335 and addresses #347 (#348)
har917 Aug 7, 2024
d395e01
Update cable_parameters.F90
rkutteh Aug 7, 2024
1239fec
Merge branch 'main' into 325-add-a-table-of-physical-constants-to-the…
ccarouge Aug 8, 2024
8b93b3b
Add a table of physical constants to the user guide (#326)
ccarouge Aug 9, 2024
fe0b80e
Always initialise canopy%DvLitt and canopy%kthLitt
Aug 13, 2024
fdcb99f
Reinstate dry and cold stress (#275)
rml599gh Aug 15, 2024
7bd295b
Correction to comments as #277 and #279
rml599gh Aug 15, 2024
4db0469
(#338) - Add namelist option for ice consistency.
Aug 15, 2024
6ed2afc
(#338) - Update doc
Aug 15, 2024
06bd3af
(#351) - correct reference for DvLitt and kthLitt
Aug 15, 2024
04e8171
Fix: uninitialised variables in cable_canopy.F90 (#352)
ccarouge Aug 15, 2024
6f22bdd
Initialise casaflux%frac_sapwood=1 for use in casa_rplant (#373)
rml599gh Aug 19, 2024
57a343d
(#338) - Add new namelist option to cable.nml
Aug 21, 2024
03f924e
Remove ESM15 case as inconsistent with current input of xkpsorb (#283)
rml599gh Aug 23, 2024
420ca49
consistency_ice_veg_soil (#349)
rkutteh Aug 26, 2024
1dd3724
Merge branch 'main' into 230-replace-cable_gw_hydrof90-with-its-new-v…
rkutteh Aug 26, 2024
d45a62c
fix bug in spitter call (MAIN) (#357)
har917 Aug 29, 2024
95b9b5e
Replace cable_gw_hydro.F90 with its new version (#231)
rkutteh Sep 1, 2024
aad87bc
(#9) - Install graphviz for readthedocs
ccarouge Sep 12, 2024
11d8197
Create call graphs in doc (#399)
ccarouge Sep 12, 2024
b1de4d8
Initialise casaflux%frac_sapwood=1 for use in casa_rplant (#373) (#374)
rml599gh Sep 15, 2024
e97c0ca
Reinstate dry and cold stress, remove double summation of btran (#372)
rml599gh Sep 15, 2024
0448257
Add src/coupled/AM3 directory (#371)
JhanSrbinovsky Sep 17, 2024
8f62897
Update build-ci version (#409)
SeanBryan51 Sep 30, 2024
66e717a
Fix compilation with gfortran: use the abort defined in cable_abort_m…
micaeljtoliveira Sep 16, 2024
d0e1995
Cleanup of mpi drivers by addressing some compiler warnings, includin…
micaeljtoliveira Sep 24, 2024
183df1f
Removed ESM15 version with hard-wired parameter, #278
rml599gh Oct 14, 2024
31db58f
Remove ESM15 case as inconsistent with current input of xkpsorb (#283…
rml599gh Oct 17, 2024
d0688cb
User guide edit to pftlookup table to note xfPleach hard-wired in CAB…
rml599gh Oct 17, 2024
41af6f7
Fix gfortran compilation and some warnings (#410)
micaeljtoliveira Oct 17, 2024
5c748af
Removed ESM15 version with hard-wired xfpleach parameter, #278 (#422)
rml599gh Oct 18, 2024
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15 changes: 15 additions & 0 deletions .github/workflows/model-build-test-ci.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
name: Test model build

on:
workflow_dispatch:
pull_request:
push:
branches:
- "master"

jobs:
build:
name: Build ${{ github.repository }} via spack
uses: access-nri/build-ci/.github/workflows/model-1-build.yml@e90ea37002e4f3aed6515482eb2cca9ac5cd2a94
permissions:
packages: read
199 changes: 101 additions & 98 deletions CMakeLists.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,163 +9,166 @@ project(
option(CABLE_MPI "Build the MPI executable" OFF)

