CESM: Difference between revisions

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(added config_compilers.xml file)
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{{draft}}
{{draft}}
"The [https://www.cesm.ucar.edu/ Community Earth System Model] is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states."


=Porting and Validating=
=Porting and Validating=
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<?xml version="1.0"?>
<?xml version="1.0"?>


<config_compilers version="2.0">
<compiler MACH="beluga">
<compiler MACH="beluga">
  <CPPDEFS>
  <CPPDEFS>
Line 539: Line 540:
  </SLIBS>
  </SLIBS>
</compiler>
</compiler>
</config_compilers>
}}
}}
</tab>
</tab>
Line 549: Line 549:
<?xml version="1.0"?>
<?xml version="1.0"?>


<config_compilers version="2.0">
<compiler MACH="cedar">
<compiler MACH="cedar">
  <CPPDEFS>
  <CPPDEFS>
Line 562: Line 561:
  </SLIBS>
  </SLIBS>
</compiler>
</compiler>
</config_compilers>
}}
}}
</tab>
</tab>
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<?xml version="1.0"?>
<?xml version="1.0"?>


<config_compilers version="2.0">
<compiler MACH="graham">
<compiler MACH="graham">
  <CPPDEFS>
  <CPPDEFS>
Line 585: Line 582:
  </SLIBS>
  </SLIBS>
</compiler>
</compiler>
</config_compilers>
}}
}}
</tab>
</tab>
Line 595: Line 591:
<?xml version="1.0"?>
<?xml version="1.0"?>


<config_compilers version="2.0">
<compiler MACH="narval">
<compiler MACH="narval">
  <CPPDEFS>
  <CPPDEFS>
Line 608: Line 603:
  </SLIBS>
  </SLIBS>
</compiler>
</compiler>
</config_compilers>
}}
}}
</tab>
</tab>
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<?xml version="1.0"?>
<?xml version="1.0"?>


<config_compilers version="2.0">
<compiler MACH="niagara">
<compiler MACH="niagara">
  <CPPDEFS>
  <CPPDEFS>
Line 631: Line 624:
  </SLIBS>
  </SLIBS>
</compiler>
</compiler>
</config_compilers>
}}
}}
</tab>
</tab>
</tabs>
</tabs>
==Checkout externals==
Before your first use of CESM, you may checkout the individual model components by running the checkout_externals script.
{{Command2
|prompt=[name@server ~]$
|/path/to/CESM/manage_externals/checkout_externals
}}
You may need to accept a certificate from the CESM repository to download input files.


==Creating a test case==
==Creating a test case==

Latest revision as of 14:14, 10 October 2024


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.




"The Community Earth System Model is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states."

Porting and Validating[edit]

The below configuration files and commands are designed for a local installation of CESM 2.1.5:

Before making the adaptations as described below, please download CESM 2.1.5 from the CESM developers in your local directory.

Local machine file[edit]

  • 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</MPILIBS>

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

    <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT>
    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <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="openmpi">
      <executable>mpirun</executable>
      <arguments>
        <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg>
      </arguments>
    </mpirun>
    <module_system type="module" allow_error="true">
      <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
      <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
      <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
      <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
      <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
      <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
      <cmd_path lang="csh">module</cmd_path>
      <cmd_path lang="sh">module</cmd_path>
      <modules>
      <command name="purge"/>
 	<command name="load">StdEnv/2023</command>
      </modules>
      <modules compiler="intel">
	<command name="load">intel/2023.2.1</command>
	<command name="load">git-annex/10.20231129</command>
	<command name="load">cmake/3.27.7</command>
      </modules>
      <modules mpilib="openmpi">
        <command name="load">openmpi/4.1.5</command>
        <command name="load">hdf5-mpi/1.14.2</command>
        <command name="load">netcdf-c++4-mpi/4.3.1</command>
        <command name="load">netcdf-fortran-mpi/4.6.1</command>
        <command name="load">netcdf-mpi/4.9.2</command>
	<command name="load">xml-libxml/2.0208</command>
	<command name="load">flexiblas/3.3.1</command>
      </modules>
    </module_system>
    <environment_variables>
            <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env>
            <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env>
            <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env>
            <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env>
	    <env name="OMP_STACKSIZE">256M</env>
            <env name="I_MPI_CC">icc</env>
            <env name="I_MPI_FC">ifort</env>
            <env name="I_MPI_F77">ifort</env>
            <env name="I_MPI_F90">ifort</env>
            <env name="I_MPI_CXX">icpc</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">300000000</resource>
    </resource_limits>
  </machine>
</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</MPILIBS>

