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

D

deepashree_dutta@student_unsw_edu_au

Member
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


When I checked the line 211 in ElementTree.py, it contains this function:
def __bool__(self):
warnings.warn(
"The behavior of this method will change in future versions. "
"Use specific 'len(elem)' or 'elem is not None' test instead.",
FutureWarning, stacklevel=2
)
return len(self._children) != 0 # emulate old behaviour, for now

Thanks!
 
J

jedwards

CSEG and Liaisons
Staff member
It looks like you have an error in config_machines.xml, this is usually caught by xmllint. emacs has a mode called nxml that will check that the file is valid.
 
D

deepashree_dutta@student_unsw_edu_au

Member
Hi Edwards,
Thanks for your reply!
I could solve that issue and create a case. But when I try to setup the case using ./case.setup I receive this error:

ERROR: Variable SUPPORTS_CXX is set ambiguously in config_build.xml. Check the file for these conflicting settings:
1: {}
2: {}

Do you have any idea why?
 
D

deepashree_dutta@student_unsw_edu_au

Member
Hi Edwards,

Running ./case.setup again solves that problem (I don't know how).

But when I run
./check_input_data --download I get
AttributeError: 'NoneType' object has no attribute 'getfile'

I checked: wget --no-check-certificate --user anonymous --password user@example.edu --spider ftp://ftp.cgd.ucar.edu/cesm/inputdata
This seems to work.

I'm enclosing here the error message for ./check_input_data and for wget commands as txt files.
Please let me know how to solve this issue and build the case.
Thanks!
 

Attachments

  • check_input_data.txt
    15.4 KB · Views: 6
  • wget.txt
    909 bytes · Views: 3
D

deepashree_dutta@student_unsw_edu_au

Member
Hi Edwards,

Thanks for your reply!
When I tried to build the case, I get the error:
ERROR: /home/561/dd7103/CESM2/CESM/cime/src/build_scripts/buildlib.pio FAILED, cat /g/data/y99/dd7103/CESM2/Test/bld/pio.bldlog.200521-074345

I checked the log file. The error I get is:
ERROR: CIME models require NETCDF in PIO build
I did include the netcdf path in the config_machine.xml and I'm using intel compiler and haven't changed anything in config_compiler.xml. Do I need to change something there?

I'm including here the config_machine.txt and the log file. Can you please have a look?
Thanks!
 

Attachments

  • pio_buildlog.txt
    45.3 KB · Views: 7
  • config_machine.txt
    2.3 KB · Views: 16
J

jedwards

CSEG and Liaisons
Staff member
Could NOT find NetCDF_Fortran you need to install the netcdf fortran build, it's easiest if you put it in the same path as the c libraries.
 
D

deepashree_dutta@student_unsw_edu_au

Member
jedwards said:
Could NOT find NetCDF_Fortran you need to install the netcdf fortran build, it's easiest if you put it in the same path as the c libraries.
Click to expand...
Hi Edwards,

Thank you for your reply!
I could solve that issue and build the case.
But I still get the same " AttributeError: 'NoneType' object has no attribute 'getfile' " when I submit the case.
The input files are missing. Please have a look at the txt file containing the complete message.

I contacted the help desk at my university. They are facing the similar problem in downloading the data.
Can you please suggest what should I do next?

Thanks!
 

Attachments

  • case_submit_error.txt
    19.8 KB · Views: 7
J

jedwards

CSEG and Liaisons
Staff member
Try reordering the download schemes in file config_inputdata.xml the first scheme in the file should be the first one attempted.
 
D

deepashree_dutta@student_unsw_edu_au

Member
jedwards said:
Try reordering the download schemes in file config_inputdata.xml the first scheme in the file should be the first one attempted.
Click to expand...
Hi Edwards,
Thanks a lot for your reply!

The order seemed to be fine.
I added a trailing slash at the end of input file and was able to download the input files in my first case. But when I tried to create another case I get the same error (I don't understand why the case was successfully created once and then fails thereafter).

I'm attaching the config_inputdata.xml and error message.
Can you please have a look and help me detect the issue?
 

Attachments

  • submit_message.txt
    6.3 KB · Views: 10
  • config_inputdata.txt
    1.4 KB · Views: 13
J

jedwards

CSEG and Liaisons
Staff member
This is a very strange path string: cisminputfile = '/g/data/y99//opt/Modules/v4.3.0/init/profile.sh{USER}/CESM2/inputs/glc/cism/Greenland/glissade/init/greenland_4km_epsg3413_c171126.nc'
I see from above that you have /g/data/$PROJECT/$USER/CESM2/inputs
It seems that the PROJECT is not resolving to a path.
 
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