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Some questions when I ./case.setup

zzwflood

zzwflood
New Member
I'm using the CLM5.0 model,after I used the command "./create_newcase --case fcama --compset I2010Clm50Sp --res f09_g17 --machine ubuntu --run-unsupported",then I got in the file of fcama to use "./case.setup",but it responded with error ---
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Machine/Decomp/Pes configuration has already been done ...skipping

ERROR: Command: '/home/zzwflood/CAMA/clm5.0/components/cism//cime_config/cism.template /home/zzwflood/CAMA/clm5.0/cime/scripts/fcama' failed with error 'b"cp: cannot stat '/home/zzwflood/CAMA/clm5.0/components/cism//source_cism/utils/build/generate_ncvars.py': No such file or directory\nERROR cism.build_usernl: cp /home/zzwflood/CAMA/clm5.0/components/cism//source_cism/utils/build/generate_ncvars.py /home/zzwflood/CAMA/clm5.0/cime/scripts/fcama/Buildconf/cismIOconf/ failed: 256"' from dir '/home/zzwflood/CAMA/clm5.0/cime/scripts/fcama'
I really don't know how to handle this question,I would appreciate it if you could help me!
 

zzwflood

zzwflood
New Member
Code:
./create_newcase --case fcama1 --compset I2010Clm50Sp --res f09_g17 --mach ubuntu --run-unsupported --compiler intel

Compset longname is 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /home/zzwflood/cesm2.1/cime/../components/clm//cime_config/config_compsets.xml
Compset forcing is
ATM component is  Data driven ATM  GSWP3v1 data set
LND component is clm5.0:Satellite phenology:
ICE component is Stub ice component
OCN component is Stub ocn component
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/zzwflood/cesm2.1/cime/../components/clm//cime_config/config_pes.xml
Could not find machine match for 'zzwflood' or 'zzwflood'
Machine is ubuntu
Pes setting: grid match    is l%0.9x1.25
Pes setting: grid          is a%0.9x1.25_l%0.9x1.25_oi%null_r%r05_g%gland4_w%null_m%gx1v7
Pes setting: compset       is 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV
Pes setting: tasks       is {'NTASKS_ATM': -4, 'NTASKS_LND': -4, 'NTASKS_ROF': -4, 'NTASKS_ICE': -4, 'NTASKS_OCN': -4, 'NTASKS_GLC': -4, 'NTASKS_WAV': -4, 'NTASKS_CPL': -4}
Pes setting: threads     is {'NTHRDS_ATM': 1, 'NTHRDS_LND': 1, 'NTHRDS_ROF': 1, 'NTHRDS_ICE': 1, 'NTHRDS_OCN': 1, 'NTHRDS_GLC': 1, 'NTHRDS_WAV': 1, 'NTHRDS_CPL': 1}
Pes setting: rootpe      is {'ROOTPE_ATM': 0, 'ROOTPE_LND': 0, 'ROOTPE_ROF': 0, 'ROOTPE_ICE': 0, 'ROOTPE_OCN': 0, 'ROOTPE_GLC': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0}
Pes setting: pstrid      is {}
Pes other settings: {}
Pes comments: none
Compset is: 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV
 Grid is: a%0.9x1.25_l%0.9x1.25_oi%null_r%r05_g%gland4_w%null_m%gx1v7
 Components in compset are: ['datm', 'clm', 'sice', 'socn', 'mosart', 'cism', 'swav', 'sesp', 'drv', 'dart']
Using project from config_machines.xml: none
No charge_account info available, using value from PROJECT
Using project from config_machines.xml: none
cesm model version found: release-cesm2.1.0
Batch_system_type is none
 Creating Case directory /home/zzwflood/cesm2.1/cime/scripts/fcama1
 
[B]./case.setup[/B]
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Creating batch scripts
Writing case.run script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
Creating user_nl_xxx files for components and cpl
If an old case build already exists, might want to run 'case.build --clean' before building
You can now run './preview_run' to get more info on how your case will be run
[B]./case.build[/B]

