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Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag
PR Checklist
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[x] This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model wiki if you are unsure how to do this.
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[x] This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR
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[ ] An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR are specified below.
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[ ] Results for one or more of the regression tests change and the reasons for the changes are understood and explained below.
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[ ] New or updated input data is required by this PR. If checked, please work with the code managers to update input data sets on all platforms.
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Description
Starting with version 10 gfortran treats mismatches between actual and dummy argument lists as errors. This error can be turned into warning (and silenced) by using '-fallow-argument-mismatch' flag. In this PR all such mismatches are fixed. Most of the errors are resolved by using mpi_f08 module which provides generic interfaces.
WARNING: We are currently using mpich MPI library with the gnu compilers on Hera and SGI MPT on Cheyenne. mpi_f08 module in mpich, when compiled with the current versions of the gnu compilers, has some issues and MPT does not provide mpi_f08 module at all. Which means this PR will require us to switch to OpenMPI, which will require hpc-stack to be rebuild on these two platforms. Do we want to do that? Do we want to make (working) mpi_f08 module a requirement for ufs-weather-model?
Issue(s) addressed
Link the issues to be closed with this PR, whether in this repository, or in another repository. (Remember, issues must always be created before starting work on a PR branch!)
- fixes #<issue_number>
- fixes noaa-emc/fv3atm/issues/<issue_number>
Testing
How were these changes tested? What compilers / HPCs was it tested with? Are the changes covered by regression tests? (If not, why? Do new tests need to be added?) Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)
- [ ] hera.intel
- [ ] hera.gnu
- [ ] orion.intel
- [ ] cheyenne.intel
- [ ] cheyenne.gnu
- [ ] gaea.intel
- [ ] jet.intel
- [ ] wcoss_cray
- [ ] wcoss_dell_p3
- [ ] opnReqTest for newly added/changed feature
- [ ] CI
Dependencies
If testing this branch requires non-default branches in other repositories, list them. Those branches should have matching names (ideally).
Do PRs in upstream repositories need to be merged first? If so add the "waiting for other repos" label and list the upstream PRs
- waiting on noaa-emc/nems/pull/<pr_number>
- waiting on noaa-emc/fv3atm/pull/<pr_number>
If mpi_f08 can fix the issue of type mismatch, I think we can add mpi_f08 module as a requirement for ufs-weather-model to support gnu compiler. @jkbk2004 would you please check if we can switch to OpenMP from SGI MPT on Cheyenne with gnu compiler and reinstall hpc-stack? Thanks
@junwang-noaa I will give a try to install openmpi/gnu and see if its doable.
@DusanJovic-NOAA @junwang-noaa @kgerheiser I captured this and related information in the spack-stack repo: https://github.com/NOAA-EMC/spack-stack/issues/109
We will try to rebuild spack-stack on the various platforms using gcc, (LLVM) clang or apple-clang with open-mpi. If that all works, then it would good to merge the changes in this ufs-weather-model PR when the switch to spack-stack is made.
@climbfuji Have you tried rebuilding spacl_stack with gcc and open-mpi? Does that work?
@climbfuji Have you tried rebuilding spacl_stack with gcc and open-mpi? Does that work?
Your question is timely, as I was about to post an update here.
There are some issues with using openmpi on macOS that I started investigating last week. The problem has to do with flat namespaces versus two-level namespaces. mpich supports two-level namespaces through a configure option, openmpi does not. I am trying to achieve the same by setting appropriate linker flags when building openmpi and when building apps with openmpi.
Without two-level namespaces, there is a problem with mixing the libc++ from macOS (part of the native clang, and similar for LLVM clang) and libstdc++ from gcc, that results in exceptions not being caught correctly etc. I hope to have a good answer in the first week of May for whether switching to openmpi is a viable solution on macOS or not.
@junwang-noaa @DusanJovic-NOAA Good news. I was able to compile openmpi such that it mimics the two-level namespace option of mpich on macOS. We can therefore switch to openmpi for supporting mpi_f08.
Still waiting on gnu/openmpi hpc-stack or spack-stack to be installed on Hera and Cheyenne.
Still waiting on gnu/openmpi hpc-stack or spack-stack to be installed on Hera and Cheyenne.
I have a gnu-openmpi spack-stack that can be used for testing on Cheyenne, but it's probably not the final location and the responsibility for Cheyenne should probably be with EPIC, not JCSDA (but it's fine to do this in the transition period).
Still waiting on gnu/openmpi hpc-stack or spack-stack to be installed on Hera and Cheyenne.
