Error in case setup step for CLM5 + Experience with ComputeCanada server???

[wvsi3w]

Hello all
this is the command for creating newcase that I used:
./create_newcase --case /home/meisam/scratch/cases/my_7th_test --compset I1850Clm50Bgc --res f19_g16 --machine narval --walltime 00:10:00 --run-unsupported
the narval machine is defined and the config file of it also the config file for the compiler is attached.

When I use the ./case.setup command, it says :
ERROR: module command None purge failed with message:
/bin/sh: None: command not found

I tried editing the init path for sh and csh but it didn't work (as you can see it's my 7th try).

Also: is there anyone with knowledge of using computecanada servers (narval and beluga)? I want to learn from anyone who did it with Canadian servers.

 

[wvsi3w]

We changed the init path again and the below error came up:

ERROR: module command /cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python purge failed with message:
The following modules were not unloaded:
(Use "module --force purge" to unload all):

1) CCconfig 3) gcccore/.9.3.0 5) intel/2020.1.217 7) libfabric/1.10.1 9) flexiblas/3.0.4 11) StdEnv/2020
2) gentoo/2020 4) imkl/2020.1.217 6) ucx/1.8.0 8) openmpi/4.0.3 10) blis/0.8.1


the init path that we used this time for the config_machine is this:
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>

 

[jedwards]

On the module_system line you can add an attribute so that the error from module load will not cause an abort:
<module_system type="module" allow_error="true">

However, the message you are getting indicates that you are not loading modules correctly for your system,
you should be able to login and execute the module commands from the command line - I would work on
getting that corrected before trying create_newcase again. You might try replacing the module purge with module reset.

 

[wvsi3w]

By adding "allow_error=true" the ./create_newcase failed with this error:

ERROR: Command: '/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/xmllint --noout --schema /home/meisam/my_cesm_sandbox/cime/config/xml_schemas/config_machines.xsd /home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml' failed with error 'b"/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml:86: element command: Schemas validity error : Element 'command', attribute 'name': '--force purge' is not a valid value of the atomic type 'xs:NCName'.\n/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml fails to validate"' from dir '/home/meisam/my_cesm_sandbox/cime/scripts'

However, with a suggestion from Digital Research Alliance of Canada I removed these two lines from config_machine.xml:

<command name="--force purge"/>
<command name="load">StdEnv/2020</command>

and the create_newcase was done correctly, BUT, by doing the ./case.setup command in the directory of this case the below error appears:

ERROR: Command: '/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/xmllint --noout --schema /home/meisam/my_cesm_sandbox/cime/config/xml_schemas/config_compilers_v2.xsd /home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml' failed with error 'b"/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml:79: element ADD_SLIBS: Schemas validity error : Element 'ADD_SLIBS': This element is not expected.\n/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml fails to validate"' from dir '/lustre07/scratch/meisam/cases/jan3_without2lines'

(for the record; I used "--force purge" command before this because I was told (by Digital Research Alliance of Canada) to use this as sticky modules (StdEnv/2020) that don't get unloaded by module purge. I used it and it didn't work and the Error "--force purge is not a valid value" appeared. Hence, I removed them as the Digital Research Alliance of Canada said so, and the above issued happened. Good news is it works for create_newcase, but it wont work for CASE.SETUP)

 

[jedwards]

Is the error message above not clear to you?
For the module issues you should work out the sequence of commands that you need to use
on the command line and then once you have established that sequence and proved to yourself that
you can apply it more than once without error then put it into config_machines.xml for your system.

 

[wvsi3w]

Sorry, I am not sure what you mean exactly. I just started using this model.

I am following steps provided by ucar in order to do a quick run on clm5. In these steps it is mentioned that I should do 4 steps which is create newcase, case setup, case built, and case submit.

I think the create new case is done but the problem with Case setup is baffling.

 

[jedwards]

You copied and pasted the following:

ERROR: Command: '/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/xmllint --noout --schema /home/meisam/my_cesm_sandbox/cime/config/xml_schemas/config_compilers_v2.xsd /home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml' failed with error 'b"/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml:79: element ADD_SLIBS: Schemas validity error : Element 'ADD_SLIBS': This element is not expected.\n/home/meisam/my_cesm_sandbox/cime/config/cesm/machines/config_compilers.xml fails to validate"' from dir '/lustre07/scratch/meisam/cases/jan3_without2lines'

which tells you exactly what you need to do to solve the problem. What is baffling about it?