CESM: Difference between revisions

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(Updated machine files and new batch file)
(Creating a test case)
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=Porting and Validating=
=Porting and Validating=
The below configuration files and commands are designed for the module of CESM version 2.1.3:
{{Command2
|prompt=[name@server ~]$
|module load cesm/2.1.3
}}


==Local machine file==
==Local machine file==
Line 224: Line 231:


{{Command2
{{Command2
|prompt=[name@server ~]$|module load cesm/2.1.3 && xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml
|prompt=[name@server ~]$
|xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml
|result=
/home/name/.cime/config_machines.xml validates
}}
{{Command2
|prompt=[name@beluga ~]$
|query_config --machines current
|result=
|result=
/home/username/.cime/config_machines.xml validates
  beluga (current) : https://docs.alliancecan.ca/wiki/Béluga/en
      os              LINUX
      compilers      intel,gnu
      pes/node        40
      max_tasks/node  40
}}
}}
</li>
</li>
Line 271: Line 289:


{{Command2
{{Command2
|prompt=[name@server ~]$|module load cesm/2.1.3 && xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
|prompt=[name@server ~]$
|xmllint --noout --schema $EBROOTCESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
|result=
|result=
/home/username/.cime/config_batch.xml validates
/home/name/.cime/config_batch.xml validates
}}
}}
</li>
</li>
Line 279: Line 298:
<li>Check the documentation for additional <b>[https://esmci.github.io/cime/versions/maint-5.6/html/xml_files/cesm.html#cimeroot-config-cesm-machines configuration parameters and examples]</b>.</li>
<li>Check the documentation for additional <b>[https://esmci.github.io/cime/versions/maint-5.6/html/xml_files/cesm.html#cimeroot-config-cesm-machines configuration parameters and examples]</b>.</li>
</ul>
</ul>
==Creating a test case==
The following command assumes the default model <code>cesm</code> and the <code>current</code> machine:
{{Command2
|prompt=[name@server ~]$
|create_newcase --case test_case --compset IHistClm50Bgc --res f19_g17
}}


=Reference=
=Reference=

Revision as of 20:55, 7 September 2023


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"