On epic side, a help desk ticket was issued to install gnu10.1 on hera. They are working on. Maybe some uodate might be available early next week. Regarding the spack-stack, there are some issues on compiling stage: git discussion #1346 Can you take a look? Sounds like we need more discussion about the issue.
On epic side, a help desk ticket was issued to install gnu10.1 on hera. They are working on. Maybe some uodate might be available early next week. Regarding the spack-stack, there are some issues on compiling stage: git discussion #1346 Can you take a look? Sounds like we need more discussion about the issue.
I do not have access to Frontera. Is spack-stack installation available on Hera?
I thought the problems on frontera were sorted out, according to the discussion. @Hang-Lei-NOAA and I will install spack-stack 1.1.0 on hera in the next few days, hopefully we can use this as a basis for the migration of the UFS to spack-stack.
Is there any progress in installing gnu/openmpi hpc-stack or spack-stack on Hera and Cheyenne?
GNU hpc-stack was there on the official hpc-stack installation.
There is a spack-stack installation on
module use /scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles module load miniconda/3.9.12 module load ecflow/5.5.3
On Mon, Oct 17, 2022 at 2:23 PM Dusan Jovic @.***> wrote:
Is there any progress in installing gnu/openmpi hpc-stack or spack-stack on Hera and Cheyenne?
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The full answer is here: https://spack-stack.readthedocs.io/en/latest/Platforms.html#noaa-rdhpcs-hera
Note that there are also two other build environments that match the hpc-stack version of the libraries in /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-gnu-9.2.0 and /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-intel-2022.0.2/.
Note also that @mark-a-potts and @AlexanderRichert-NOAA are testing the ufs-weather-model with these software stacks.
GNU hpc-stack was there on the official hpc-stack installation.
@Hang-Lei-NOAA Do you mean the installation here /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/gnu-9.2.0 ?
I see only mpich not openmpi library.
The full answer is here: https://spack-stack.readthedocs.io/en/latest/Platforms.html#noaa-rdhpcs-hera
Note that there are also two other build environments that match the hpc-stack version of the libraries in
/scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-gnu-9.2.0and/scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-intel-2022.0.2/.Note also that @mark-a-potts and @AlexanderRichert-NOAA are testing the ufs-weather-model with these software stacks.
I tried to build and run the control regression test using /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack. I addition to using this stack and loading stack-gcc/9.2.0 and stack-openmpi/3.1.4 I had to rename two modules in ufs_common (netcdf to netcdf-c and pio to parallelio) and remove one (gftl-shared) which apparently is missing.
Model then compiled successfully, but unfortunately it crashes with this error:
85: /scratch1/NCEPDEV/stmp2/Dusan.Jovic/FV3_RT/rt_40700/control/./fv3.exe: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-gnu-9.2.0/install/gcc/9.2.0/libpng-1.6.37-7jlo63z/lib/libpng16.so.16)
We do not have openmpi versions installed. Could you please create a ticket in hpc-stack, if it is required on hera. I can start to develop these sets of libs.
On Mon, Oct 17, 2022 at 4:11 PM Dusan Jovic @.***> wrote:
The full answer is here: https://spack-stack.readthedocs.io/en/latest/Platforms.html#noaa-rdhpcs-hera
Note that there are also two other build environments that match the hpc-stack version of the libraries in /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-gnu-9.2.0 and /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-intel-2022.0.2/ .
Note also that @mark-a-potts https://github.com/mark-a-potts and @AlexanderRichert-NOAA https://github.com/AlexanderRichert-NOAA are testing the ufs-weather-model with these software stacks.
I tried to build and run the control regression test using /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack. I addition to using this stack and loading stack-gcc/9.2.0 and stack-openmpi/3.1.4 I had to rename two modules in ufs_common (netcdf to netcdf-c and pio to parallelio) and remove one (gftl-shared) which apparently is missing. Model then compiled successfully, but unfortunately it crashes with this error:
85: /scratch1/NCEPDEV/stmp2/Dusan.Jovic/FV3_RT/rt_40700/control/./fv3.exe: /usr/lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /scratch1/NCEPDEV/global/spack-stack/spack-stack-v1/envs/hpc-stack-dev-gnu-9.2.0/install/gcc/9.2.0/libpng-1.6.37-7jlo63z/lib/libpng16.so.16)
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I also tried this stack /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-2.0.0-intel-19.1.1.217/install/modulefiles/Core, as described in redathedocs link in the above comment. In order to use this stack I had to update versions of several libraries (zlib, jasper, hdf5, netcdf) in addition to renaming two modules listed above. But then one module is missing w3emc/2.9.2
It will be difficult to transition to spack-stack from hpc-stack with so many inconsistencies between the two, in module names, module versions, the content of the stacks etc.
