errors after ./case.build

[yangx2]

Hi,
I am testing another experiment by setting :
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$./create_newcase --case b.e20.B1850.f19_g17.test --compset B1850 --res f19_g17
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$cd b.e20.B1850.f19_g17.test/
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$./case.setup
.[yangx2@node-0003 b.e20.B1850.f19_g17.test]$/case.build
Then I got this (below):

****************************************************************************************************************
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$ ./case.build
Building case in directory /home/yangx2/my_cesm_sandbox/cime/scripts/b.e20.B1850.f19_g17.test
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Generating component namelists as part of build
Creating component namelists
Calling /home/yangx2/my_cesm_sandbox/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /home/yangx2/my_cesm_sandbox/cime/scripts/b.e20.B1850.f19_g17.test/Buildconf/camconf/atm_in file2 /mnt/scratch/nfs_fs02/yangx2/b.e20.B1850.f19_g17.test/run/atm_in
Calling /home/yangx2/my_cesm_sandbox/components/clm//cime_config/buildnml
ERROR: Command /home/yangx2/my_cesm_sandbox/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /home/yangx2/my_cesm_sandbox/components/clm/bld /home/yangx2/my_cesm_sandbox/components/clm/bld /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib /home/yangx2/my_cesm_sandbox/components/clm/bld /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /home/yangx2/my_cesm_sandbox/components/clm/bld/CLMBuildNamelist.pm line 413.
****************************************************************************************************************
I assume it probably is related to the Perl module, but I did not know how to solve it.
By the way, when I created another case (./create_newcase --case mycase --compset X --res f19_g16), it all worked. I submitted and got the output. Then I decided to change "--compsets" from "dead(X)" mode to "active" mode. And I get this error.

Thanks for your help!
Best,
Skylar

 

[yangx2]

By the way, I am running experiments on my university HPC, therefore I do not have root.

 

[zongy17]

Hi,
I am testing another experiment by setting :
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$./create_newcase --case b.e20.B1850.f19_g17.test --compset B1850 --res f19_g17
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$cd b.e20.B1850.f19_g17.test/
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$./case.setup
.[yangx2@node-0003 b.e20.B1850.f19_g17.test]$/case.build
Then I got this (below):

****************************************************************************************************************
[yangx2@node-0003 b.e20.B1850.f19_g17.test]$ ./case.build
Building case in directory /home/yangx2/my_cesm_sandbox/cime/scripts/b.e20.B1850.f19_g17.test
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Generating component namelists as part of build
Creating component namelists
Calling /home/yangx2/my_cesm_sandbox/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /home/yangx2/my_cesm_sandbox/cime/scripts/b.e20.B1850.f19_g17.test/Buildconf/camconf/atm_in file2 /mnt/scratch/nfs_fs02/yangx2/b.e20.B1850.f19_g17.test/run/atm_in
Calling /home/yangx2/my_cesm_sandbox/components/clm//cime_config/buildnml
ERROR: Command /home/yangx2/my_cesm_sandbox/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /home/yangx2/my_cesm_sandbox/components/clm/bld /home/yangx2/my_cesm_sandbox/components/clm/bld /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib /home/yangx2/my_cesm_sandbox/components/clm/bld /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /home/yangx2/my_cesm_sandbox/cime/utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /home/yangx2/my_cesm_sandbox/components/clm/bld/CLMBuildNamelist.pm line 413.
****************************************************************************************************************
I assume it probably is related to the Perl module, but I did not know how to solve it.
By the way, when I created another case (./create_newcase --case mycase --compset X --res f19_g16), it all worked. I submitted and got the output. Then I decided to change "--compsets" from "dead(X)" mode to "active" mode. And I get this error.

Thanks for your help!
Best,
Skylar

Hi, I got the same problem as you, but I met it during the phase ./case.submit
Do you solve the problem now?

 

[jrvb]

Hi Skylar -

My guess is that you'll need to install the perl XML libraries under your home dir. Something like the instructions here may help:

How can I install Perl modules without root privileges?
Installing Perl Modules as a Normal User

It looks like the XML::LibXML library needs some specific shared libraries installed on the system too, though:

Installing XML::LibXML — Perl XML::LibXML by Example documentation

Hence, the simplest may be to ask your systema admin if they are willing to install XML::LibXML globally. If that doesn't fly, you should be able to install the shared libraries in a local directory as well, and set the appropriate LD_LIBRARY_PATH variables and such so they can be found.

Best of luck!

-Rob