CLM build error in CESM2.3 port

[James King]

Hi all,

I'm trying to port CESM2.3.alpha17 to my HPC. When I run the ensemble test for F2000climo after installing the model:

:/$CESMROOT/tools/statistical_ensemble_test> python ensemble.py --case $CESMROOT/runs/F2000climo_CESM2.3.alpha17.uf.0000 --ect cam --uf --mach archer2 --compset F2000climo --res f19_f19_mg17 --compiler gnu

I get the following error:

ERROR: Command /mnt/lustre/a2fs-work2/work/n02/n02/jking/cesm/CESM2.3/my_cesm_sandbox/components/clm/bld/build-namelist failed rc=2
out=
err=Can't load '/work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML/LibXML.so' for module XML::LibXML: /work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML/LibXML.so: undefined symbol: PL_hash_seed at /home1/home/n02/n02/jking/miniconda3/lib/5.34.0/x86_64-linux-thread-multi/DynaLoader.pm line 193.
at /work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/XML/LibXML.pm line 156.
BEGIN failed--compilation aborted at /work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/XML/LibXML.pm line 156.
Compilation failed in require at /mnt/lustre/a2fs-work2/work/n02/n02/jking/cesm/CESM2.3/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /mnt/lustre/a2fs-work2/work/n02/n02/jking/cesm/CESM2.3/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /mnt/lustre/a2fs-work2/work/n02/n02/jking/cesm/CESM2.3/my_cesm_sandbox/components/clm/bld/CLMBuildNamelist.pm line 421.

The file:

/work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML/LibXML.so

exists, so I'm not sure what the problem is about loading it. Any suggestions would be most welcome.

Thanks,

James

 

[jedwards]

We don't have an ensemble prepared yet for the cesm2.3 series since we are still in a rapid development phase.
That said it looks like maybe it found XML::LibXML but then had an error loading the .so file therein - are you sure that the
file in path /work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML/LibXML.so was built for the platform you are attempting to run on?

 

[James King]

Hi Jim,

That's fair enough, I suspected not - I didn't choose the model version to use here. One potential issue here is that

perl -v

tells me I am using perl v5.34.0 installed in my home area, whereas the model is looking for v5.26.2 installed in a shared area. Do you think this could be part of the problem?
I will check with the system admins that this file (/work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML/LibXML.so) has been built and installed properly.

Thanks,

James

 

[jedwards]

I think that the perl mismatch is the problem - can you try modifying your path so that you are using the system perl?
Or you can try installing XML::LibXML in your version.

 

[James King]

Hi Jim,

Just to check, would I do this by:

export PATH=/work/n02/shared/perl/5.26.2/x86_64-linux-thread-multi/auto/XML/LibXML:$PATH

Thanks,

James