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xml.etree.ElementTree.ParseError: not well-formed (invalid token): error after adding a new grid to CLM

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akhtert

Tanjila Akhter
New Member
Hello,

I am trying to add new land, atm, and rtm grid to my CLM.

I added the grid alias, domain files for lnd and rof, and mapping files for atm<>lnd and lnd<>rof. I am getting error in creating new case as below:

Compset longname is 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV
Compset specification file is /glade/work/akhtert/CLM5_gw/clm5/cime/../cime_config/config_compsets.xml
Traceback (most recent call last):
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./create_newcase", line 220, in <module>
_main_func(__doc__)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./create_newcase", line 208, in _main_func
case.create(casename, srcroot, compset, grid, user_mods_dir=user_mods_dir,
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1436, in create
self.configure(compset_name, grid_name, machine_name=machine_name,
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 781, in configure
grids = Grids(gridfile)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/grids.py", line 22, in __init__
GenericXML.__init__(self, infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__
self.read(infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd
self.tree = ET.parse(fd)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 1229, in parse
tree.parse(source, parser)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 580, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1433, column 14

I am getting the error below in ./query_config --grids:

Traceback (most recent call last):
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 350, in <module>
_main_func(__doc__)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 334, in _main_func
query_grids(long_output=args.long)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 31, in query_grids
grids = Grids(config_file)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/grids.py", line 22, in __init__
GenericXML.__init__(self, infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__
self.read(infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd
self.tree = ET.parse(fd)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 1229, in parse
tree.parse(source, parser)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 580, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1433, column 14

My config_grids.xml file is attached here. 'mygrid' is commented for the lines I added.
Any help regarding this will be highly appreciated!
 
A

akhtert

Tanjila Akhter
New Member
akhtert said:
Hello,

I am trying to add new land, atm, and rtm grid to my CLM.

I added the grid alias, domain files for lnd and rof, and mapping files for atm<>lnd and lnd<>rof. I am getting error in creating new case as below:

Compset longname is 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV
Compset specification file is /glade/work/akhtert/CLM5_gw/clm5/cime/../cime_config/config_compsets.xml
Traceback (most recent call last):
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./create_newcase", line 220, in <module>
_main_func(__doc__)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./create_newcase", line 208, in _main_func
case.create(casename, srcroot, compset, grid, user_mods_dir=user_mods_dir,
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1436, in create
self.configure(compset_name, grid_name, machine_name=machine_name,
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 781, in configure
grids = Grids(gridfile)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/grids.py", line 22, in __init__
GenericXML.__init__(self, infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__
self.read(infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd
self.tree = ET.parse(fd)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 1229, in parse
tree.parse(source, parser)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 580, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1433, column 14

I am getting the error below in ./query_config --grids:

Traceback (most recent call last):
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 350, in <module>
_main_func(__doc__)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 334, in _main_func
query_grids(long_output=args.long)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/./query_config", line 31, in query_grids
grids = Grids(config_file)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/grids.py", line 22, in __init__
GenericXML.__init__(self, infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__
self.read(infile, schema)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/glade/work/akhtert/CLM5_gw/clm5/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd
self.tree = ET.parse(fd)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 1229, in parse
tree.parse(source, parser)
File "/glade/u/home/akhtert/anaconda3/lib/python3.9/xml/etree/ElementTree.py", line 580, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1433, column 14

My config_grids.xml file is attached here. 'mygrid' is commented for the lines I added.
Any help regarding this will be highly appreciated!
Click to expand...
I figured out one problem and the case created! Thank you!
 
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