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Error in porting CESM2

F

fkc000@163_com

Member
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 siliconCompset longname is 2000_CAM60%WCTS_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAVCompset specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_compsets.xmlCompset forcing is 1972-2004ATM 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 ciceOCN component is DOCN   prescribed ocean modeROF component is MOSART: MOdel for Scale Adaptive River TransportGLC 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 componentESP component is Pes     specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_pes.xmlCompset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1x1_2000climo_c180511.ncTraceback (most recent call last):  File "./create_newcase", line 218, in     _main_func(__doc__)  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/case.py", line 1431, in create    input_dir=input_dir, driver=driver)  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 808, in configure    machobj = Machines(machine=machine_name)  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/machines.py", line 36, in __init__    GenericXML.__init__(self, infile, schema)  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__    self.read(infile, schema)  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read    self.read_fd(fd)  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd    self.tree = ET.parse(fd)  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1182, in parse    tree.parse(source, parser)  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 656, in parse    parser.feed(data)  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1642, in feed    self._raiseerror(v)  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror    raise errxml.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 ElementTree.py). 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!
 
J

jedwards

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

jedwards

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

jedwards

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

fkc000@163_com

Member
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.
 
F

fkc000@163_com

Member
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.
 
F

fkc000@163_com

Member
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.
 
J

jedwards

CSEG and Liaisons
Staff member
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.
 
J

jedwards

CSEG and Liaisons
Staff member
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.
 
J

jedwards

CSEG and Liaisons
Staff member
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.
 
J

jedwards

CSEG and Liaisons
Staff member
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.xmlafter the entry you have two lines in a row, remove one of them.  Then run the xmllint command again to make sure everything is okay.
 
J

jedwards

CSEG and Liaisons
Staff member
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.xmlafter the entry you have two lines in a row, remove one of them.  Then run the xmllint command again to make sure everything is okay.
 
J

jedwards

CSEG and Liaisons
Staff member
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.xmlafter the entry you have two lines in a row, remove one of them.  Then run the xmllint command again to make sure everything is okay.
 
X

xueyanzhang520@gmail_com

New Member
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?
 
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