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--- howto:r [2016/04/05 11:31]
dane updated for new cluster
+++ howto:r [2021/12/09 16:42] (current)
@@ Line 9: / Line 9: @@
-=====Parallel R=====
+===== Parallel R =====
 The ''Rmpi'', ''doMPI'' and other packages are already installed to allow R to use MPI to distribute its work across multiple nodes of the cluster. **Please submit a request to helpdesk should you need any other packages installed.**
@@ Line 19: / Line 19: @@
 <file bash my_R_job.qsub>
 #!/bin/bash
-#PBS -l select=10:ncpus=24:mpiprocs=24:nodetype=haswell_reg
+#PBS -l select=2:ncpus=24:mpiprocs=24
 #PBS -P SHORTNAME
 #PBS -q normal
@@ Line 47: / Line 47: @@
   * And replace ''my_R_data'' with your program's //working directory// (which **must** be under ''/mnt/lustre/users/USERNAME/'').
   * And change ''myScRipt.r'' to be your //script file name//.
+===Running the script===
+Submit to the scheduler
+<code>
+qsub my_R_job.qsub
+</code>
+Check the list of current jobs in the queue
+<code>
+qstat -w
+</code>
+==== R/bioconductor ====
+Here is a more complete example
+=== pbdR example ===
+== Job scripts ==
+<file bash pbdtest.qsub>
+#PBS -l select=2:ncpus=24:mpiprocs=24:place=excl
+#PBS -l walltime=00:01:00
+#PBS -q normal
+#PBS -P SHORTNAME
+#PBS -M YOUREMAILADDRESS
+#PBS -m be
+#PBS -e /mnt/luster/users/USERNAME/pbdR_test/std_err.txt
+#PBS -o /mnt/lustre/users/USERNAME/pbdR_test/std_out.txt
+#PBS -N PBDR_TEST
+#PBS -mb
+module add chpc/R/3.2.3-gcc5.1.0
+NP=`cat ${PBS_NODEFILE} | wc -l`
+cd /mnt/lustre/users/USERNAME/pbdR_test/
+mpirun -np ${NP} -machinefile ${PBS_NODEFILE} Rscript test_script.R
+</file>
+Note: __USERNAME__ should contain your actual user name!
+<file R test_script.R>
+library(pbdMPI, quiet=TRUE)
+init()
+my.rank <- comm.rank()
+comm.print(my.rank, all.rank=TRUE)
+finalize()
+</file>
+== Submit your job ==
+Finally submit your job using:<code bash>user@login01:~ $ qsub pbdtest.qsub</code>

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