creat new case error

[wannh]

I download CESM2.1.3 on my laptop and try to creat a new case,
cd cime/scripts/
./create_newcase --case ~/cases/b.day1.0 --res f19_g17 --compset B1850

the result show

Compset longname is 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO%ABIO-DIC_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD
Compset specification file is /home/wannh/CESM/cime/../cime_config/config_compsets.xml
Compset forcing is 1850
Com forcing is Biogeochemistry intercomponent with diagnostic CO2
ATM component is CAM cam6 physics:
LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:
ICE component is Sea ICE (cice) model version 5
OCN component is POP2 EcosystemAbiotic DIC/DIC14
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 Wave Watch
ESP component is
Pes specification file is /home/wannh/CESM/cime/../cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 0001-01-01
Compset specific settings: name is RUN_REFDATE and value is 0301-01-01
Compset specific settings: name is RUN_TYPE and value is hybrid
Compset specific settings: name is RUN_REFCASE and value is b.e20.B1850.f19_g17.release_cesm2_1_0.020
Compset specific settings: name is CLM_NAMELIST_OPTS and value is use_init_interp=.true.
ERROR: Makes no sense to have empty read-only file

how can I solve this problem? any suggests would be helpful.

 

[sacks]

Can you please send the results of running ./describe_version from the top level of your CESM checkout?

 

[wannh]

Can you please send the results of running ./describe_version from the top level of your CESM checkout?

attached is the results

 

[sacks]

Thanks. I see nothing unusual there. (I assume you intended to change config_compilers and config_machines for your case.)

Can you please edit the file cime/scripts/lib/CIME/XML/generic_xml.py, changing line 61 from this:

expect(not self.read_only, "Makes no sense to have empty read-only file")

to this:

expect(not self.read_only, "Makes no sense to have empty read-only file: {}".format(infile))

Then remove the case directory (~/cases/b.day1.0) and rerun your create_newcase command. This should tell us which file is causing the problem, which will hopefully help with tracking down the issue.

 

[wannh]

Thank you sir, according to your suggestion, the error happans in config_machines.xml file, I don't know where is the error of xml file, but I redownload the CESM code and run again, it succeed

 

[sacks]

Great, I'm glad it works for you now!

 

[wannh]

hi, sir, when I set up a new case with code:

./create_newcase --case ~/cases/b.day2.0 --res f19_g17 --compset B1850

the same error happen again：

Compset longname is 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO%ABIO-DIC_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD
Compset specification file is /home/wannh/CESM/cime/../cime_config/config_compsets.xml
Compset forcing is 1850
Com forcing is Biogeochemistry intercomponent with diagnostic CO2
ATM component is CAM cam6 physics:
LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:
ICE component is Sea ICE (cice) model version 5
OCN component is POP2 EcosystemAbiotic DIC/DIC14
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 Wave Watch
ESP component is
Pes specification file is /home/wannh/CESM/cime/../cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 0001-01-01
Compset specific settings: name is RUN_REFDATE and value is 0301-01-01
Compset specific settings: name is RUN_TYPE and value is hybrid
Compset specific settings: name is RUN_REFCASE and value is b.e20.B1850.f19_g17.release_cesm2_1_0.020
Compset specific settings: name is CLM_NAMELIST_OPTS and value is use_init_interp=.true.
ERROR: Makes no sense to have empty read-only file: /home/wannh/CESM/cime/config/cesm/machines/config_machines.xml

here is what I changed the config_machines.xml file. is there any wrong with my xml file?

<machine MACH="AGR-1711-WAN">
<DESC>
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
</DESC>
<NODENAME_REGEX>AGR-1711-WAN</NODENAME_REGEX>
<OS>LINUX</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>gnu</COMPILERS>
<MPILIBS>mpich</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/CESM/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>$ENV{HOME}/CESM/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/CESM/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$ENV{HOME}/CESM/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/CESM/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/CESM/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>8</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>8</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpiexec</executable>
<arguments>
<arg name="anum_tasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<mpirun mpilib="openmpi">
<executable>mpirun</executable>
<arguments>
<arg name="anum_tasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>

<module_system type="none"/>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
</machine>

 

[sacks]

Can you please attach the complete config_machines.xml file? That will be easier for me to see than this pasted version. Also, can you describe what (if anything) you changed between your successful case and this new, failed case?

 

[taoliu_tech]

I got the same error. Changing this line "expect(not self.read_only, "Makes no sense to have empty read-only file: {}".format(infile))" told me the error is due to the config_compilers.xml. It turned out I accidently put an extra space in the name of config_compilers.xml file. The file was wrongly named "config_compilers .xml', and the correct name is "config_compilers.xml". The difference is a space before .xml.