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#!/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 64 -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 |
The run.mitgcm.96np.debug 20yr is similar except for the fact that it requests SLURM to give it more CPUs and a longer amount of run time:
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#!/bin/bash #SBATCH -n 128 #SBATCH -N 2 #SBATCH -t 601-00:00 #SBATCH -p regal #SBATCH --mem-per-cpu=3750 #SBATCH --mail-type=ALL #EOC #------------------------------------------------------------------------------ # Harvard Biogeochemistry of GEOS-Chem Global ChemicalPollutants Transport ModelGroup ! #------------------------------------------------------------------------------ #BOP # # !IROUTINEMODULE: run.mitgcm.96np.debug20yr # # !DESCRIPTION: Script to runsubmit a debug long (e.g. 20 yr) MITgcm Hgsimulation # simulation withusing 96 CPUs. #\\ #\\ # !CALLING SEQUENCE: # sbatch run.mitgcm.96np.debug20yr # To submit a batch job # # !REMARKS: # Consider requesting 2 entire nodes (-n 128 -N 2), which will prevent # outside jobs from slowing down your simulation. # # Also note: Make your timestep edits in "data.debug20yr_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.debug.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 |
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If you need to run MITgcm for a different amount of time, we recommend that you copy one of the existing data* files and edit the time stepping parameters accordingly.
Submitting a MITgcm
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simulation
10-hour debug run
To submit a 10-hour debugging run (on 13 CPUs), type the following commands:
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#### 10-hr debug Hg simulation #### cd MITgcm_code/ # Switch to main code directory cd verification/global_hg_llc90/run # Change to the Hg run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### 10-hr debug PFOS simulation #### cd MITgcm_code/ # Switch to main code directory cd verification/pfos/run # Change to the PFOS run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### 10-hr debug PCB simulation #### cd MITgcm_code/ # Switch to main code directory cd verification/pfos/run # Change to the PCB run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job |
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1-month run
To submit a 1-month MITgcm run (on 13 CPUs), type the following commands:
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#### 1-month Hg simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/global_hg_llc90/run # Change to the Hg run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### 1-month PFOS simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/pfos/run # Change to the PFOS run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### 1-month PCB simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/pfos/run # Change to the PCB run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job |
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20-year run
To submit a 20-year MITgcm simulation (on 96 CPUs), type the following commands:
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#### To run a debug Hg simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/global_hg_llc90/run # Change to the Hg run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### To run a debug PFOS simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/pfos/run # Change to the PFOS run directory sbatch run.mitgcm.13np.1month # Sets the proper data and data.exch files; submits job #### To run a debug PCB simulation ### cd MITgcm_code/ # Switch to main code directory cd verification/pcb/run # Change to the PCB run directory sbatch run.mitgcm.96np.20yr # Sets the proper data and data.exch files; submits job |
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Runs for other lengths of time
To run a MITgcm simulation for a different length of time:
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cp data.20yr_run data.myrun # Copy an existing data template file to a new file
cp run.mitgcm.96np.20yr run.mitgcm.96np.myrun # Copy an existing run.mitgcm* file to a new file |
Then in data.myrun, you can change the time stepping parameters (number of timesteps and frequency of diagnostic output) accordingly.
Lastly, in the new run file run.mitgcm.96np.myrun, change this line:
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Change this line from:
cp -f data.20yr_run datato:
cp -f data.myrun data |
and if necessary, also increase the amount of run time that you are requesting (e.g.the #SBATCH -t setting).