So in this PR I'm going to focus to get hpc-stack working. If possible.
That’s why we created the “other” hpc-stack-dev environments (in addition to the skylab-2.0.0 envs) on hera for transitioning ...
On Oct 17, 2022, at 2:46 PM, Dusan Jovic @.***> wrote:
I also tried this stack /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-2.0.0-intel-19.1.1.217/install/modulefiles/Core, as described in redathedocs link in the above comment. In order to use this stack I had to update versions of several libraries (zlib, jasper, hdf5, netcdf) in addition to renaming two modules listed above. But then one module is missing w3emc/2.9.2
It will be difficult to transition to spack-stack from hpc-stack with so many inconsistencies between the two, in module names, module versions, the content of the stacks etc.
So in this PR I'm going to focus to get hpc-stack working. If possible.
— Reply to this email directly, view it on GitHub https://github.com/ufs-community/ufs-weather-model/pull/1147#issuecomment-1281474186, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5C2RKQHCY745LDFTQS7LDWDW3JNANCNFSM5R6RO57Q. You are receiving this because you were mentioned.
@BrianCurtis-NOAA tried to run this branch on Cheyenne using gnu compiler and mpt, and it failed to compile. I suspect we'll need to switch from mpt to openmpi.
@jkbk2004 Can somebody from EPIC build gnu/openmpi stack on cheyenne. Thanks.
@BrianCurtis-NOAA tried to run this branch on Cheyenne using gnu compiler and mpt, and it failed to compile. I suspect we'll need to switch from mpt to openmpi.
@jkbk2004 Can somebody from EPIC build gnu/openmpi stack on cheyenne. Thanks.
It's really a pity that we didn't coordinate this PR with switching to spack-stack - spack-stack is on Cheyenne and should be able to support the ufs-weather-model. It uses Intel + Intel-MPI and GNU + OpenMPI.
I do not have access to cheyenne, so I can not run any tests. But it looks like the gnu/openmpi hpc-stack on hera is finally ready (see https://github.com/ufs-community/ufs-weather-model/issues/1465), so I do not see why we can not switch to gnu/openmpi hpc-stack on Hera and gnu/openmpi spack-stack on Cheyenne and finally get this PR merged.
Command:
CMAKE_FLAGS="-DAPP=S2SWA -DCCPP_SUITES=FV3_GFS_v17_coupled_p8,FV3_GFS_cpld_rasmgshocnsstnoahmp_ugwp" ./build.sh
module list:
Currently Loaded Modules:
1) cmake/3.22.0 7) ncarcompilers/0.5.0 13) libpng/1.6.37 19) bacio/2.4.1 25) w3emc/2.9.2
2) miniconda3/4.12.0 8) hpc/1.2.0 14) hdf5/1.10.6 20) crtm/2.4.0 26) gftl-shared/v1.5.0
3) python/3.7.9 9) hpc-gnu/11.2.0 15) netcdf/4.7.4 21) g2/3.4.5 27) mapl/2.22.0-esmf-8.3.0b09
4) ncarenv/1.3 10) hpc-mpt/2.25 16) pio/2.5.7 22) g2tmpl/1.10.0 28) ufs_common
5) gnu/11.2.0 11) jasper/2.0.25 17) esmf/8.3.0b09 23) ip/3.3.3 29) ufs_cheyenne.gnu
6) mpt/2.25 12) zlib/1.2.11 18) fms/2022.01 24) sp/2.3.3
Output at linking stage:
[100%] Linking Fortran executable ufs_model
/usr/bin/ld: /usr/bin/ld: DWARF error: can't find .debug_ranges section.
FV3/libfv3atm.a(module_fcst_grid_comp.F90.o): in function `__module_fcst_grid_comp_MOD_fcst_initialize':
module_fcst_grid_comp.F90:(.text+0x2711): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_fcst_grid_comp.F90:(.text+0x277d): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: module_fcst_grid_comp.F90:(.text+0x27c0): undefined reference to `sgi_mpi_f08_logical'
/usr/bin/ld: module_fcst_grid_comp.F90:(.text+0x27e1): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: module_fcst_grid_comp.F90:(.text+0x4675): undefined reference to `sgi_mpi_f08_logical'
/usr/bin/ld: module_fcst_grid_comp.F90:(.text+0x46b6): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: /usr/bin/ld: DWARF error: can't find .debug_ranges section.
