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Warning

This is as a Lab Notebook which describes how to solve a specific problem at a specific time. Please keep this in mind as you read and use the content. Please pay close attention to the date, version information and other details.

CTSM and LILAC

CTSM (Community Terrestrial Systems Model) is a land model for geographic data. The latest version is built with LILAC (Lightweight Infrastructure for Land Atmosphere Coupling) to connect land models with atmosphere models.

Extensive documentation for CTSM, CESM et al. is available at https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html (CTSM-LILAC) and https://escomp.github.io/CESM/versions/master/html/index.html (CESM).

Installation on ICER

The installation of CTSM requires CESM (Community Earth System Model) and its dependencies to be installed first.

  1. Log in to a gateway node. Do not connect to a development node yet.

  2. Load git and Subversion.

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module purge
module load Subversion
module load git
  1. Clone the latest CESM release (2.2.2 as of this notebook) into your working directory.
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git clone -b release-cesm2.2.2 https://github.com/ESCOMP/cesm.git cesm-2.2.2
  1. Download the external packages for CESM (this will take time).
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cd cesm-2.2.2
./manage_externals/checkout_externals

  1. Connect to a development node (this is because CTSM uses Python to handle its dependencies, and the Subversion module does not have a new enough matching Python module.)

  2. Clone CTSM.

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cd ..
git clone https://github.com/ESCOMP/CTSM.git
  1. Download the external packages for CTSM.
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cd CTSM
./bin/git-fleximod update
  1. Load the required modules for building CTSM.
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module purge
module load ESMF/8.6.0-foss-2023a
module load CMake Python lxml Perl XML-LibXML PnetCDF git git-lfs
  1. Try building CTSM.
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./lilac/build_ctsm ../ctsm_build --os linux --compiler gnu --netcdf-path $EBROOTNETCDF --esmf-mkfile-path $EBROOTESMF/lib/esmf.mk --max-mpitasks-per-node 20 --pnetcdf-path $EBROOTPNETCDF --pio-filesystem-hints gpfs

Configuration

Warning

ESMF is compiled with the FOSS (GNU/GCC) toolchain. Make sure you specify the GNU gcc compiler when building your models.

CESM and CTSM use "machine files" to understand the environment they are running in. You will need to set up a config_machines.xml file containing the appropriate settings for ICER.

These files should be in this directory for a user $USER /mnt/home/$USER/.cime

config_machines.xml

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<?xml version="1.0"?>

<!-- This is a partial cime machine port which should be able to get
          through the case.build step. Trying to get further than that will
     cause problems, because various directory paths won't be set up
     properly.

     If you are looking at the template file: Variable names prefixed
     with a dollar sign will be replaced with machine-specific values. A
     double dollar sign gets replaced with a single dollar sign, so
     something like $MYVAR refers to the MYVAR cime variable.
     -->

<config_machines version="2.0">
  <machine MACH="dev-amd20">

    <!-- Text description of the machine -->
    <DESC>Temporary build information for a CTSM build</DESC>

    <!-- OS: the operating system of this machine. Passed to cppflags for
                  compiled programs as -DVALUE  recognized are LINUX, AIX, Darwin, CNL -->
    <OS>UBUNTU</OS>

    <!-- COMPILERS: compilers supported on this machine, comma seperated list, first is default -->
    <COMPILERS>gnu</COMPILERS>

    <!-- MPILIBS: mpilibs supported on this machine, comma seperated list,
                  first is default, mpi-serial is assumed and not required in
         this list.

         It appears that the particular value is not important here: all
         that matters is that we're self-consistent. (See
         https://github.com/ESMCI/cime/issues/3537)
    -->
    <MPILIBS>mpich</MPILIBS>

    <!-- CIME_OUTPUT_ROOT: Base directory for case output,
                  the case/bld and case/run directories are written below here -->
    <CIME_OUTPUT_ROOT>/mnt/scratch/$USER/</CIME_OUTPUT_ROOT>

    <!-- DIN_LOC_ROOT: location of the inputdata data directory
                  inputdata is downloaded automatically on a case by case basis as
         long as the user has write access to this directory. -->
    <DIN_LOC_ROOT>/mnt/scratch/$USER/</DIN_LOC_ROOT>

    <!-- DIN_LOC_ROOT_CLMFORC: override of DIN_LOC_ROOT specific to CLM
                  forcing data -->
    <DIN_LOC_ROOT_CLMFORC>$DIN_LOC_ROOT/</DIN_LOC_ROOT_CLMFORC>

    <!-- DOUT_S_ROOT: root directory of short term archive files, short term
               archiving moves model output data out of the run directory, but
      keeps it on disk-->
    <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

    <!-- GMAKE: gnu compatible make tool, default is 'gmake' -->
    <GMAKE>gmake</GMAKE>

    <!-- GMAKE_J: optional number of threads to pass to the gmake flag -->
    <GMAKE_J>12</GMAKE_J>

    <!-- BATCH_SYSTEM: batch system used on this machine,
                  supported values are: none, cobalt, lsf, pbs, slurm.