# third party libs
if(CABLE_MPI)
find_package(MPI REQUIRED COMPONENTS Fortran)
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(NETCDF REQUIRED IMPORTED_TARGET "netcdf-fortran")

set(CABLE_INTEL_Fortran_FLAGS -fp-model precise)
set(CABLE_INTEL_Fortran_FLAGS_DEBUG -O0 -g -traceback -fpe0)
set(CABLE_INTEL_Fortran_FLAGS_RELEASE -O2)
set(CABLE_Intel_Fortran_FLAGS -fp-model precise)
set(CABLE_Intel_Fortran_FLAGS_DEBUG -O0 -g -traceback -fpe0)
set(CABLE_Intel_Fortran_FLAGS_RELEASE -O2)
if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
add_compile_options(
${CABLE_Intel_Fortran_FLAGS}
"$<$<CONFIG:Release>:${CABLE_Intel_Fortran_FLAGS_RELEASE}>"
"$<$<CONFIG:Debug>:${CABLE_Intel_Fortran_FLAGS_DEBUG}>"
)
endif()

# CMake $<...> syntax is explained here:
# https://cmake.org/cmake/help/latest/manual/cmake-generator-expressions.7.html#introduction
set(CABLE_EXE_NAME "$<IF:$<BOOL:${CABLE_MPI}>,cable-mpi,cable>")
set(CABLE_GNU_Fortran_FLAGS -cpp -ffree-form -ffixed-line-length-132)
set(CABLE_GNU_Fortran_FLAGS_DEBUG -O -g -pedantic-errors -Wall -W -Wno-maybe-uninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan)
set(CABLE_GNU_Fortran_FLAGS_RELEASE -O3 -Wno-aggressive-loop-optimizations)
if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
add_compile_options(
${CABLE_GNU_Fortran_FLAGS}
"$<$<CONFIG:Release>:${CABLE_GNU_Fortran_FLAGS_RELEASE}>"
"$<$<CONFIG:Debug>:${CABLE_GNU_Fortran_FLAGS_DEBUG}>"
)
endif()

