Difference between revisions of "Submit R jobs on Abel"
From mn/geo/geoit
(Created page with "<div class="vrtx-introduction"> This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at [http://www.uio.no/english/services/it/re...") |
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For normal off-line non-parallell R running on any Linux server, you can simply do e.g. | For normal off-line non-parallell R running on any Linux server, you can simply do e.g. | ||
<pre>module load R | <pre>module load R | ||
− | + | R CMD BATCH R_program.r | |
</pre> | </pre> | ||
For large jobs, this script should set you up OK at the Abel cluster: | For large jobs, this script should set you up OK at the Abel cluster: | ||
− | #!/bin/bash<br/># Job name:<br/>#SBATCH --job-name=R<br/>#<br/># Project (change to your :<br/>#SBATCH --account=geofag<br/>#<br/># Wall clock limit:<br/>#SBATCH --time=1000:0:0<br/>#<br/># Max memory usage per core (MB):<br/>#SBATCH --mem-per-cpu=2000M<br/>#<br/># Number of tasks (cores):<br/>#SBATCH --ntasks-per-cpu=12<br/># | + | <pre>#!/bin/bash<br/># Job name:<br/>#SBATCH --job-name=R<br/>#<br/># Project (change to your :<br/>#SBATCH --account=geofag<br/>#<br/># Wall clock limit:<br/>#SBATCH --time=1000:0:0<br/>#<br/># Max memory usage per core (MB):<br/>#SBATCH --mem-per-cpu=2000M<br/>#<br/># Number of tasks (cores):<br/>#SBATCH --ntasks-per-cpu=12<br/># |
− | ## Setup job environment<br/>source /cluster/bin/jobsetup | + | ##Setup job environment<br/>source /cluster/bin/jobsetup |
#Load R module | #Load R module | ||
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export OMP_NUM_<span id="cke_bm_104E" style="display: none" data-cke-bookmark="1"> </span>THREADS=12 | export OMP_NUM_<span id="cke_bm_104E" style="display: none" data-cke-bookmark="1"> </span>THREADS=12 | ||
− | + | module load R openmpi.gnu</pre><pre>mpirun -np 1 R CMD BATCH --no-save --no-restore R_program.r | |
− | #End of script | + | #End of script</pre> |
− | </pre> | + | |
− | [[Category:Tools]] | + | [[Category:Tools]] [[Category:Software]] [[Category:R]] [[Category:Abel]] |
Revision as of 11:01, 27 April 2015
This is an example of a Matlab submit script for use on the Abel cluster. Abel usage is documented at UiOs HPC pages
For normal off-line non-parallell R running on any Linux server, you can simply do e.g.
module load R R CMD BATCH R_program.r
For large jobs, this script should set you up OK at the Abel cluster:
#!/bin/bash<br/># Job name:<br/>#SBATCH --job-name=R<br/>#<br/># Project (change to your :<br/>#SBATCH --account=geofag<br/>#<br/># Wall clock limit:<br/>#SBATCH --time=1000:0:0<br/>#<br/># Max memory usage per core (MB):<br/>#SBATCH --mem-per-cpu=2000M<br/>#<br/># Number of tasks (cores):<br/>#SBATCH --ntasks-per-cpu=12<br/># ##Setup job environment<br/>source /cluster/bin/jobsetup #Load R module module load R<br/><br/>#Set variable with number of processors and load mpi export OMP_NUM_<span id="cke_bm_104E" style="display: none" data-cke-bookmark="1"> </span>THREADS=12 module load R openmpi.gnu
mpirun -np 1 R CMD BATCH --no-save --no-restore R_program.r
- End of script