Running CESM2 on derecho with new environment setting

Y

ylee

Yu-Chi Lee
New Member
What version of the code are you using?
CESM 2.1.5

Have you made any changes to files in the source tree?
This simulation requires topography modifications, and I've made related xml file changes.
please find more details in the case create shell script.

Describe every step you took leading up to the problem:
Peviously I have successfully run the cases for several members, but since last maintance, I encountered mismatched running environment issues.

Describe your problem or question:
I am running CESM2 simulation on Derecho, as mentioned previously, I was successfully running the experiments for a while.
However, since last maintanance and the updated ncarenv, it kept encountering modules mismatch issues.
I was successfully adopted the model from ncarenv/23.9 -> ncarenv/24.12 by making changes in env_mach_specific.xml; but the same approach seems not working this time for the new enviroment.

Inactive Modules:
1) cray-mpich/8.1.29 3) hdf5-mpi/1.12.3 5) netcdf-mpi/4.9.2
2) esmf/8.7.0 4) ncarcompilers/1.0.0 6) parallel-netcdf/1.14.0

The following have been reloaded with a version change:
1) cmake/3.26.6 => cmake/3.31.8
2) craype/2.7.31 => craype/2.7.34
3) intel/2024.2.1 => intel/2025.2.1
4) libfabric/1.15.2.0 => libfabric/1.22.0
5) mkl/2024.2.2 => mkl/2025.3.1
6) ncarenv/24.12 => ncarenv/25.10

ERROR: module command $LMOD_ROOT/lmod/libexec/lmod python load cesmdev/1.0 ncarenv/24.12 failed with message:
Lmod has detected the following error: These module(s) or extension(s) exist
but cannot be loaded as requested: "esmf/8.7.0", "ncarcompilers/1.0.0",
"netcdf-mpi/4.9.2", "netcdf", "hdf5/1.14.6", "ncview", "hdf5-mpi/1.12.3",
"nco", "ncl", "cray-mpich/8.1.29", "parallel-netcdf/1.14.0", "mkl", "libfabric"
Try: "module spider esmf/8.7.0 ncarcompilers/1.0.0 netcdf-mpi/4.9.2 netcdf
hdf5/1.14.6 ncview hdf5-mpi/1.12.3 nco ncl cray-mpich/8.1.29
parallel-netcdf/1.14.0 mkl libfabric" to see how to load the module(s).

While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
hdf5-mpi/1.12.3 /glade/u/apps/derecho/modules/24.12/cray-mpich/8.1.29/oneapi/2024.2.1/hdf5-mpi/1.12.3.lua
Click to expand...

Please let me know if more details needed. Thank you so much for the help!
 
Y

ylee

Yu-Chi Lee
New Member
I wan't able to attach the files previously.
Here is the script for creating and setting the changes:
#!/bin/csh

set casedir = /glade/u/home/yuchilee/cesm2/cases
set ens = 003
set dateres = 1942-01-01-00000
set refdate = 1942-01-01
set casename = b.e21.BHIST.f09_g17.CMIP6-historical.rmBS.$ens.test
set refcase = b.e21.BHIST.f09_g17.CMIP6-historical.rmBS.$ens
set restdir = /glade/derecho/scratch/yuchilee/archive/$refcase/rest/$dateres
set workdir = /glade/derecho/scratch/yuchilee
set rundir = run

cd /glade/u/home/yuchilee/cesm2/my_cesm_code_v1/cime/scripts
./create_newcase --case $casedir/$casename --res f09_g17 --compset BHIST --project UCLR0006

mkdir $workdir/$casename
mkdir $workdir/$casename/$rundir
cp $restdir/* $workdir/$casename/$rundir/.

cd $casedir/$casename

./xmlchange --file env_run.xml --id RUN_TYPE --val hybrid
./xmlchange --file env_run.xml --id RUN_REFCASE --val $refcase
./xmlchange --file env_run.xml --id RUN_REFDATE --val $refdate
./xmlchange --file env_run.xml --id GET_REFCASE --val FALSE
./xmlchange --file env_run.xml --id STOP_OPTION --val nmonths
./xmlchange --file env_run.xml --id STOP_N --val 12
./xmlchange ATM_DOMAIN_FILE="domain.lnd.fv09_gx1v7_rmBS.250206.nc"
./xmlchange ATM_DOMAIN_PATH="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/"
./xmlchange LND_DOMAIN_FILE="domain.lnd.fv09_gx1v7_rmBS.250206.nc"
./xmlchange LND_DOMAIN_PATH="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/"
./xmlchange ICE_DOMAIN_FILE="domain.ocn.gx1v7_rmBS.250206.nc"
./xmlchange ICE_DOMAIN_PATH="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/"
./xmlchange OCN_DOMAIN_FILE="domain.ocn.gx1v7_rmBS.250206.nc"
./xmlchange OCN_DOMAIN_PATH="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/"
./xmlchange ROF2LND_FMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_r05_nomask_TO_fv09_aave.250206.nc"
./xmlchange LND2ROF_FMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_fv09_TO_r05_nomask_aave.250206.nc"
./xmlchange ROF2OCN_LIQ_RMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_r05_to_gx1v7_rmBS_merged_250206.nc"
./xmlchange ROF2OCN_ICE_RMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_r05_to_gx1v7_rmBS_nnsm_e1000r300_250206.nc"
./xmlchange ATM2OCN_FMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_fv09_TO_gx1v7_rmBS_aave.250206.nc"
./xmlchange ATM2OCN_VMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_fv09_TO_gx1v7_rmBS_patc.250206.nc"
./xmlchange OCN2ATM_FMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_gx1v7_rmBS_TO_fv09_aave.250206.nc"
./xmlchange OCN2ATM_SMAPNAME="/glade/derecho/scratch/yuchilee/data/04-Project_bering_strait/modified_topo/map_gx1v7_rmBS_TO_fv09_aave.250206.nc"
./xmlchange CLM_NAMELIST_OPTS="use_init_interp=.true. init_interp_method='general'"
Click to expand...

And current settings in env_mach_specific.xml is for ncarenv/24.12.
 
J

jedwards

CSEG and Liaisons
Staff member
You should be able to continue to use the ncarenv/24.12 - an issue may occur if you have changed some settings in your login dot files related
to the new ncarenv or other modules?
 
Y

ylee

Yu-Chi Lee
New Member
Thank you for the reply!

I just checked the .bashrc, and found out one command out line:
# export LD_LIBRARY_PATH=/glade/u/apps/casper/23.10/spack/opt/spack/netcdf/4.9.2/packages/netcdf-c/4.9.2/oneapi/2023.2.1/esck/lib:$LD_LIBRARY_PATH
Click to expand...

I think it may be related, is it the one should be address with? If so, can you tell how to make it correct? Thank you!
 
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