Run Jobs on NERSC
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First, download the RMCProfile package on Linux platform here and untar it somewhere in our home directory. Once logged onto NERSC from terminal, we can do this,
cd SOMEWHERE wget https://yr.iris-home.net/rmclinux -O RMCProfile_V6.7.9_Linux_64.tgz tar xzvf RMCProfile_V6.7.9_Linux_64.tgz -
Prepare the job submission script -- see the example below -- and put the script to somewhere in your home directory. I would suggest put the script in the same directory where the RMC run will be happening so that we can easily keep track of which one is for which one.
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Several notes about the script,
3.1.
<YOUR_JOB_NAME>is a name that we can give to the running job, which can be any meaningful name to us.3.2.
<YOUR_OUTPUT_FILE>is the name for the output file of the running job, meaning that all the terminal output during the job running will go into this file.3.3.
<YOUR_EMAIL>is our email address -- status (e.g., started, or stopped, or failure, etc.) of the job will be sent to this email.3.4.
<FULL_PATH_TO_RMCPROFILE_PACKAGE>is the full path to the RMCProfile package directory.3.5.
<RMC_RUNNING_DIR>is the RMC running directory and<YOUR_RMC_STEM_NAME>is the stem name of the RMC setup. -
Submit the job by running
sbatch submit.slurmfrom where thesubmit.slurmscript is located, on the terminal.
| 1 | #!/bin/bash |
| 2 | #SBATCH --job-name=<YOUR_JOB_NAME> |
| 3 | #SBATCH --output=<YOUR_OUTPUT_FILE> |
| 4 | #SBATCH -t 24:00:00 |
| 5 | #SBATCH -N 1 |
| 6 | #SBATCH -q regular |
| 7 | #SBATCH -C cpu |
| 8 | #SBATCH --mail-user=<YOUR_EMAIL> |
| 9 | #SBATCH --mail-type=ALL |
| 10 | |
| 11 | #OpenMP settings: |
| 12 | export OMP_NUM_THREADS=8 |
| 13 | export OMP_PLACES=threads |
| 14 | export OMP_PROC_BIND=spread |
| 15 | |
| 16 | RMCProfile_PATH=<FULL_PATH_TO_RMCPROFILE_PACKAGE> |
| 17 | export PGPLOT_DIR=$RMCProfile_PATH/exe/libs |
| 18 | export LD_LIBRARY_PATH=$RMCProfile_PATH/exe/libs |
| 19 | export LIBRARY_PATH=$RMCProfile_PATH/exe/libs |
| 20 | export PATH=$PATH:$RMCProfile_PATH/exe |
| 21 | cd <RMC_RUNNING_DIR> |
| 22 | $RMCProfile_PATH/exe/rmcprofile <YOUR_RMC_STEM_NAME> |