Something strange when running case.submit.

[icbj007]

case.submit was executed. However,

env_batch.xml appears to have changed, regenerating batch scripts manually edits to these files will be lost!

Creating batch scripts
Writing case.run script from input template /home/hanulsol/model/cesm2/cesm2.2.1/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/hanulsol/model/cesm2/cesm2.2.1/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
Setting Environment NETCDF_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_C_PATH=/usr /local/netcdf/4.6.1_intel21
Setting Environment NETCDF_FORTRAN_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment HDF5_PATH=/usr/local/hdf5/1.10.5
Setting Environment PNETCDF_PATH=/usr/local/pnetcdf/1.11.2_intel21_mpich-3.4.1

Can you tell me why I'm creating batch scripts? In the tutorial video, that part Because this doesn't come out.

And then when I run ./preview_run

CASE INFO:
nodes: 6
total tasks: 48
tasks per node: 8
thread count: 1

BATCH INFO:
FOR JOB: case.run
ENV:
module command is /usr/bin/modulecmd python purge
module command is /usr/bin/modulecmd python load intel21/compiler-21 intel21/mkl intel21/mpich-3.4.1 intel21/netcdf-4.6.1 intel21/pnetcdf-1.11.2 gcc/hdf5-1.10.5
Setting Environment NETCDF_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_C_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_C_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_FORTRAN_PATH=/usr/local/netcdf/4.6.1_intel21
Setting Environment NETCDF_FORTRAN_PATH=/usr/local/netcdf /4.6.1_intel21
Setting Environment HDF5_PATH=/usr/local/hdf5/1.10.5
Setting Environment HDF5_PATH=/usr/local/hdf5/1.10.5
Setting Environment PNETCDF_PATH=/usr/local/pnetcdf/1.11.2_intel21_mpich-3.4.1 Setting Environment PNETCDF_PATH=/usr/local/pnetcdf/1.11.2_intel21_mpich-3.4.1
Setting Environment OMP_NUM_THREADS=1

SUBMIT CMD:
qsub -q workq -l walltime=9999:00:00 -v ARGS_FOR_SCRIPT='--resubmit' .case.run MPIRUN (job=case.run):
ERROR: Undefined env var 'PBS_NODEFILE'

Why does this happen? Pls help me...

 

[erik]

Hello

We need some more context around what you are trying to do here. I can tell you are using cesm2.2.1 here, and using intel21 compiler. But, it's not clear what machine you are trying to run on, and if it's a supported machine or one that you made the port to. From the context it's also clear that the setup is assuming you have the PBS batch system on your machine.

I also suggest that you use cesm2.2.2 which is the recent update to the previous cesm2.2.1 version.

In terms of the question...

Can you tell me why I'm creating batch scripts?

Part of what CESM does is to create batch scripts for you based on what it knows about the machine you are using. If you are using a system without batch you should configure it to not use a batch system.


And for this question...

SUBMIT CMD:
qsub -q workq -l walltime=9999:00:00 -v ARGS_FOR_SCRIPT='--resubmit' .case.run MPIRUN (job=case.run):
ERROR: Undefined env var 'PBS_NODEFILE'

Why does this happen? Pls help me...

PBS_NODEFILE is an environment variable that the PBS job scheduler sets for you when a job is submitted to it. The error saying it's NOT defined means that it wasn't defined and it's aborting early. Was this message part of "preview_run" or on the job submission? If in preview_run there may be a bug where it doesn't realize the command is NOT run under batch and so the variable isn't set. If under the batch submission this indicates that PBS didn't set the expected variable, so either your system doesn't use PBS or something else went wrong.