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Setup a CESM 1.0.x benchmark run on a generic system

This is a cookbook to setup a CESM 1.0 benchmark run on a generic (Linux) system.
See also porting CESM in the CESM user's guide: http://www.cesm.ucar.edu/models/cesm1.0/cesm/cesm_doc/c2161.html

System requirements

  • Compilers known to work: intel 10.1, pgi 7.2, 8.0, 9.0, (pathscale 3.2)
  • MPI implementations known to work: openmpi 1.4, 1.5, mvapich2 1.4, 1.5
  • tcsh CESM setup scripts are written in tcsh

Compile NETCDF (Requirement)

  • Download NETCDF
    wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.1.tar.gz
    tar xfvz netcdf-4.1.1.tar.gz
    cd netcdf-4.1.1

  • Compile netcdf with the compiler you use later to compile the model. For example for intel compiler do:
    export FC=ifort
    export F77=ifort
    export F90=ifort
    export CPPFLAGS="-fPIC -DpgiFortran"
    ./configure --prefix=/usr/local/netcdf-4.1.1-intel --disable-netcdf-4 --disable-dap
    make test

  • Install NETCDF
    make install

Download CESM source code

Adapt configuration files

  • Change to Machines directory
    cd cesm1_0_2
    cd scripts/ccsm_utils/Machines/

  • Meaning of filenames

    Filename Purpose
    env_machopts.* Set environment: Can be used to set paths to compiler, MPI library, NETCDF library
    Macros.* Set compiler name and paths to MPI library, NETCDF library. Set compiler options
    mkbatch.* Setting for queuing system
    where * corresponds to a machine.

  • As starting point take configuration files of a machine that is close to your environment. For example if you run on Linux, have a look at brutus_io, brutus_im, brutus_po or brutus_pm where i=intel, p=pgi, o=openmpi, m=mvapich2. You can get a list of pre-configured machines with
    cd cesm1_0_2/scripts
    ./create_newcase -l

  • Let's assume you use intel and openmpi, start with *.brutus_io files:
    cp env_machopts.brutus_io env_machopts.your_machine
    cp Macros.brutus_io       Macros.your_machine
    cp mkbatch.brutus_io      mkbatch.your_machine

  • Add to config_machines.xml a configuration tag for your machine (your_machine) - only the important lines are listed below
    <machine MACH="your_machine"
             DESC="Test System"
             BATCHQUERY="qstat -f"
    please set the following variables:
    EXEROOT=                     # working directory, final location of binary and output files
    DIN_LOC_ROOT_CSMDATA=        # input data, date will be downloaded on the fly
    DIN_LOC_ROOT_CLMQIAN=        # input data, data will be downloaded on the fly
    MAX_TASKS_PER_NODE=          # define cores per node

  • Configure mpirun execution: Search in mkbatch.your_machine for the line starting the executable ccsm.exe and replace it with the correct mpirun command for your system, for example something like
    mpirun -np ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID
    # or
    mpirun -x LD_LIBRARY_PATH -np ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID

Create a new case

  • Change to scripts directory
    cd cesm1_0_2
    cd scripts

  • Define the machine type (MACH), resolution (RES), compset (COMP=B: fully coupled model)
    Possible values for RES are T31_gx3v7 (~3), 1.9x2.5_gx1v6 (2) or 0.9x1.25_gx1v6 (1).

  • Define a case name (in principle, can be any name)

  • Create case
    ./create_newcase -res $RES -compset $COMP -mach $MACH -case $CASE