Building case in directory /home/zzwflood/cesm2.1/cime/scripts/fcama1
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
   Calling /home/zzwflood/cesm2.1/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/home/zzwflood/cesm2.1/output/inputdata//share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc", will attempt to download in check_input_data phase
   Calling /home/zzwflood/cesm2.1/components/clm//cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/sice/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/socn/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/components/mosart//cime_config/buildnml
File not found: frivinp_rtm = "/home/zzwflood/cesm2.1/output/inputdata//rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
   Running /home/zzwflood/cesm2.1/components/cism//cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/swav/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/sesp/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/buildnml
File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/0.9x1.25/map_0.9x1.25_nomask_to_0.5x0.5_nomask_aave_da_c120522.nc", will attempt to download in check_input_data phase
File not found: rof2lnd_fmapname = "lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_nomask_to_0.9x1.25_nomask_aave_da_c121019.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv0.9x1.25/map_fv0.9x1.25_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv0.9x1.25/map_fv0.9x1.25_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv0.9x1.25_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv0.9x1.25_aave.170429.nc", will attempt to download in check_input_data phase
Finished creating component namelists
Building gptl with output to file /home/zzwflood/cesm2.1/output/fcama1/bld/gptl.bldlog.221116-205338
   Calling /home/zzwflood/cesm2.1/cime/src/build_scripts/buildlib.gptl
ERROR: /home/zzwflood/cesm2.1/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/zzwflood/cesm2.1/output/fcama1/bld/gptl.bldlog.221116-205338
Sorry for that I reply so late,I download a whole package of CESM2.1,then checkout the externals successfully,and I created case,after ./case.build I got an error,Could you please help me to see how to solve this problem? Thank you very much for your help! The gptl.bldlog.221116-205338,config_machines.xml and config_compilers.xml are in the attach files.
 

Attachments

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zzwflood

zzwflood
New Member
I am sorry for that last file is wrong.The 2022-11.zip is new one.
 

Attachments

  • 2022-11.zip
    4.1 KB · Views: 3

oleson

Keith Oleson
CSEG and Liaisons
Staff member
I'm going to move this to the infrastructure forum, since this now seems like a porting problem.
 

jedwards

CSEG and Liaisons
Staff member
It doesn't seem to find the c compiler - can you send the contents of Macros.make from your case directory?
 

zzwflood

zzwflood
New Member
Code:
zzwflood@zzwflood:~/cesm2.1/cime/scripts/fcama1$ sudo ./case.setup --reset --debug
[sudo] password for zzwflood:
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_case.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_case.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_run.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_run.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_build.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_build.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_pes.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_mach_pes.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_mach_pes.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_batch.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_batch.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_batch.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_specific.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_mach_specific.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_mach_specific.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_archive.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_archive.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/env_archive.xml validates

Successfully cleaned batch script .case.run
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama1/LockedFiles/env_case.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama1/LockedFiles/env_case.xml validates

Creating batch scripts
Writing case.run script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
RUN: /home/zzwflood/cesm2.1/components/cism//cime_config/cism.template /home/zzwflood/cesm2.1/cime/scripts/fcama1
If an old case build already exists, might want to run 'case.build --clean' before building
RUN: echo -e '
' && env
You can now run './preview_run' to get more info on how your case will be run
Thank you very much for your reply. This is the result after running. I don't see any problem.
 

zzwflood

zzwflood
New Member
It's still running,but I got a file like before.I put it in the attachment.Could you please give me some advises from it?Thanks!!!
Code:
zzwflood@zzwflood:~/cesm2.1/cime/scripts/fcama3$ sudo ./case.build --debug
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_case.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_case.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_run.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_run.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_build.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_build.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_pes.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_pes.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_pes.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_batch.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_batch.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_batch.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_specific.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_specific.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_specific.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_archive.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_archive.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_archive.xml validates

Building case in directory /home/zzwflood/cesm2.1/cime/scripts/fcama3
sharedlib_only is False
model_only is False
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_pes.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/LockedFiles/env_mach_pes.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/LockedFiles/env_mach_pes.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/LockedFiles/env_case.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/LockedFiles/env_case.xml validates

Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
   Calling /home/zzwflood/cesm2.1/cime/src/components/data_comps/datm/cime_config/buildnml
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/entry_id_namelist.xsd /home/zzwflood/cesm2.1/cime/src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
  errput: /home/zzwflood/cesm2.1/cime/src/components/data_comps/datm/cime_config/namelist_definition_datm.xml validates