set(
CABLE_SRCS_SERIAL
src/offline/cable_driver.F90
)
set(
CABLE_SRCS_MPI
src/offline/cable_mpidrv.F90
src/offline/cable_mpicommon.F90
src/offline/cable_mpimaster.F90
src/offline/cable_mpiworker.F90
src/science/pop/pop_mpi.F90
)
set(
CABLE_SRCS_COMMON
src/science/casa-cnp/bgcdriver.F90
src/science/casa-cnp/biogeochem_casa.F90
add_library(
cable_common_objlib
OBJECT
src/offline/cable_abort.F90
src/science/misc/cable_air.F90
src/science/canopy/cable_canopy.F90
src/science/misc/cable_carbon.F90
src/offline/cable_checks.F90
src/science/misc/cable_climate.F90
src/util/cable_climate_type_mod.F90
src/util/cable_common.F90
src/offline/cable_cru_TRENDY.F90
src/offline/cable_define_types.F90
src/science/gw_hydro/cable_gw_hydro.F90
src/offline/cable_initialise.F90
src/offline/cable_input.F90
src/offline/cable_iovars.F90
src/offline/cable_LUC_EXPT.F90
src/params/cable_maths_constants_mod.F90
src/offline/cable_metutils.F90
src/offline/cable_namelist_input.F90
src/params/cable_other_constants_mod.F90
src/offline/cable_output.F90
src/offline/cable_parameters.F90
src/offline/cable_pft_params.F90
src/offline/cable_phenology.F90
src/params/cable_photo_constants_mod.F90
src/params/cable_phys_constants_mod.F90
src/offline/cable_plume_mip.F90
src/science/gw_hydro/cable_psm.F90
src/offline/cable_read.F90
src/science/roughness/cable_roughness.F90
src/util/cable_runtime_opts_mod.F90
src/offline/cable_site.F90
src/science/sli/cable_sli_main.F90
src/science/sli/cable_sli_numbers.F90
src/science/sli/cable_sli_roots.F90
src/science/sli/cable_sli_solve.F90
src/science/sli/cable_sli_utils.F90
src/offline/cable_soil_params.F90
src/offline/cable_weathergenerator.F90
src/offline/cable_write.F90
src/offline/casa_cable.F90
src/offline/casa_ncdf.F90
src/offline/casa_offline_inout.F90
src/offline/CASAONLY_LUC.F90
src/offline/cbl_model_driver_offline.F90
src/offline/landuse_inout.F90
src/offline/spincasacnp.F90
src/params/cable_maths_constants_mod.F90
src/params/cable_other_constants_mod.F90
src/params/cable_photo_constants_mod.F90
src/params/cable_phys_constants_mod.F90
src/params/grid_constants_cbl.F90
src/science/albedo/cbl_albedo.F90
src/science/albedo/cbl_snow_albedo.F90
src/science/albedo/cbl_soilColour_albedo.F90
src/science/canopy/cable_canopy.F90
src/science/canopy/cbl_dryLeaf.F90
src/science/canopy/cbl_friction_vel.F90
src/science/canopy/cbl_fwsoil.F90
src/science/canopy/cbl_latent_heat.F90
src/science/canopy/cbl_photosynthesis.F90
src/science/canopy/cbl_pot_evap_snow.F90
src/science/canopy/cbl_qsat.F90
src/science/canopy/cbl_SurfaceWetness.F90
src/science/canopy/cbl_wetleaf.F90
src/science/canopy/cbl_within_canopy.F90
src/science/canopy/cbl_zetar.F90
src/science/casa-cnp/bgcdriver.F90
src/science/casa-cnp/biogeochem_casa.F90
src/science/casa-cnp/casa_cnp.F90
src/science/casa-cnp/casa_dimension.F90
src/science/casa-cnp/casa_feedback.F90
src/science/casa-cnp/casa_inout.F90
src/offline/casa_ncdf.F90
src/offline/casa_offline_inout.F90
src/offline/CASAONLY_LUC.F90
src/science/casa-cnp/casa_param.F90
src/science/casa-cnp/casa_phenology.F90
src/science/casa-cnp/casa_readbiome.F90
src/science/casa-cnp/casa_rplant.F90
src/science/casa-cnp/casa_sumcflux.F90
src/science/casa-cnp/casa_variable.F90
src/science/albedo/cbl_albedo.F90
src/science/gw_hydro/cable_gw_hydro.F90
src/science/gw_hydro/cable_psm.F90
src/science/landuse/landuse3.F90
src/science/landuse/landuse_constant.F90
src/science/misc/cable_air.F90
src/science/misc/cable_carbon.F90
src/science/misc/cable_climate.F90
src/science/pop/pop_constants.F90
src/science/pop/pop_def.F90
src/science/pop/POP.F90
src/science/pop/pop_io.F90
src/science/pop/POPLUC.F90
src/science/pop/pop_types.F90
src/science/radiation/cbl_init_radiation.F90
src/science/radiation/cbl_radiation.F90
src/science/radiation/cbl_rhoch.F90
src/science/radiation/cbl_sinbet.F90
src/science/radiation/cbl_spitter.F90
src/science/roughness/cable_roughness.F90
src/science/roughness/roughnessHGT_effLAI_cbl.F90
src/science/sli/cable_sli_main.F90
src/science/sli/cable_sli_numbers.F90
src/science/sli/cable_sli_roots.F90
src/science/sli/cable_sli_solve.F90
src/science/sli/cable_sli_utils.F90
src/science/soilsnow/cbl_conductivity.F90
src/science/canopy/cbl_dryLeaf.F90
src/science/canopy/cbl_friction_vel.F90
src/science/canopy/cbl_fwsoil.F90
src/science/soilsnow/cbl_GW.F90
src/science/soilsnow/cbl_hyd_redistrib.F90
src/science/radiation/cbl_init_radiation.F90
src/science/canopy/cbl_latent_heat.F90
src/offline/cbl_model_driver_offline.F90
src/science/soilsnow/cbl_Oldconductivity.F90
src/science/canopy/cbl_photosynthesis.F90
src/science/canopy/cbl_pot_evap_snow.F90
src/science/canopy/cbl_qsat.F90
src/science/radiation/cbl_radiation.F90
src/science/soilsnow/cbl_remove_trans.F90
src/science/radiation/cbl_rhoch.F90
src/science/radiation/cbl_sinbet.F90
src/science/soilsnow/cbl_smoisturev.F90
src/science/soilsnow/cbl_snowAccum.F90
src/science/soilsnow/cbl_snow_aging.F90
src/science/albedo/cbl_snow_albedo.F90
src/science/soilsnow/cbl_snowCheck.F90
src/science/soilsnow/cbl_snowDensity.F90
src/science/soilsnow/cbl_snowl_adjust.F90
src/science/soilsnow/cbl_snowMelt.F90
src/science/albedo/cbl_soilColour_albedo.F90
src/science/soilsnow/cbl_soilfreeze.F90
src/science/soilsnow/cbl_soilsnow_data.F90
src/science/soilsnow/cbl_soilsnow_init_special.F90
src/science/soilsnow/cbl_soilsnow_main.F90
src/science/radiation/cbl_spitter.F90
src/science/soilsnow/cbl_stempv.F90
src/science/canopy/cbl_SurfaceWetness.F90
src/science/soilsnow/cbl_surfbv.F90
src/science/soilsnow/cbl_thermal.F90
src/science/soilsnow/cbl_trimb.F90
src/science/canopy/cbl_wetleaf.F90
src/science/canopy/cbl_within_canopy.F90
src/science/canopy/cbl_zetar.F90
src/params/grid_constants_cbl.F90
src/science/landuse/landuse3.F90
src/science/landuse/landuse_constant.F90
src/offline/landuse_inout.F90
src/util/cable_climate_type_mod.F90
src/util/cable_common.F90
src/util/cable_runtime_opts_mod.F90
src/util/masks_cbl.F90
src/science/pop/pop_constants.F90
src/science/pop/pop_def.F90
src/science/pop/pop_io.F90
src/science/pop/POPLUC.F90
src/science/pop/POP.F90
src/science/pop/pop_types.F90
src/science/roughness/roughnessHGT_effLAI_cbl.F90
src/offline/spincasacnp.F90
)
set(
CABLE_SRCS
"$<IF:$<BOOL:${CABLE_MPI}>,${CABLE_SRCS_MPI},${CABLE_SRCS_SERIAL}>"
${CABLE_SRCS_COMMON}
)

