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Error in porting CESM2

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Error in porting CESM2

Hello there, I'm trying to build CESM2 in our server. But I couldn't even creat a new case. 

The result of create_newcase is like below:

./create_newcase --case test --compset FW2000 --res f09_g16 --machine silicon


Compset specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is CAM cam6 physics:WACCM with tropospheric, stratospheric, mesospheric, and lower thermospheric chemistry:

LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:

ICE component is Sea ICE (cice) model version 5 :prescribed cice

OCN component is DOCN   prescribed ocean mode

ROF component is MOSART: MOdel for Scale Adaptive River Transport

GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):

WAV component is Stub wave component

ESP component is 

Pes     specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_pes.xml

Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/

Traceback (most recent call last):

  File "./create_newcase", line 218, in <module>


  File "./create_newcase", line 213, in _main_func

    input_dir=input_dir, driver=driver)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/case/", line 1431, in create

    input_dir=input_dir, driver=driver)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/case/", line 808, in configure

    machobj = Machines(machine=machine_name)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 36, in __init__

    GenericXML.__init__(self, infile, schema)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 57, in __init__, schema)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 87, in read


  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/", line 112, in read_fd

    self.tree = ET.parse(fd)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/", line 1182, in parse

    tree.parse(source, parser)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/", line 656, in parse


  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/", line 1642, in feed


  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/", line 1506, in _raiseerror

    raise err

xml.etree.ElementTree.ParseError: mismatched tag: line 2313, column 6


Besides, when I run query_config and other executables in /scripts, similar errors occured(also traced back to So I guess there might be something wrong with my python 2.7, but python seemed work well and I don't know how to fix it. Should I build python2.7 again or a new python3.7?

Thank you in advance!


I think that there is a problem with something in your config_machines.xml file - do you have an xmllint program on your system?

CESM Software Engineer


Thank you for your reply.

Yes, we do have xmllint installed and the version of xmllint is 20908.

And the odd thing is, I got the same error even running query_config. I'm a little confused because running query_config should have nothing to do with config_machine.xml.


Query_config does parse the config_machines.xml file - please post that file and I'll try to spot the error.   You can add that file as an attachment here by adding a .txt to the filename.

CESM Software Engineer


Here's my config_machines.xml, and my machine name is silicon.

Thank you for your reply!


You have an error in this file - you should have seen it with the command 

xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_machines.xsd config_machines.xml

after the <cmd_path> entry you have two <modules> lines in a row, remove one of them.  Then run the xmllint command again to make sure everything is okay.

CESM Software Engineer


It worked! Thank you very very much!


Hi, I have the same error and I use your idea: xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_machines.xsd config_machines.xml to see the error in my config_machines.xml, but I got Segmentation fault (core dumped).

Work hard


Hi, I have the same error with you, but when I tried xmllint --noout --schema ../../../config/xml_schemas/config_machines.xsd config_machines.xml --debugent, I met an error: 

new input from file: ../../../config/xml_schemas/config_machines.xsd
Segmentation fault (core dumped)
 How to solve it?

Work hard


I'm not sure what the --debugent flag is about.   But you should be able to run the xmllint tool on the unmodified config_machines.xml file.   

Then add a little at a time until you find the error.

CESM Software Engineer


Sorry, I am not sure what you said the unmodified config_machines.xml file, you mean the original file in clm5?

Work hard

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