CESM

Revision as of 20:35, 7 September 2023 by Plstonge (talk | contribs) (Updated machine files and new batch file)

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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

Local machine file

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

BelugaCedarGrahamNarvalNiagara

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 ~]$ module load cesm/2.1.3 && xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml
/home/username/.cime/config_machines.xml validates

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 ~]$ module load cesm/2.1.3 && xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
/home/username/.cime/config_batch.xml validates

Check the documentation for additional configuration parameters and examples.

Reference

Main website
- CESM Quickstart Guide (CESM2.1)
- CESM Coupled Model XML Files

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