Failed to create a case in CESM2 using out-of-box machine

[deepashree_dutta@student_unsw_edu_au]

Hi all,

I'm trying to create a case using CESM2 after editing config_machines.xml and config_compilers.xml files to use an out-of-box machine 'gadi'. I tried to create a case using:
./create_newcase --case /g/data/y99/dd7103/CESM2/case/Test --compset FHIST --res f09_f09_mg17

I don't understand the xml.etree.ElementTree.ParseError I got. Can anyone please suggest how to resolve this?

Compset specification file is /home/561/dd7103/CESM2/CESM/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
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 /home/561/dd7103/CESM2/CESM/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1979-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/share/domains/domain.ocn.fv0.9x1.25_gx1v7.151020.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Compset specific settings: name is RUN_TYPE and value is hybrid
Compset specific settings: name is RUN_REFCASE and value is f.e20.FHIST.f09_f09.cesm2_1.001_v2
Compset specific settings: name is RUN_REFDATE and value is 1979-01-01
Compset specific settings: name is RUN_REFDIR and value is cesm2_init
Traceback (most recent call last):
File "./create_newcase", line 218, in <module>
_main_func(__doc__)
File "./create_newcase", line 213, in _main_func
input_dir=input_dir, driver=driver, workflowid=workflow)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1448, in create
input_dir=input_dir, driver=driver, workflowid=workflowid)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 813, in configure
machobj = Machines(machine=machine_name)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/XML/machines.py", line 36, in __init__
GenericXML.__init__(self, infile, schema)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__
self.read(infile, schema)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/home/561/dd7103/CESM2/CESM/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd
self.tree = ET.parse(fd)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1196, in parse
tree.parse(source, parser)
File "/usr/lib64/python3.6/xml/etree/ElementTree.py", line 597, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: junk after document element: line 211, column 2

Thanks!

 

[jedwards]

Look at file config_machines.xml - according to the error message the file is corrupt at around line 211.
You can test the integrity of the xml file with the command:
xmllint --no-out --schema cime/config/xml_schemas/config_machines.xsd config_machines.xml