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---+!! Setup a CESM 1.0.x benchmark run on a generic Linux system
%TOC%

This is a *cookbook* to setup a CESM 1.0 benchmark run on a generic Linux system. This page is *still work in progress*, but will give already an idea what has to be done.
See also porting CESM in the CESM user's guide: http://www.cesm.ucar.edu/models/cesm1.0/cesm/cesm_doc/c2161.html


---++ Compile NETCDF (Requirement)
   * See also http://www.ncl.ucar.edu/Download/build_from_src.shtml#NetCDF

   * Download NETCDF 
 <verbatim>
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
</verbatim>


   * Compile netcdf with the compiler you use later to compile the model. For example for intel compiler do:
 <verbatim>
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
make test
</verbatim>

   * Install NETCDF
 <verbatim>
make install
</verbatim>

---++ Download CESM source code

   * From SVN. Password needed to checkout. Please register at: http://www.cesm.ucar.edu/models/cesm1.0/register/register_cesm1.0.cgi
 <verbatim>
svn export https://svn-ccsm-release.cgd.ucar.edu/model_versions/cesm1_0_2 cesm1_0_2
</verbatim>
 

---++ Adapt configuration files
   * Change to ==Machines== directory
 <verbatim>
cd cesm1_0_2
cd scripts/ccsm_utils/Machines/
</verbatim>

   * 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.

   * For example modify brutus_io, brutus_im, brutus_po, brutus_pm to fit the local environment. (i=intel, p=pgi, o=openmpi, m=mvapich2). For example if you have intel and openmpi start with ==*.brutus_io== files:
 <verbatim>
emacs env_machopts.brutus_io
emacs Macros.brutus_io
emacs mkbatch.brutus_io
</verbatim>

   * Modify ==config_machines.xml== and set the following variables. For example for brutus_io :
 <verbatim>
EXEROOT=                     # working directory, final location of binary, output files
DIN_LOC_ROOT_CSMDATA=        # input data
DIN_LOC_ROOT_CLMQIAN=        # input data
MAX_TASKS_PER_NODE=          # how many cores per node?
</verbatim>


---++ Compile and setup simulation

   * Change to ==scripts== directory
 <verbatim>
cd cesm1_0_2
cd scripts
</verbatim>

   * Define a case name (can be any name), for example 2° resolution (1.9x2.5_gx1v6), fully coupled model (B), running with intel (i) and openmpi (o)
 <verbatim>
CASE=1.9x2.5_gx1v6-B-benchmark-io
</verbatim>

   * Define the machine type, resolution, compset
 <verbatim>
MACH=brutus_im
RES=1.9x2.5
COMP=B
</verbatim>

   * Create case
 <verbatim>
./create_newcase -res $RES -compset $COMP -mach $MACH -case $CASE
</verbatim>

   * Change into case directory
 <verbatim>
cd $CASE
</verbatim>

   * Define layout, for example run with 128 task on 128 cores
 <verbatim>
NTASKS=128
./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 $NTASKS
./xmlchange -file env_mach_pes.xml -id TOTALPES   -val $NTASKS
</verbatim>

   * Simulation should run for 1 month and no restart files should be produced:
 <verbatim>
./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 never
</verbatim>

   * Configure case
 <verbatim>
./configure -case
</verbatim>

   * Build/Compile the model
 <verbatim>
./$CASE.$MACH.build
</verbatim>


---++ Run the model

   * Run the model, for example with LSF queuing system
 <verbatim>
bsub < $CASE.$MACH.run
</verbatim>

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


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Changed by UrsBeyerle on 15 Feb 2011 - 16:49 - r1
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