Change the layout

  • The layout will define which model component (ATM, LND, ICE, OCN, CPL) will run on how many cores.
  • To change the layout you don't have to recreate the case (but you can if you like).
  • Change into case directory
    cd $CASE
  • Clean the case
    ./configure -cleanmach
  • Configure layout (all components will run on all cores)
    NTASKS=16 #or# NTASKS=32 #or# NTASKS=64 #or# NTASKS=128 #or# NTASKS=256 #or# NTASKS=512
    ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 1
    ./xmlchange -file env_mach_pes.xml -id TOTALPES   -val $NTASKS
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_OCN -val 0
  • Exception: For resolution T31_gx3v7 with NTASKS=32, NTASKS=64
    NTASKS=32 #or# NTASKS=64
    F=$(( $NTASKS / $NTASKS_TOTAL ))
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_GLC -val 0
    ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 1
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_ATM -val 0
    ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val $(( $NTASKS_ATM * $F ))
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_LND -val 0
    ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val $(( $NTASKS_LND * $F ))
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_ICE -val 0
    ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val $(( $NTASKS_ICE * $F ))
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_OCN -val $(( $NTASKS_ATM * $F ))
    ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val $(( $NTASKS_OCN * $F ))
    ./xmlchange -file env_mach_pes.xml -id ROOTPE_CPL -val 0
    ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val $(( $NTASKS_CPL * $F ))
    ./xmlchange -file env_mach_pes.xml -id TOTALPES   -val $NTASKS

Set simulation length

  • In general, CESM is hardwired to generate monthly average data. In principle this can be turned of but needs a lot of code changes. Therefore it's not considered here. The following two cases are suggested instead:

  • CASE 1: Run a short simulation (10 days) with producing no restart files (REST_OPTION=never) and no archiving (DOUT_S=FALSE)
    ./xmlchange -file env_run.xml -id STOP_OPTION -val 'ndays'
    ./xmlchange -file env_run.xml -id STOP_N      -val '10'
    ./xmlchange -file env_run.xml -id REST_OPTION -val 'never'
    ./xmlchange -file env_run.xml -id DOUT_S      -val 'FALSE'

  • CASE 2: Run a longer simulation (1 months) with producing restart files at the end
    ./xmlchange -file env_run.xml -id STOP_OPTION -val 'nmonths'
    ./xmlchange -file env_run.xml -id STOP_N      -val '1'
    ./xmlchange -file env_run.xml -id REST_OPTION -val '$STOP_OPTION'
    ./xmlchange -file env_run.xml -id DOUT_S      -val 'FALSE'

Configure the case

  • Configure case
    ./configure -case

Change history file output frequency of atmosphere model (cam)

  • CASE 1: leave the default which is monthly output data
  • CASE 2: change history file output frequency to one hour. Edit Buildconf/cam.buildnml.csh and set just after &cam_inparm the variable nhtfrq = -1
    cat Buildconf/cam.buildnml.csh
     nhtfrq  = -1
     absems_data            = '$DIN_LOC_ROOT/atm/cam/rad/abs_ems_factors_fastvx.c030508.nc'
    ALERT! In case you change Buildconf/cam.buildnml.csh, you can not go back by just deleting the lines. You have configure an new case with with ./create_newcase !

Build the case

  • Build and compile the model

Run the model

  • Run the model, for example with LSF queuing system
    bsub < $CASE.$MACH.run

  • To start without a queuing system just execute:

  • Timing results can be found after the run has been successfully completed in folder timing
    cat timing/ccsm_timing.$CASE.*
    Model Throughput:         6.39   simulated_years/day 

Change the resolution

  • Recommended resolutions are T31_gx3v7 (~3), 1.9x2.5_gx1v6 (2), 0.9x1.25_gx1v6 (1)
  • ALERT! Create for each resolutions a separate cases !

Produce a summary

  • Create performance matrix for CASE 1 and CASE 2. Fill in Model Throughput in simulated_years/day

  • CASE 1: Run a short simulation with producing almost no output (I/O) - Values are from brutus.ethz.ch

    resolution / layout (NTASKS) 16 32 64 128 192 256 512
    T31_gx3v7 12.0 18.3 26.9 -- -- -- --
    1.9x2.5_gx1v6 -- 2.27/2.60         --
    0.9x1.25_gx1v6 -- -- 1.88        

  • CASE 2: Run a longer simulation with producing hourly output data - Values are from brutus.ethz.ch

    resolution / layout (NTASKS) 16 32 64 128 192 256 512
    T31_gx3v7 7.9 10.8 13.6 -- -- -- --
    1.9x2.5_gx1v6 --           --
    0.9x1.25_gx1v6 -- --          


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