FV3/libfv3atm.a(module_wrt_grid_comp.F90.o): in function `__module_wrt_grid_comp_MOD_wrt_run':
module_wrt_grid_comp.F90:(.text+0x126b4): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x126c1): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x12741): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x1274e): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x127ce): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x127db): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x1285b): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x12868): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x12c52): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x12c5f): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: FV3/libfv3atm.a(module_wrt_grid_comp.F90.o): in function `__module_wrt_grid_comp_MOD_wrt_initialize_p1':
module_wrt_grid_comp.F90:(.text+0x13f9b): undefined reference to `mpi_comm_dup_f08_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x172f3): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x17314): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x1737b): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x1739c): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x17403): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x17424): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x17489): undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: module_wrt_grid_comp.F90:(.text+0x174aa): undefined reference to `mpi_allgather_f08ts_'
/usr/bin/ld: FV3/libfv3atm.a(post_fv3.F90.o): in function `__post_fv3_MOD_post_run_fv3':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/FV3/io/post_fv3.F90:209: undefined reference to `mpi_barrier_f08_'
/usr/bin/ld: /usr/bin/ld: DWARF error: can't find .debug_ranges section.
FV3/libfv3atm.a(atmos_model.F90.o): in function `__atmos_model_mod_MOD_update_atmos_radiation_physics':
atmos_model.F90:(.text+0x2695d): undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: atmos_model.F90:(.text+0x2696a): undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: atmos_model.F90:(.text+0x26a27): undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: atmos_model.F90:(.text+0x26a42): undefined reference to `sgi_mpi_f08_maxloc'
/usr/bin/ld: atmos_model.F90:(.text+0x26a5a): undefined reference to `sgi_mpi_f08_2double_precision'
/usr/bin/ld: atmos_model.F90:(.text+0x26b53): undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: atmos_model.F90:(.text+0x26bc4): undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: atmos_model.F90:(.text+0x26bde): undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: /usr/bin/ld: DWARF error: can't find .debug_ranges section.
FV3/libfv3atm.a(module_write_netcdf.F90.o): in function `__module_write_netcdf_MOD_write_netcdf':
module_write_netcdf.F90:(.text+0x51e3): undefined reference to `sgi_mpi_f08_info_null'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x8f6c): undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x8f7d): undefined reference to `sgi_mpi_f08_real4'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x9005): undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x9012): undefined reference to `sgi_mpi_f08_real4'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x9028): undefined reference to `sgi_mpi_f08_min'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x90b1): undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x90fb): undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x9100): undefined reference to `sgi_mpi_f08_real4'
/usr/bin/ld: module_write_netcdf.F90:(.text+0x918e): undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: /usr/bin/ld: DWARF error: can't find .debug_ranges section.
FV3/ccpp/physics/libccpp_physics.a(module_mp_thompson.F90.o): in function `__module_mp_thompson_MOD_freezeh2o':
module_mp_thompson.F90:(.text+0x5d97): undefined reference to `mpi_barrier_f08_'
/usr/bin/ld: FV3/ccpp/physics/libccpp_physics.a(module_mp_thompson.F90.o): in function `__module_mp_thompson_MOD_qr_acr_qs':
module_mp_thompson.F90:(.text+0x6737): undefined reference to `mpi_barrier_f08_'
/usr/bin/ld: FV3/ccpp/physics/libccpp_physics.a(module_mp_thompson.F90.o): in function `__module_mp_thompson_MOD_qr_acr_qg':
module_mp_thompson.F90:(.text+0x87d7): undefined reference to `mpi_barrier_f08_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_alltoall_r4_1darr':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:710: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:710: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:710: undefined reference to `mpi_alltoallv_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_i8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:685: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:685: undefined reference to `sgi_mpi_f08_integer8'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:685: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:660: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:660: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:660: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r8_2darr':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:640: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:640: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:640: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r8_1darr':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:616: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:616: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:616: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r8_1d':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:594: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:594: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:594: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r4_1d':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:566: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:566: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:566: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r4_2darr':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:537: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:537: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:537: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r4_1darr':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:514: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:514: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:514: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:491: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:491: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:491: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_sum_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:471: undefined reference to `sgi_mpi_f08_sum'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:471: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:471: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_max_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:451: undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:451: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:451: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_min_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:431: undefined reference to `sgi_mpi_f08_min'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:431: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:431: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_min_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:419: undefined reference to `sgi_mpi_f08_min'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:419: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:419: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_max_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:407: undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:407: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:407: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_max_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:390: undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:390: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:390: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_max_r8_1d':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:370: undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:370: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:370: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_reduce_max_r4_1d':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:349: undefined reference to `sgi_mpi_f08_max'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:349: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:349: undefined reference to `mpi_allreduce_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_4d_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:330: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:330: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_2d_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:314: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:314: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_1d_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:298: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:298: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_3d_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:282: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:282: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_4d_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:266: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:266: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_4d_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:250: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:250: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_3d_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:234: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:234: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_3d_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:218: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:218: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_2d_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:202: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:202: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_2d_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:186: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:186: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_1d_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:170: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:170: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_1d_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:154: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:154: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_r8':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:138: undefined reference to `sgi_mpi_f08_double_precision'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:138: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_r4':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:123: undefined reference to `sgi_mpi_f08_real'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:123: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mp_bcst_i':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:108: undefined reference to `sgi_mpi_f08_integer'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:108: undefined reference to `mpi_bcast_f08ts_'
/usr/bin/ld: stochastic_physics/libstochastic_physics.a(mpi_wrapper.F90.o): in function `__mpi_wrapper_MOD_mpi_wrapper_initialize':
/glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:86: undefined reference to `mpi_comm_rank_f08_'
/usr/bin/ld: /glade/work/briancurtis/git/DusanJovic-NOAA/ufs-weather-model/stochastic_physics/mpi_wrapper.F90:87: undefined reference to `mpi_comm_size_f08_'
collect2: error: ld returned 1 exit status
CMakeFiles/ufs_model.dir/build.make:155: recipe for target 'ufs_model' failed
make[2]: *** [ufs_model] Error 1
CMakeFiles/Makefile2:773: recipe for target 'CMakeFiles/ufs_model.dir/all' failed
make[1]: *** [CMakeFiles/ufs_model.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2
I do not have access to cheyenne, so I can not run any tests. But it looks like the gnu/openmpi hpc-stack on hera is finally ready (see #1465), so I do not see why we can not switch to gnu/openmpi hpc-stack on Hera and gnu/openmpi spack-stack on Cheyenne and finally get this PR merged.
Yes, I hear you ... not exactly my job anymore, but I am going to give it a shot on Cheyenne. I will need to extend the existing environment with a few missing packages for the fully-coupled UFS. Then change the build environment for Cheyenne with GNU and see what happens ...
@BrianCurtis-NOAA tried to run this branch on Cheyenne using gnu compiler and mpt, and it failed to compile. I suspect we'll need to switch from mpt to openmpi.
@jkbk2004 Can somebody from EPIC build gnu/openmpi stack on cheyenne. Thanks.
i can install gnu/openmpi in the official space on cheyenne, unless @climbfuji has already done so. @DusanJovic-NOAA : can you confirm which gnu/openmpi you prefer? there is much more flexibility for combinations out-of-the-box on cheyenne.
Any supported gnu compiler version >= 9, and any supported opemnpi. I do not have any preference.
I was able to compile the UFS on Cheyenne using spack-stack with gcc-10.1.0 and openmpi-4.1.1.
I ran rt.sh for the control test first, and it passed against the existing baseline:
...
+ cat /glade/scratch/heinzell/ufs-weather-model-dusan-no-arg-mismatch-spack-stack/tests/log_cheyenne.gnu/compile_001_time.log
+ cat /glade/scratch/heinzell/ufs-weather-model-dusan-no-arg-mismatch-spack-stack/tests/log_cheyenne.gnu/rt_001_control.log
+ FILES='fail_test_* fail_compile_*'
+ for f in '$FILES'
+ [[ -f fail_test_* ]]
+ for f in '$FILES'
+ [[ -f fail_compile_* ]]
+ [[ -e fail_test ]]
+ echo
+ echo REGRESSION TEST WAS SUCCESSFUL
REGRESSION TEST WAS SUCCESSFUL
+ echo
+ echo REGRESSION TEST WAS SUCCESSFUL
+ rm -f 'fv3_*.x' fv3_001.exe modules.fv3
It requires small changes in the ufs-weather-model which I would be happy to contribute to this PR, but we need a clear path forward with the remaining applications and how to manage this spack-stack installation.
@DusanJovic-NOAA Do we need to change the ufs_hera.gnu.lua and ufs_hera.gnu_debug.lua too?
Both hera and cheyenne gnu module files will eventually need to be changed to use updated gnu and openmpi modules. But I'm not sure if that's ready at this moment. Ideally we should update to the new mpi library in a separate commit so that this PR only updates the code without needing new baselines.