File not found: domainfile = "/home/zzwflood/cesm2.1/output/inputdata//share/domains/domain.lnd.fv1.9x2.5_gx1v7.170518.nc", will attempt to download in check_input_data phase
   Calling /home/zzwflood/cesm2.1/components/clm//cime_config/buildnml
RUN: /home/zzwflood/cesm2.1/components/clm/bld/build-namelist -cimeroot /home/zzwflood/cesm2.1/cime -infile /home/zzwflood/cesm2.1/cime/scripts/fcama3/Buildconf/clmconf/namelist -csmdata /home/zzwflood/cesm2.1/output/inputdata/ -inputdata /home/zzwflood/cesm2.1/cime/scripts/fcama3/Buildconf/clm.input_data_list -ignore_ic_year -namelist "&clm_inparm  start_ymd=00010101 / "  -use_case 2000_control -res 1.9x2.5  -clm_start_type default -envxml_dir /home/zzwflood/cesm2.1/cime/scripts/fcama3 -l_ncpl 48 -lnd_frac /home/zzwflood/cesm2.1/output/inputdata//share/domains/domain.lnd.fv1.9x2.5_gx1v7.170518.nc -glc_nec 10 -co2_ppmv 367.0 -co2_type constant -config /home/zzwflood/cesm2.1/cime/scripts/fcama3/Buildconf/clmconf/config_cache.xml -bgc sp -clm_accelerated_spinup off  -lnd_tuning_mode clm5_0_GSWP3v1  -mask gx1v7
  output: CLM adding use_case 2000_control defaults for var 'sim_year' with val '2000'
CLM adding use_case 2000_control defaults for var 'sim_year_range' with val 'constant'
CLM adding use_case 2000_control defaults for var 'stream_year_first_urbantv' with val '2000'
CLM adding use_case 2000_control defaults for var 'stream_year_last_urbantv' with val '2000'
CLM adding use_case 2000_control defaults for var 'use_case_desc' with val 'Conditions to simulate 2000 land-use'

  errput: File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/zzwflood/cesm2.1/components/clm/bld/CLMBuildNamelist.pm line 4209.

   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/sice/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/socn/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/components/mosart//cime_config/buildnml
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/entry_id_namelist.xsd /home/zzwflood/cesm2.1/components/mosart/cime_config/namelist_definition_mosart.xml
  errput: /home/zzwflood/cesm2.1/components/mosart/cime_config/namelist_definition_mosart.xml validates

File not found: frivinp_rtm = "/home/zzwflood/cesm2.1/output/inputdata//rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
   Running /home/zzwflood/cesm2.1/components/cism//cime_config/buildnml
RUN: /home/zzwflood/cesm2.1/components/cism//cime_config/buildnml /home/zzwflood/cesm2.1/cime/scripts/fcama3
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_case.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_case.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_run.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_run.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_entry_id.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_build.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_build.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_pes.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_pes.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_pes.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_batch.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_batch.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_batch.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_mach_specific.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_specific.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_mach_specific.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/env_archive.xsd /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_archive.xml
  errput: /home/zzwflood/cesm2.1/cime/scripts/fcama3/env_archive.xml validates

   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/swav/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/components/stub_comps/sesp/cime_config/buildnml
   Calling /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/buildnml
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/entry_id_namelist.xsd /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_drv.xml
  errput: /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_drv.xml validates

File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_1.9x2.5_nomask_to_0.5x0.5_nomask_aave_da_c120522.nc", will attempt to download in check_input_data phase
File not found: rof2lnd_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_nomask_to_1.9x2.5_nomask_aave_da_c120709.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/config_grids_v2.xsd /home/zzwflood/cesm2.1/cime/config/cesm/config_grids.xml
  errput: /home/zzwflood/cesm2.1/cime/config/cesm/config_grids.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/entry_id_namelist.xsd /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_drv_flds.xml
  errput: /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_drv_flds.xml validates

RUN: /usr/bin/xmllint --noout --schema /home/zzwflood/cesm2.1/cime/config/xml_schemas/entry_id_namelist.xsd /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_modelio.xml
  errput: /home/zzwflood/cesm2.1/cime/src/drivers/mct/cime_config/namelist_definition_modelio.xml validates

Finished creating component namelists
Building gptl with output to file /home/zzwflood/cesm2.1/output/fcama3/bld/gptl.bldlog.221117-232448
   Calling /home/zzwflood/cesm2.1/cime/src/build_scripts/buildlib.gptl
 

Attachments

  • gptl.bldlog(1).zip
    807 bytes · Views: 2

jedwards

CSEG and Liaisons
Staff member
The Macros.make file is created at line 102 of file cime/scripts/lib/CIME/case/case_setup.py.
You can add a print statement to make sure it is being called:
print("Create Macros.make file")
that print should show up in the output of ./case.setup --reset
right after this line: Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
if you are familiar with python debugging you can try
adding the lines
import pdb
pdb.set_trace()
there and stepping into the configure subroutine with the debugger.

