CESM

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This site replaces the former Compute Canada documentation site, and is now being managed by the Digital Research Alliance of Canada.

Ce site remplace l'ancien site de documentation de Calcul Canada et est maintenant géré par l'Alliance de recherche numérique du Canada.


This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.




Porting and Validating

The below configuration files and commands are designed for the module of CESM version 2.1.3: 

[name@server ~]$ module load cesm/2.1.3


Local machine file

  • Create and edit the file ~/.cime/config_machines.xml from the following minimal content per cluster:
    File : ~/.cime/config_machines.xml

    <?xml version="1.0"?>

<config_machines version="2.0">
  <machine MACH="beluga">
    <DESC>https://docs.alliancecan.ca/wiki/Béluga/en</DESC>
    <NODENAME_REGEX>b[cegl].*.int.ets1.calculquebec.ca</NODENAME_REGEX>

    <OS>LINUX</OS>
    <COMPILERS>intel,gnu</COMPILERS>
    <MPILIBS>openmpi,intelmpi</MPILIBS>

    <PROJECT>def-EDIT_THIS</PROJECT>
    <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT>

    <CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>40</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>40</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>

    <mpirun mpilib="default">
      <executable>srun</executable>
    </mpirun>
  </machine>

  <default_run_suffix>
    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
  </default_run_suffix>
</config_machines>


    File : ~/.cime/config_machines.xml

    <?xml version="1.0"?>

<config_machines version="2.0">
  <machine MACH="cedar">
    <DESC>https://docs.alliancecan.ca/wiki/Cedar</DESC>
    <NODENAME_REGEX>c[de].*.computecanada.ca</NODENAME_REGEX>

    <OS>LINUX</OS>
    <COMPILERS>intel,gnu</COMPILERS>
    <MPILIBS>openmpi,intelmpi</MPILIBS>

    <PROJECT>def-EDIT_THIS</PROJECT>
    <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT>

    <CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>48</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>48</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>

    <mpirun mpilib="default">
      <executable>srun</executable>
    </mpirun>
  </machine>

  <default_run_suffix>
    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
  </default_run_suffix>
</config_machines>


    File : ~/.cime/config_machines.xml

    <?xml version="1.0"?>

<config_machines version="2.0">
  <machine MACH="graham">
    <DESC>https://docs.alliancecan.ca/wiki/Graham</DESC>
    <NODENAME_REGEX>gra.*</NODENAME_REGEX>

    <OS>LINUX</OS>
    <COMPILERS>intel,gnu</COMPILERS>
    <MPILIBS>openmpi,intelmpi</MPILIBS>

    <PROJECT>def-EDIT_THIS</PROJECT>
    <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT>

    <CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>44</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>44</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>

    <mpirun mpilib="default">
      <executable>srun</executable>
    </mpirun>
  </machine>

  <default_run_suffix>
    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
  </default_run_suffix>
</config_machines>


    File : ~/.cime/config_machines.xml

    <?xml version="1.0"?>

<config_machines version="2.0">
  <machine MACH="narval">
    <DESC>https://docs.alliancecan.ca/wiki/Narval/en</DESC>
    <NODENAME_REGEX>n[acgl].*.narval.calcul.quebec</NODENAME_REGEX>

    <OS>LINUX</OS>
    <COMPILERS>intel,gnu</COMPILERS>
    <MPILIBS>openmpi,intelmpi</MPILIBS>

    <PROJECT>def-EDIT_THIS</PROJECT>
    <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT>

    <CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>64</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>64</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>

    <mpirun mpilib="default">
      <executable>srun</executable>
    </mpirun>
  </machine>

  <default_run_suffix>
    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
  </default_run_suffix>
</config_machines>


    File : ~/.cime/config_machines.xml

    <?xml version="1.0"?>

<config_machines version="2.0">
  <machine MACH="niagara">
    <DESC>https://docs.alliancecan.ca/wiki/Niagara</DESC>
    <NODENAME_REGEX>nia.*.scinet.local</NODENAME_REGEX>

    <OS>LINUX</OS>
    <COMPILERS>intel,gnu</COMPILERS>
    <MPILIBS>openmpi,intelmpi</MPILIBS>

    <PROJECT>def-EDIT_THIS</PROJECT>
    <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT>

    <CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>
    <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>40</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>40</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>

    <mpirun mpilib="default">
      <executable>srun</executable>
    </mpirun>
  </machine>

  <default_run_suffix>
    <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
    <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1 </default_run_misc_suffix>
  </default_run_suffix>
</config_machines>


  • Validate your XML machine file with the following commands: 
    [name@server ~]$ xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml
/home/name/.cime/config_machines.xml validates

    [name@beluga ~]$ query_config --machines current
beluga (current) : https://docs.alliancecan.ca/wiki/Béluga/en
      os              LINUX
      compilers       intel,gnu
      pes/node        40
      max_tasks/node  40
  • Check the official template for additional parameters: 
    [name@server ~]$ less $EBROOTCESM/cime/config/xml_schemas/config_machines_template.xml

Local batch file

  • Create and edit the file ~/.cime/config_batch.xml from the following minimal content:
    File : ~/.cime/config_batch.xml

    <?xml version="1.0"?>

<config_batch version="2.1">
  <batch_system type="slurm">
    <batch_submit>sbatch</batch_submit>
    <submit_args>
      <arg flag="--time" name="$JOB_WALLCLOCK_TIME"/>
      <arg flag="--account" name="$PROJECT"/>
    </submit_args>
    <directives>
      <directive>--mem=0</directive>
    </directives>
    <queues>
      <queue default="true">default</queue>
    </queues>
  </batch_system>
</config_batch>


  • Validate your XML machine file with the following commands: 
    [name@server ~]$ xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
/home/name/.cime/config_batch.xml validates
  • Check the documentation for additional configuration parameters and examples.

Creating a test case

The following command assumes the default model cesm and the current machine: 

[name@server ~]$ create_newcase --case test_case --compset IHistClm50Bgc --res f19_g17


Reference

Retrieved from "https://docs.alliancecan.ca/mediawiki/index.php?title=CESM&oldid=143338"