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

    <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT>
    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <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="openmpi">
      <executable>mpirun</executable>
      <arguments>
        <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg>
      </arguments>
    </mpirun>
    <module_system type="module" allow_error="true">
      <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
      <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
      <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
      <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
      <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
      <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
      <cmd_path lang="csh">module</cmd_path>
      <cmd_path lang="sh">module</cmd_path>
      <modules>
      <command name="purge"/>
 	<command name="load">StdEnv/2023</command>
      </modules>
      <modules compiler="intel">
	<command name="load">intel/2023.2.1</command>
	<command name="load">git-annex/10.20231129</command>
	<command name="load">cmake/3.27.7</command>
      </modules>
      <modules mpilib="openmpi">
        <command name="load">openmpi/4.1.5</command>
        <command name="load">hdf5-mpi/1.14.2</command>
        <command name="load">netcdf-c++4-mpi/4.3.1</command>
        <command name="load">netcdf-fortran-mpi/4.6.1</command>
        <command name="load">netcdf-mpi/4.9.2</command>
	<command name="load">xml-libxml/2.0208</command>
	<command name="load">flexiblas/3.3.1</command>
      </modules>
    </module_system>
    <environment_variables>
            <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env>
            <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env>
            <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env>
            <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env>
	    <env name="OMP_STACKSIZE">256M</env>
            <env name="I_MPI_CC">icc</env>
            <env name="I_MPI_FC">ifort</env>
            <env name="I_MPI_F77">ifort</env>
            <env name="I_MPI_F90">ifort</env>
            <env name="I_MPI_CXX">icpc</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">300000000</resource>
    </resource_limits>
  </machine>
</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</MPILIBS>

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

    <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT>
    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <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="openmpi">
      <executable>mpirun</executable>
      <arguments>
        <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg>
      </arguments>
    </mpirun>
    <module_system type="module" allow_error="true">
      <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
      <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
      <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
      <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
      <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
      <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
      <cmd_path lang="csh">module</cmd_path>
      <cmd_path lang="sh">module</cmd_path>
      <modules>
      <command name="purge"/>
 	<command name="load">StdEnv/2023</command>
      </modules>
      <modules compiler="intel">
	<command name="load">intel/2023.2.1</command>
	<command name="load">git-annex/10.20231129</command>
	<command name="load">cmake/3.27.7</command>
      </modules>
      <modules mpilib="openmpi">
        <command name="load">openmpi/4.1.5</command>
        <command name="load">hdf5-mpi/1.14.2</command>
        <command name="load">netcdf-c++4-mpi/4.3.1</command>
        <command name="load">netcdf-fortran-mpi/4.6.1</command>
        <command name="load">netcdf-mpi/4.9.2</command>
	<command name="load">xml-libxml/2.0208</command>
	<command name="load">flexiblas/3.3.1</command>
      </modules>
    </module_system>
    <environment_variables>
            <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env>
            <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env>
            <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env>
            <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env>
	    <env name="OMP_STACKSIZE">256M</env>
            <env name="I_MPI_CC">icc</env>
            <env name="I_MPI_FC">ifort</env>
            <env name="I_MPI_F77">ifort</env>
            <env name="I_MPI_F90">ifort</env>
            <env name="I_MPI_CXX">icpc</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">300000000</resource>
    </resource_limits>
  </machine>
</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</MPILIBS>

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

    <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT>
    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <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="openmpi">
      <executable>mpirun</executable>
      <arguments>
        <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg>
      </arguments>
    </mpirun>
    <module_system type="module" allow_error="true">
      <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
      <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
      <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
      <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
      <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
      <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
      <cmd_path lang="csh">module</cmd_path>
      <cmd_path lang="sh">module</cmd_path>
      <modules>
      <command name="purge"/>
 	<command name="load">StdEnv/2023</command>
      </modules>
      <modules compiler="intel">
	<command name="load">intel/2023.2.1</command>
	<command name="load">git-annex/10.20231129</command>
	<command name="load">cmake/3.27.7</command>
      </modules>
      <modules mpilib="openmpi">
        <command name="load">openmpi/4.1.5</command>
        <command name="load">hdf5-mpi/1.14.2</command>
        <command name="load">netcdf-c++4-mpi/4.3.1</command>
        <command name="load">netcdf-fortran-mpi/4.6.1</command>
        <command name="load">netcdf-mpi/4.9.2</command>
	<command name="load">xml-libxml/2.0208</command>
	<command name="load">flexiblas/3.3.1</command>
      </modules>
    </module_system>
    <environment_variables>
            <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env>
            <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env>
            <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env>
            <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env>
	    <env name="OMP_STACKSIZE">256M</env>
            <env name="I_MPI_CC">icc</env>
            <env name="I_MPI_FC">ifort</env>
            <env name="I_MPI_F77">ifort</env>
            <env name="I_MPI_F90">ifort</env>
            <env name="I_MPI_CXX">icpc</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">300000000</resource>
    </resource_limits>
  </machine>
</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</MPILIBS>