The code that writes the Macros file is in cime/scripts/lib/CIME/XML/compilers.py
 

zzwflood

zzwflood
New Member
Code:
zzwflood@zzwflood:~/cesm2.1/cime/scripts/fcama3$ sudo ./case.setup --reset
[sudo] password for zzwflood:
Successfully cleaned batch script .case.run
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Create Macros.make file
Creating batch scripts
Writing case.run script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/zzwflood/cesm2.1/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
If an old case build already exists, might want to run 'case.build --clean' before building
You can now run './preview_run' to get more info on how your case will be run
zzwflood@zzwflood:~/cesm2.1/cime/scripts/fcama3$ sudo ./case.setup --reset
> /home/zzwflood/cesm2.1/cime/scripts/lib/CIME/XML/compilers.py(16)<module>()
-> logger = logging.getLogger(__name__)
(Pdb)
Sorry,I'm not familiar with python...:(
 

jedwards

CSEG and Liaisons
Staff member
Just to make sure that you have the most up to date version it should be clm5.0.35 - is it?
 

zzwflood

zzwflood
New Member
It's part of CESM2.1.It seems to be Community Land Surface Model (CLM) science version 5.0.0.From the README.
Code:
$CTSMROOT/README                                          06/08/2018

Community Land Surface Model (CLM) science version 5.0.0  series -- source code, tools,
offline-build and test scripts. This gives you everything you need
to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in
place of a modeled atmosphere.
 

jedwards

CSEG and Liaisons
Staff member
try updating to the latest in the cesm2.1 series:
cd cesm2.1
git checkout cesm2.1-alphabranch
git pull origin cesm2.1-alphabranch
./manage_externals/checkout_externals
 

zzwflood

zzwflood
New Member
Dear Jedwards,after your help,my model had the Macros.make.But I have CLM5.0(release-clm5.0.35-4-g9399250c0) & cesm2.1(release-cesm2.1.0).And I didn't create .cime under the root directory,I just change the config_compilers.xml and config_machines.xml separately.
sudo ./case.build & ./case.build had different errors...but I got the Macros.make,you can see it in the attachment.
./create_newcase --case xxx --compset I2000Clm50Sp --res f19_g17 --mach ubuntu --compiler intel --run-unsupported
First,it's CLM5.0-------
Code:
zzwflood@zzwflood:~/CAMA/clm5.0/cime/scripts/fcama6$ sudo ./case.build
Building case in directory /home/zzwflood/CAMA/clm5.0/cime/scripts/fcama6
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/home/zzwflood/CAMA/clm5.0/output/inputdata/share/domains/domain.lnd.fv1.9x2.5_gx1v7.181205.nc", will attempt to download in check_input_data phase
   Calling /home/zzwflood/CAMA/clm5.0/cime_config/buildnml
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/components/stub_comps/sice/cime_config/buildnml
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/components/stub_comps/socn/cime_config/buildnml
   Calling /home/zzwflood/CAMA/clm5.0/components/mosart//cime_config/buildnml
File not found: frivinp_rtm = "/home/zzwflood/CAMA/clm5.0/output/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
   Running /home/zzwflood/CAMA/clm5.0/components/cism//cime_config/buildnml 
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/components/stub_comps/swav/cime_config/buildnml
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/components/stub_comps/sesp/cime_config/buildnml
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/drivers/mct/cime_config/buildnml
File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_1.9x2.5_nomask_to_0.5x0.5_nomask_aave_da_c120522.nc", will attempt to download in check_input_data phase
File not found: rof2lnd_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_nomask_to_1.9x2.5_nomask_aave_da_c120709.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
Finished creating component namelists
Building gptl with output to file /home/zzwflood/CAMA/clm5.0/output/fcama6/bld/gptl.bldlog.221118-211544
   Calling /home/zzwflood/CAMA/clm5.0/cime/src/build_scripts/buildlib.gptl
ERROR: /home/zzwflood/CAMA/clm5.0/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/zzwflood/CAMA/clm5.0/output/fcama6/bld/gptl.bldlog.221118-211544------------------------------------------------------------------------------------------------------------------------------------------------------------------
make -f /home/zzwflood/CAMA/clm5.0/cime/src/share/timing/Makefile install -C /home/zzwflood/CAMA/clm5.0/output/fcama6/bld/intel/intelmpi/nodebug/nothreads/gptl MACFILE=/home/zzwflood/CAMA/clm5.0/cime/scripts/fcama6/Macros.make MODEL=gptl GPTL_DIR=/home/zzwflood/CAMA/clm5.0/cime/src/share/timing GPTL_LIBDIR=/home/zzwflood/CAMA/clm5.0/output/fcama6/bld/intel/intelmpi/nodebug/nothreads/gptl SHAREDPATH=/home/zzwflood/CAMA/clm5.0/output/fcama6/bld/intel/intelmpi/nodebug/nothreads
make: Entering directory '/home/zzwflood/CAMA/clm5.0/output/fcama6/bld/intel/intelmpi/nodebug/nothreads/gptl'
mpiicc -c -I/home/zzwflood/CAMA/clm5.0/cime/src/share/timing -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -debug minimal -DFORTRANUNDERSCORE -DCPRINTEL -DHAVE_MPI /home/zzwflood/CAMA/clm5.0/cime/src/share/timing/gptl.c
/home/zzwflood/CAMA/clm5.0/cime/src/share/timing/Makefile:57: recipe for target 'gptl.o' failed
make: Leaving directory '/home/zzwflood/CAMA/clm5.0/output/fcama6/bld/intel/intelmpi/nodebug/nothreads/gptl'
make: mpiicc: Command not found
make: *** [gptl.o] Error 127
ERROR: make: mpiicc: Command not found

