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---+!! Setup a CESM 1.0.x benchmark run on a generic 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

---++ 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



---++ 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

   * Download from NCAR SVN. A password is needed to checkout. Please register at: http://www.cesm.ucar.edu/models/cesm1.0/register/register_cesm1.0.cgi In case you don't have time to register ask urs.beyerle@env.ethz.ch
 <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.

   * As starting point take configuration files of a machine that is close to your environment. For example have a look at brutus_io, brutus_im, brutus_po or brutus_pm where i=intel, p=pgi, o=openmpi, m=mvapich2

   * Let's assume you use intel and openmpi, start with ==*.brutus_io== files:
 <verbatim>
cp env_machopts.brutus_io env_machopts.your_machine
cp Macros.brutus_io       Macros.your_machine
cp mkbatch.brutus_io      mkbatch.your_machine
</verbatim>

   * Add to ==config_machines.xml== a configuration tag for your machine (your_machine) - only the important lines are listed below
 <verbatim>
<machine MACH="your_machine"
         DESC="Test System"
         EXEROOT="/scratch/$CCSMUSER/$CASE"
         OBJROOT="$EXEROOT"
         INCROOT="$EXEROOT/lib/include" 
         DIN_LOC_ROOT_CSMDATA="/scratch/cesm1/inputdata"
         DIN_LOC_ROOT_CLMQIAN="/scratch/cesm1/inputdata/atm/datm7/atm_forcing.datm7.Qian.T62.c080727"
         BATCHQUERY="qstat -f"
         BATCHSUBMIT="qsub" 
         GMAKE_J="4" 
         MAX_TASKS_PER_NODE="4"
         MPISERIAL_SUPPORT="FALSE" />
</verbatim>
 please set the following variables:
 <verbatim>
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
</verbatim>

   * 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
 <verbatim>
mpirun -np ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID
# or
mpirun -x LD_LIBRARY_PATH -np ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID
</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)
 <verbatim>
CASE=1.9x2.5_gx1v6-B-benchmark
</verbatim>

   * Define the machine type, resolution, compset
 <verbatim>
MACH=your_machine
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>

   * 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 with producing almost no output (I/O) %BR%
  Simulation should run only for 20 days and no restart files should be produced at the end:
 <verbatim>
./xmlchange -file env_run.xml -id STOP_OPTION -val ndays
./xmlchange -file env_run.xml -id STOP_N      -val 20
./xmlchange -file env_run.xml -id REST_OPTION -val never
</verbatim>

   * *CASE 2*: Run a larger simulation with producing monthly (*better daily? - CKECK THIS*) output data %BR%
  Simulation should run for 2 months and restart files should be produced at the end:
 <verbatim>
./xmlchange -file env_run.xml -id STOP_OPTION -val nmonths
./xmlchange -file env_run.xml -id STOP_N      -val 2
./xmlchange -file env_run.xml -id REST_OPTION -val $STOP_N
</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>

   * To start without a queuing system just execute:
 <verbatim>
./$CASE.$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>


---++ Change the layout

   * To *change the layout* you don't have to recreate the case (but you can if you wish).
   * Change into case directory and re-define layout
 <verbatim>
cd $CASE
NTASKS=64
./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>
   * Clean the case and re-configure it 
 <verbatim>
./configure -cleanmach
./configure -case
</verbatim>

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

---++ Change the resolution
   * Recommended resolutions are T31_gx3v7 (~3°), 1.9x2.5_gx1v6 (2°), 0.9x1.25_gx1v6 (1°)
   * %X% To *change the resolution* create a *new* case !


---++ 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)
   |  *resolution / layout (NTASKS)*   |  16  |   32  |  64  |  128  |  256  |  512  |  1024 (a)  |
   | T31_gx3v7                         |      |       |      |       |   --  |   --  |  --    |
   | 1.9x2.5_gx1v6                     |  --  |       |      |       |       |       |  --    |
   | 0.9x1.25_gx1v6                    |  --  |  --   |      |       |       |       |        |

   * *CASE 2*: Run a larger simulation with producing monthly (*better daily? - CKECK THIS*) output data
   |  *resolution / layout (NTASKS)*   |  16  |   32  |  64  |  128  |  256  |  512  |  1024 (a)  |
   | T31_gx3v7                         |      |       |      |       |   --  |   --  |  --    |
   | 1.9x2.5_gx1v6                     |  --  |       |      |       |       |       |  --    |
   | 0.9x1.25_gx1v6                    |  --  |  --   |      |       |       |       |        |
 (a) *optional*

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Changed by UrsBeyerle on 22 Feb 2011 - 14:01 - r4
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