CESM2.3.beta08 porting issue

[James King]

That's why you should really try to avoid hardcoded paths. All of these ESMF_ variables
are set by ESMFMKFILE and they should not need to be set individually. Just make sure
that ESMFMKFILE is in the environment.

Yes agreed! I will add ESMFMKFILE to my path and see if that makes any difference.

I've submitted a support ticket to ARCHER2's help desk summarising this discussion - thanks a lot for your advice. If it's an issue around compiler installations and/or the content of centrally located module files then it'll be beyond my power to fix but hopefully we've been able to identify some of the reasons why the case is failing.

 

[viswanathvelamuri]

EDIT - fixed this, ignore. Previous question about cmake macros still stands.

Hi James,
I am facing a similar issue when I try to create a new case for the local HPC. Can you please share how you rectified the mistake?
I am attaching the error below.

Using project from config_machines.xml: USER_REQUESTED_PROJECT
No charge_account info available, using value from PROJECT
cesm model version found: release-cesm2.2.2-2-g488ecf9
Batch_system_type is pbs
job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S
WARNING: No queue on this system met the requirements for this job. Falling back to defaults
ERROR: No queues found

Thanks in advance

 

[James King]

Hi James,
I am facing a similar issue when I try to create a new case for the local HPC. Can you please share how you rectified the mistake?
I am attaching the error below.

Using project from config_machines.xml: USER_REQUESTED_PROJECT
No charge_account info available, using value from PROJECT
cesm model version found: release-cesm2.2.2-2-g488ecf9
Batch_system_type is pbs
job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S
WARNING: No queue on this system met the requirements for this job. Falling back to defaults
ERROR: No queues found

Thanks in advance

Hi Viswanath,

This error is probably because you need to provide details of your HPC's batch system, including the names and properties of the various job queues, in cime/config/cesm/machines/config_batch.xml.

Hope that helps,

James

 

[viswanathvelamuri]

Hi James,

Thank you for the answer.

Do you know why the following error is occuring while building the case:
[cez238111@login02 ~/scratch/new_case/test1]
$ ./case.build
Building case in directory /scratch/civil/phd/cez238111/new_case/test1
sharedlib_only is False
model_only is False
Setting Environment NETCDF=/home/soft/centOS/lib/intel/2020/netcdf/c-4.8.0-cxx-4.3.1-f-4.5.3
Setting Environment PNETCDF=/home/soft/centOS/lib/intel/2020/pnetcdf/1.12.2
Setting Environment HDF5=/home/soft/centOS/lib/intel/2020/hdf5/1.12.1
Setting Environment PHDF5=/home/soft/centOS/lib/intel/2020/hdf5/1.12.1
Setting Environment MPIROOT=/home/soft/intel2020u4/impi/2019.9.304/intel64
Setting Environment CIMEROOT=/home/soft/centOS/apps/cesm/2.2.0/my_cesm_sandbox/cime
Generating component namelists as part of build
Creating component namelists
2024-05-20 19:10:42 atm
Calling /scratch/civil/phd/cez238111/{my_cesm_sandbox}/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
ERROR: Command /scratch/civil/phd/cez238111/{my_cesm_sandbox}/components/cam/bld/build-namelist -ntasks 160 -csmdata /home/civil/phd/cez238111/scratch/inputdata -infile /home/civil/phd/cez238111/scratch/new_case/test1/Buildconf/camconf/namelist -start_ymd 20100101 -ignore_ic_year -use_case hist_trop_strat_nudged_cam6 -inputdata /home/civil/phd/cez238111/scratch/new_case/test1/Buildconf/cam.input_data_list -namelist " &atmexp /" failed rc=2
out=
err=CAM build-namelist - ERROR: invalid value of use_case (hist_trop_strat_nudged_cam6) specified in commandline
expected one of:

 

[jedwards]

This error appears to be due to specifying a cam use_case "hist_trop_strat_nudged_cam6" which is not defined in the version of cam that you have checked out.

 

[James King]

Yes, I would advise using a defined compset for testing purposes first (e.g. F2000climo) before attempting something more complicated. You may be able to define this particular use_case in one of the namelist files in the CAM src but that's not something I've done before.

 

[inos@bas_ac_uk]

OK thanks. With this line in gnu_archer2.cmake, I can build and submit a case. However we're still having fun with compilers as the run fails with this line in the cesm.log:

/work/n02/n02/jking/cesm/CESM2.3.beta08/cesm_sims/runs/F2000climo_test/bld/cesm.exe: error while loading shared libraries: libnetcdf_parallel_gnu_91.so.18: cannot open shared object file: No such file or directory'

I have the module

cray-parallel-netcdf/1.12.3.1

loaded in my environment.

Hi James,

I'm also using ARCHER2 and getting the exact same error message about the netcdf library when trying to re-run a case I ran previously without any problem back in Oct 2022 (I just wanted to re-run to add a variable to my output that I missed that time - not as easy as I thought it'd be!). I'm guessing this is due to a module change on ARCHER2 in the meantime, but I haven't been able to pinpoint the issue or fix it. I followed the rest of this thread, but that hasn't led me to the solution either. Could you share how you fixed it in the end (assuming you did)?

Thanks!
Ingrid

 

[jedwards]

You may need to set an rpath in the executable to find the library. Add flag

string(APPEND LDFLAGS " -Wl,-rpath,${NETCDF_PATH}/lib")