add_executable(cable ${CABLE_SRCS})

set_target_properties(cable PROPERTIES OUTPUT_NAME ${CABLE_EXE_NAME})

if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
target_compile_options(
cable
PRIVATE
${CABLE_INTEL_Fortran_FLAGS}
"$<$<CONFIG:Release>:${CABLE_INTEL_Fortran_FLAGS_RELEASE}>"
"$<$<CONFIG:Debug>:${CABLE_INTEL_Fortran_FLAGS_DEBUG}>"
)
endif()
target_link_libraries(cable_common_objlib PRIVATE PkgConfig::NETCDF)

target_link_libraries(
add_executable(
cable
PkgConfig::NETCDF
src/offline/cable_driver.F90
"$<TARGET_OBJECTS:cable_common_objlib>"
)

target_link_libraries(cable PRIVATE PkgConfig::NETCDF)
install(TARGETS cable RUNTIME)

if(CABLE_MPI)
add_executable(
cable-mpi
src/offline/cable_mpicommon.F90
src/offline/cable_mpidrv.F90
src/offline/cable_mpimaster.F90
src/offline/cable_mpiworker.F90
src/science/pop/pop_mpi.F90
"$<TARGET_OBJECTS:cable_common_objlib>"
)
target_link_libraries(cable-mpi PRIVATE PkgConfig::NETCDF MPI::MPI_Fortran)
install(TARGETS cable-mpi RUNTIME)
endif()
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