make: *** [gptl.o] Error 127
Second,it's cesm2.1--- the Macros.make of cesm2.1 is a strange type,you also can find it in the attachment.
Code:
zzwflood@zzwflood:~/CAMA/cesm2.1/cime/scripts/fcama5$ sudo ./case.build
Building case in directory /home/zzwflood/CAMA/cesm2.1/cime/scripts/fcama5
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/home/zzwflood/CAMA/cesm2.1/output/inputdata//share/domains/domain.lnd.fv1.9x2.5_gx1v7.170518.nc", will attempt to download in check_input_data phase
   Calling /home/zzwflood/CAMA/cesm2.1/components/clm//cime_config/buildnml
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/components/stub_comps/sice/cime_config/buildnml
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/components/stub_comps/socn/cime_config/buildnml
   Calling /home/zzwflood/CAMA/cesm2.1/components/mosart//cime_config/buildnml
File not found: frivinp_rtm = "/home/zzwflood/CAMA/cesm2.1/output/inputdata//rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
   Running /home/zzwflood/CAMA/cesm2.1/components/cism//cime_config/buildnml 
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/components/stub_comps/swav/cime_config/buildnml
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/components/stub_comps/sesp/cime_config/buildnml
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/drivers/mct/cime_config/buildnml
File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_1.9x2.5_nomask_to_0.5x0.5_nomask_aave_da_c120522.nc", will attempt to download in check_input_data phase
File not found: rof2lnd_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_0.5x0.5_nomask_to_1.9x2.5_nomask_aave_da_c120709.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
Finished creating component namelists
Building gptl with output to file /home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/gptl.bldlog.221118-211245
   Calling /home/zzwflood/CAMA/cesm2.1/cime/src/build_scripts/buildlib.gptl
ERROR: /home/zzwflood/CAMA/cesm2.1/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/gptl.bldlog.221118-211245-----------------------------------------------------------------------------------------------------------------------------------------------------------
make -f /home/zzwflood/CAMA/cesm2.1/cime/src/share/timing/Makefile install -C /home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/intel/intelmpi/nodebug/nothreads/gptl MACFILE=/home/zzwflood/CAMA/cesm2.1/cime/scripts/fcama5/Macros.make MODEL=gptl GPTL_DIR=/home/zzwflood/CAMA/cesm2.1/cime/src/share/timing GPTL_LIBDIR=/home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/intel/intelmpi/nodebug/nothreads/gptl SHAREDPATH=/home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/intel/intelmpi/nodebug/nothreads
make: Entering directory '/home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/intel/intelmpi/nodebug/nothreads/gptl'
mpiicc -c -I/home/zzwflood/CAMA/cesm2.1/cime/src/share/timing -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -debug minimal -DFORTRANUNDERSCORE -DCPRINTEL -DHAVE_MPI /home/zzwflood/CAMA/cesm2.1/cime/src/share/timing/gptl.c
/home/zzwflood/CAMA/cesm2.1/cime/src/share/timing/Makefile:55: recipe for target 'gptl.o' failed
make: Leaving directory '/home/zzwflood/CAMA/cesm2.1/output/fcama5/bld/intel/intelmpi/nodebug/nothreads/gptl'
make: mpiicc: Command not found
make: *** [gptl.o] Error 127
ERROR: make: mpiicc: Command not found

make: *** [gptl.o] Error 127
 

Attachments

  • Macros.make.zip
    1.7 KB · Views: 3

jedwards

CSEG and Liaisons
Staff member
It doesn't find mpiicc in your path - are you sure that you have the intel compiler and mpi libraries installed and available?
 
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