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Code Block

#!/bin/bash 
#SBATCH -n 13
#SBATCH -N 1
#SBATCH -t 60
#SBATCH -p regal
#SBATCH --mem-per-cpu=3750
#SBATCH --mail-type=ALL 
#EOC
#------------------------------------------------------------------------------
#              Harvard Biogeochemistry of Global Pollutants Group             !
#------------------------------------------------------------------------------
#BOP
#
# !IROUTINE: run.mitgcm.13np.debug
#
# !DESCRIPTION: Script to run a debug MITgcm simulation with 13 CPUs.
#\\
#\\
# !CALLING SEQUENCE:
#  sbatch run.mitgcm.13np.debug       # To submit a batch job
#  ./run.mitgcm.hg.13np.debug         # To run in an interactive session
#
# !REMARKS:
#  Consider requesting an entire node (-N 6416 -n 1), which will prevent
#  outside jobs from slowing down your simulation.
#
#  Also note: Make your timestep edits in "data.debug_run", which will
#  automatically be copied to "data" by this script.
#
# !REVISION HISTORY:
#  17 Feb 2015 - R. Yantosca - Initial version
#EOP
#------------------------------------------------------------------------------
#BOC

# Make sure we apply the .bashrc_mitgcm settings
source ~/.bashrc_mitgcm

# Copy run-time parameter input files for the 13 CPU run
cp -f data.debug_run   data
cp -f data.exch2.13np  data.exch2

# Remove old output files
rm -f STDOUT.*
rm -f STDERR.*
rm -f PTRACER*

# Run MITgcm with 13 CPUs
time -p ( mpirun -np 13  ./mitgcmuv )
exit 0
#EOC

...

Code Block

#!/bin/bash 
#SBATCH -n 12896
#SBATCH -N 26
#SBATCH -t 1-00:00
#SBATCH -p regal
#SBATCH --mem-per-cpu=3750
#SBATCH --mail-type=ALL 

#EOC
#------------------------------------------------------------------------------
#              Harvard Biogeochemistry of Global Pollutants Group             !
#------------------------------------------------------------------------------
#BOP
#
# !MODULE: run.mitgcm.96np.20yr
#
# !DESCRIPTION: Script to submit a long (e.g. 20 yr) MITgcm simulation 
#  using 96 CPUs.
#\\
#\\
# !CALLING SEQUENCE:
#  sbatch run.mitgcm.96np.20yr    # To submit a batch job
#
# !REMARKS:
#  Consider requesting 26 entire nodes (-n 12896 -N 26), which will prevent
#  outside jobs from slowing down your simulation.
#
#  Also note: Make your timestep edits in "data.20yr_run", which will
#  automatically be copied to "data" by this script.
#
# !REVISION HISTORY:
#  17 Feb 2015 - R. Yantosca - Initial version
#EOP
#------------------------------------------------------------------------------
#BOC

# Make sure we apply the .bashrc_mitgcm settings
source ~/.bashrc_mitgcm

# Copy run-time parameter input files for the 96 CPU run
cp -f data.20yr_run    data
cp -f data.exch2.96np  data.exch2

# Remove old output files
rm -f STDOUT.*
rm -f STDERR.*
rm -f PTRACER.*

# Run MITgcm with 96 CPUs
time -p ( mpirun -np 96  ./mitgcmuv )
exit 0
#EOC

...

Gets the proper compiler and library settings from your ~/.bashrc_mitgcm file.
Reserves CPUs for the MITgcm run.
- NOTE: For MITgcm production runs, we recommend that you request 128 96 CPUs (i.e. 2 6 entire nodes) even though the MITgcm only uses 96. This will reserve both all nodes exclusively for your MITgcm simulation, and will prevent other Odyssey jobs from running on the same node and competing for resources.
Creates the proper data file for your simulation from a template. This file contains basic information for the simulation, including
- The number of timesteps for the simulation to run;
- How frequently diagnostics are saved to disk (i.e. dumpFreq);
- How frequenlty statistics are written to the log file (i.e. monitorFreq)
Creates the proper data.exch file for your simulation from a template.
- The data.exch file, which is described below, contains information about the tiles used for the horizontal grid specification.
Runs the MITgcm simulation and prints the user, cpu, and system time in seconds.

...

and if necessary, also increase the amount of run time that you are requesting (e.g.the #SBATCH -t setting).

Then submit the job to the queue:

Code Block
sbatch run.mitgcm.96np.myrun

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