         This is irrelevant for this build-only port.
    -->
    <BATCH_SYSTEM>slurm</BATCH_SYSTEM>

    <!-- SUPPORTED_BY: contact information for support for this system
               this field is not used in code -->
    <SUPPORTED_BY>CTSM</SUPPORTED_BY>

    <!-- MAX_TASKS_PER_NODE: maximum number of threads*tasks per shared
                  memory node on this machine, should always be >=
         MAX_MPITASKS_PER_NODE.

         This is irrelevant for this build-only port.
    -->
    <MAX_TASKS_PER_NODE>28</MAX_TASKS_PER_NODE>

    <!-- MAX_MPITASKS_PER_NODE: number of physical PES per shared node
                  on this machine, in practice the MPI tasks per node will not
         exceed this value.
    -->
    <MAX_MPITASKS_PER_NODE>28</MAX_MPITASKS_PER_NODE>

    <!-- mpirun: The mpi exec to start a job on this machine, supported values
                  are values listed in MPILIBS above, default and mpi-serial.

         This is irrelevant for this build-only port.
    -->
    <mpirun mpilib="default">
      <!-- name of the exectuable used to launch mpi jobs -->
      <executable>srun</executable>
      <!-- arguments to the mpiexec command, the name attribute here is ignored-->
      <arguments>
              <!-- <arg name="anum_tasks"> -ntasks $TOTALPES</arg>
                        <arg name="labelstdout">-prepend-rank</arg>-->
        <arg name="num_tasks">--ntasks={{ total_tasks }}</arg>
      </arguments>
    </mpirun>

    <!-- module system: allowed module_system type values are:
                  module  http://www.tacc.utexas.edu/tacc-projects/mclay/lmod
         soft http://www.mcs.anl.gov/hs/software/systems/softenv/softenv-intro.html
         none

         For this build-only port, we don't specify a module system:
         instead, we assume that the user has loaded all relevant
         modules prior to starting the build. (Similarly, we assume that
         the user has set all relevant environment variables, so don't
         specify any environment variables here.)
      -->
    <module_system type="none"/>

    <environment_variables comp_interface="nuopc">
            <env name="ESMFMKFILE">/opt/software-current/2023.06/x86_64/generic/software/ESMF/8.6.0-foss-2023a/lib/esmf.mk</env>
            <env name="NETCDF_PATH">/opt/software-current/2023.06/x86_64/generic/software/netCDF/4.9.2-gompi-2023a</env>
            <env name="PNETCDF_PATH">/opt/software-current/2023.06/x86_64/generic/software/PnetCDF/1.12.3-gompi-2023a</env>
    </environment_variables>

  </machine>
</config_machines>

config_compiler.xml

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<?xml version="1.0" encoding="UTF-8"?>

<compiler COMPILER="gnu" MACH="dev-amd20">

</compiler>

config_batch.xml

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<?xml version="1.0"?>

 <batch_system type="slurm" MACH="dev-amd20">
    <batch_query per_job_arg="-j">squeue</batch_query>
    <batch_submit>sbatch</batch_submit>
    <batch_cancel>scancel</batch_cancel>
    <batch_directive>#SBATCH</batch_directive>
    <jobid_pattern>(\d+)$</jobid_pattern>
    <depend_string> --dependency=afterok:jobid</depend_string>
    <depend_allow_string> --dependency=afterany:jobid</depend_allow_string>
    <depend_separator>,</depend_separator>
    <walltime_format>%H:%M:%S</walltime_format>
    <!-- replace $USER with your username -->
    <batch_mail_flag>--mail-user=$USER@msu.edu</batch_mail_flag> 
    <batch_mail_type_flag>--mail-type=$USER@msu.edu</batch_mail_type_flag>
    <batch_mail_type>end</batch_mail_type>
    <directives>
      <directive> --job-name={{ job_id }}</directive>
      <directive> --nodes={{ num_nodes }}</directive>
      <directive> --ntasks-per-node={{ tasks_per_node }}</directive>
      <directive> --output={{ job_id }}   </directive>
      <directive> --time=02:00:00   </directive>
      <directive> --mem=205G                 </directive>
    </directives>
    <queues>
      <queue default="true"></queue>
    </queues>
  </batch_system>