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

    <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT>
    <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT>
    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <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="openmpi">
      <executable>mpirun</executable>
      <arguments>
        <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg>
      </arguments>
    </mpirun>
    <module_system type="module" allow_error="true">
      <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path>
      <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path>
      <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path>
      <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path>
      <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path>
      <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path>
      <cmd_path lang="csh">module</cmd_path>
      <cmd_path lang="sh">module</cmd_path>
      <modules>
      <command name="purge"/>
 	<command name="load">StdEnv/2023</command>
      </modules>
      <modules compiler="intel">
	<command name="load">intel/2023.2.1</command>
	<command name="load">git-annex/10.20231129</command>
	<command name="load">cmake/3.27.7</command>
      </modules>
      <modules mpilib="openmpi">
        <command name="load">openmpi/4.1.5</command>
        <command name="load">hdf5-mpi/1.14.2</command>
        <command name="load">netcdf-c++4-mpi/4.3.1</command>
        <command name="load">netcdf-fortran-mpi/4.6.1</command>
        <command name="load">netcdf-mpi/4.9.2</command>
	<command name="load">xml-libxml/2.0208</command>
	<command name="load">flexiblas/3.3.1</command>
      </modules>
    </module_system>
    <environment_variables>
            <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env>
            <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env>
            <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env>
            <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env>
	    <env name="OMP_STACKSIZE">256M</env>
            <env name="I_MPI_CC">icc</env>
            <env name="I_MPI_FC">ifort</env>
            <env name="I_MPI_F77">ifort</env>
            <env name="I_MPI_F90">ifort</env>
            <env name="I_MPI_CXX">icpc</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">300000000</resource>
    </resource_limits>
  </machine>
</config_machines>


  • Validate your XML machine file with the following commands: 
    [name@server ~]$ xmllint --noout --schema /path/to/CESM/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 /path/to/CESM/cime/config/xml_schemas/config_machines_template.xml

Local batch file[edit]

  • 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 /path/to/CESM/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.

Local compilers file[edit]

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

    <?xml version="1.0"?>

	<compiler MACH="beluga">
	  <CPPDEFS>
	    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
	  </CPPDEFS>
	  <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH>
	  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
	  <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH>
	  <SLIBS>
	    <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append>
	  </SLIBS>
	</compiler>


    File : ~/.cime/config_compilers.xml

    <?xml version="1.0"?>

	<compiler MACH="cedar">
	  <CPPDEFS>
	    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
	  </CPPDEFS>
	  <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH>
	  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
	  <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH>
	  <SLIBS>
	    <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append>
	  </SLIBS>
	</compiler>


    File : ~/.cime/config_compilers.xml

    <?xml version="1.0"?>

	<compiler MACH="graham">
	  <CPPDEFS>
	    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
	  </CPPDEFS>
	  <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH>
	  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
	  <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH>
	  <SLIBS>
	    <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append>
	  </SLIBS>
	</compiler>


    File : ~/.cime/config_compilers.xml

    <?xml version="1.0"?>

	<compiler MACH="narval">
	  <CPPDEFS>
	    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
	  </CPPDEFS>
	  <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH>
	  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
	  <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH>
	  <SLIBS>
	    <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append>
	  </SLIBS>
	</compiler>


    File : ~/.cime/config_compilers.xml

    <?xml version="1.0"?>

	<compiler MACH="niagara">
	  <CPPDEFS>
	    <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
	  </CPPDEFS>
	  <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH>
	  <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
	  <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH>
	  <SLIBS>
	    <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append>
	  </SLIBS>
	</compiler>


    Checkout externals[edit]

    Before your first use of CESM, you may checkout the individual model components by running the checkout_externals script. 

    [name@server ~]$ /path/to/CESM/manage_externals/checkout_externals

    You may need to accept a certificate from the CESM repository to download input files.


    Creating a test case[edit]

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

    [name@server ~]$ /path/to/CESM/cime/scripts/create_newcase --case test_case --compset IHistClm50Bgc --res f19_g17


    Reference[edit]

Message Passing Interface

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