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Error in porting clm5 and creating a new case

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Error in porting clm5 and creating a new case

Hi, everyone! I am new fro porting CLM5 on a Linux platform. When I did a out-of-the-box case using the following command in cime/scripts/.

./create_newcase --case qian-20190102 --compset I1PtClm45SpGs  --res f19_g16 --mach xyz --run-unsupported --debug

There is an error

RUN: /usr/bin/xmllint --noout --schema /stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/config/xml_schemas/config_compsets.xsd /stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/../cime_config/config_compsets.xml

  stat: -11


> /stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/lib/CIME/

-> try:

(Pdb) q

Traceback (most recent call last):

  File "./create_newcase", line 210, in <module>


  File "./create_newcase", line 205, in _main_func

    input_dir=input_dir, driver=driver)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/", line 1453, in create

    input_dir=input_dir, driver=driver)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/", line 787, in configure

    compset_name, files)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/", line 453, in _set_compset

    compsets = Compsets(compsets_filename)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 18, in __init__

    GenericXML.__init__(self, infile, schema=schema)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 56, in __init__, schema)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 87, in read

    self.validate_xml_file(infile, schema)

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 460, in validate_xml_file

    run_cmd_no_fail("{} --noout --schema {} {}".format(xmllint, schema, filename))

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/", line 453, in run_cmd_no_fail

    expect(False, "Command: '{}' failed with error '{}' from dir '{}'".format(cmd, errput.encode('utf-8'), os.getcwd() if from_dir is None else from_dir))

  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/", line 107, in expect


  File "/stor9000/apps/users/NWSUAF/2014011989/CLM5/clm5/cime/scripts/Tools/../../scripts/lib/CIME/", line 107, in expect


  File "/stor9000/apps/appsoftware/python2.7.10/lib/python2.7/", line 49, in trace_dispatch

    return self.dispatch_line(frame)

  File "/stor9000/apps/appsoftware/python2.7.10/lib/python2.7/", line 68, in dispatch_line

    if self.quitting: raise BdbQuit



Now, I have no idea about this error. I have tried xmllint --noout --schema ../../config/xml_schemas/config_machines.xsd config_machines.xml to find the error but got another error:

Segmentation fault.


I attached my create_newcase.log and config_machines.xml.


May you have a look at my problem? Thank you very much!

Work hard

I experienced similar errors in my early stages of porting CLM5. It is usually caused by some error in the config_* files, like missing or duplicated xml tags. I would recommend starting from scratch and carefully double-checking each change you make in the files.

Thiago V. dos Santos
Postdoctoral Fellow
Department of Climate and Space Sciences and Engineering
University of Michigan

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