Questions about install CTSM

[lfu]

Hi,

I cannot successfully install CTSM. The following is my code in the terminal.
Do you know how to fix it? Thank you.

> git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM) ctsm_MYBRANCH_b
> cd ctsm_MYBRANCH_b
> git checkout -b MYBRANCH master
> ./bin/git-fleximod update
e fates not checked out, aligned at tag sci.1.78.3_api.36.1.0
fates up to date.
Recursively checking out submodules of cism
e source_cism not checked out, aligned at tag cism_main_2.01.013
cism up to date.
rtm up to date.
mosart up to date.
mizuRoute up to date.
ccs_config updated to ccs_config_cesm1.0.0
Recursively checking out submodules of cime
e CIME/non_py/cprnc has no fxtag defined in .gitmodules
cime up to date.
cmeps up to date.
Recursively checking out submodules of cdeps
e fox not checked out, aligned at tag 4.1.2.1
e genf90 not checked out, aligned at hash 4816965
cdeps up to date.
share up to date.
mct up to date.
parallelio up to date.
Skipping optional component doc-builder

 

[slevis]

I don't see error messages included in the post, but I moved the thread to "porting" regardless.

 

[lfu]

I don't see error messages included in the post, but I moved the thread to "porting" regardless.

Thank you.
I got an error when I submitted my case. Is it because of the model installation?

 

[jedwards]

No error here - check the associated cesm.log file

 

[slevis]

I see that you're working on derecho, so you should not have porting or installation problems.

In cesm.log I see
dec1885.hsn.de.hpc.ucar.edu 0: /glade/u/apps/derecho/23.09/spack/opt/spack/esmf/8.6.0/cray-mpich/8.1.27/oneapi/2023.2.1/7haa/lib/libesmf.so(_ZN5ESMCI6FTable12callVFuncPtrEPKcPNS_2VMEPi+0x444) [0x154613c12884]
dec1885.hsn.de.hpc.ucar.edu 0: MPICH ERROR [Rank 0] [job id 4d4119af-606f-4628-bdaa-ea1691e48b7f] [Sun Oct 13 21:28:14 2024] [dec1885] - Abort(-1) (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
dec1885.hsn.de.hpc.ucar.edu 0:
dec1885.hsn.de.hpc.ucar.edu: rank 0 exited with code 255

This is a 1x1 simulation (single point) and I wonder whether you used this flag when you created the case:
--mpilib mpi-serial

 

[lfu]

I see that you're working on derecho, so you should not have porting or installation problems.

In cesm.log I see
dec1885.hsn.de.hpc.ucar.edu 0: /glade/u/apps/derecho/23.09/spack/opt/spack/esmf/8.6.0/cray-mpich/8.1.27/oneapi/2023.2.1/7haa/lib/libesmf.so(_ZN5ESMCI6FTable12callVFuncPtrEPKcPNS_2VMEPi+0x444) [0x154613c12884]
dec1885.hsn.de.hpc.ucar.edu 0: MPICH ERROR [Rank 0] [job id 4d4119af-606f-4628-bdaa-ea1691e48b7f] [Sun Oct 13 21:28:14 2024] [dec1885] - Abort(-1) (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
dec1885.hsn.de.hpc.ucar.edu 0:
dec1885.hsn.de.hpc.ucar.edu: rank 0 exited with code 255

This is a 1x1 simulation (single point) and I wonder whether you used this flag when you created the case:
--mpilib mpi-serial

Thank you for your suggestion! But here is another error:

/glade/derecho/scratch/lfu/I2000_CTSM_singlept_single_CR_N_spinup/bld/cesm.exe() [0x5a8a7e]
/glade/u/apps/derecho/23.09/spack/opt/spack/esmf/8.6.0/mpi-serial/2.3.0/oneapi/2023.2.1/juyc/lib/libesmf.so(_ZN5ESMCI6FTable12callVFuncPtrEPKcPNS_2VMEPi+0x444) [0x1508eefbd594]
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libpthread-2.31.s 00001508ECB3C8C0 Unknown Unknown Unknown
libc-2.31.so 00001508EB9FBCBB gsignal Unknown Unknown
libc-2.31.so 00001508EB9FD355 abort Unknown Unknown
libpioc.so 00001508F9AD4C01 Unknown Unknown Unknown
libpioc.so 00001508F9AD84CC PIOc_openfile_ret Unknown Unknown
libpioc.so 00001508F9AD3B13 PIOc_openfile Unknown Unknown
libpiof.so 00001508F9D2BB34 piolib_mod_mp_pio Unknown Unknown
cesm.exe 00000000005C3407 ncdio_pio_mp_ncd_ 211 ncdio_pio.F90.in
cesm.exe 000000000078B1B4 surfrdmod_mp_surf 147 surfrdMod.F90
cesm.exe 0000000000606AFC clm_initializemod 103 clm_initializeMod.F90
cesm.exe 00000000005A8A7E lnd_comp_nuopc_mp 629 lnd_comp_nuopc.F90
libesmf.so 00001508EEFBD594 _ZN5ESMCI6FTable1 Unknown Unknown
libesmf.so 00001508EEFBD07E ESMCI_FTableCallE Unknown Unknown

Could you help me check it again? Thank you very much!

 

[jedwards]

You need to learn to read the logs and correctly identify errors. Please review more carefully yourself before asking for help.

cat user_nl_clm
!----------------------------------------------------------------------------------
! Users should add all user specific namelist changes below in the form of
! namelist_var = new_namelist_value
!
! EXCEPTIONS:
! Set use_cndv           by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
! Set use_vichydro       by the compset you use and the CLM_BLDNML_OPTS -vichydro           setting
! Set use_cn             by the compset you use and CLM_BLDNML_OPTS -bgc  setting
! Set use_crop           by the compset you use and CLM_BLDNML_OPTS -crop setting
! Set spinup_state       by the CLM_BLDNML_OPTS -bgc_spinup      setting
! Set co2_ppmv           with CCSM_CO2_PPMV                      option
! Set fatmlndfrc         with LND_DOMAIN_PATH/LND_DOMAIN_FILE    options
! Set finidat            with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
!                        (includes $inst_string for multi-ensemble cases)
!                        or with CLM_FORCE_COLDSTART to do a cold start
!                        or set it with an explicit filename here.
! Set maxpatch_glc       with GLC_NEC                            option
! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
!----------------------------------------------------------------------------------

fsurdat = '/glade/u/home/lfu/CostaRica_single/I2000_CTSM_singlept_single_CR_N_spinup/surface_data/surfdata_CO_point_hist_2000_78pfts_c241013.nc'
derecho7: /glade/u/home/lfu/CostaRica_single/I2000_CTSM_singlept_single_CR_N_spinup
:) ls -ltr /glade/u/home/lfu/CostaRica_single/I2000_CTSM_singlept_single_CR_N_spinup/surface_data/surfdata_CO_point_hist_2000_78pfts_c241013.nc
ls: cannot access '/glade/u/home/lfu/CostaRica_single/I2000_CTSM_singlept_single_CR_N_spinup/surface_data/surfdata_CO_point_hist_2000_78pfts_c241013.nc': No such file or directory

 

[jedwards]

I think that you mean

fsurdat = '/glade/u/home/lfu/CostaRica_single/surface_data/surfdata_CO_point_hist_2000_78pfts_c241013.nc'

 

[lfu]

I think that you mean

fsurdat = '/glade/u/home/lfu/CostaRica_single/surface_data/surfdata_CO_point_hist_2000_78pfts_c241013.nc'

You are right. Thank you very much! I will check it more carefully.