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--- howto:r [2015/05/04 11:30]
dane Updated for PBSPro
+++ howto:r [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
 ====== Using R ======
-**R** is installed in ''/opt/gridware/applications/R/R-3.1.3/'' and is compiled using openmpi 1.6.5 with the GNU compilers. Simply adding:
+**R** has been installed in ''/apps/chpc/bio/R/?'' and is compiled using openmpi and the GNU compilers. R modules have been created so simply adding:
 <code>
-export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH
+module add chpc/R/3.2.3-gcc5.1.0
-module add R/3.1.3
 </code>
-to your **''.bashrc''**  file in your home directory will set up the appropriate paths to R, the compilers (if you want to add your own R packages) and the mpi libraries. Note that there are several versions of R installed and can be seen by running the: <code>module avail</code> command.
+to your scripts will set up the appropriate paths to R, the compilers (if you want to add your own R packages) and the mpi libraries. Note that there may be several versions of R installed and can be seen by running the: <code>module avail 2>&1 | grep "R"</code> command.
-==== Changes to .profile file ====
-On the CHPC clusters the ''.bashrc'' file is not automatically run for interactive logins, only the ''.profile'' file is.  To rectify this add the following lines to the **end** of your ''.profile'' file:
+===== Parallel R =====
-<code bash>
+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.**
-if [ -f ~/.bashrc ]; then
-    . ~/.bashrc
-fi
-</code>
-Then make any changes to the ''PATH'' variable in your ''.bashrc'' file.
+Once you've created your R script file, called ''myScRipt.r'', you will need to create a job script file to submit to the PBSPro scheduler.
-=====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.
-Once you've created your R script file, called '''myScRipt.r''', you will need to create a job script file to submit to the Moab scheduler.
 Example job script file:
@@ Line 32: / Line 19: @@
 <file bash my_R_job.qsub>
 #!/bin/bash
-#PBS -l select=2:ncpus=12:jobtype=dell,place=excl
+#PBS -l select=2:ncpus=24:mpiprocs=24
-#PBS -l walltime=1:00:00
+#PBS -P SHORTNAME
-#PBS -q workq
+#PBS -q normal
-#PBS -V
+#PBS -l walltime=4:00:00
-#PBS -o /export/home/username/scratch5/my_R_data/stdout.txt
+#PBS -o /mnt/lustre/users/USERNAME/my_R_data/stdout.txt
-#PBS -e /export/home/username/scratch5/my_R_data/stderr.txt
+#PBS -e /mnt/lustre/users/USERNAME/my_R_data/stderr.txt
 #PBS -N RJob
 #PBS -M myemailaddress@someplace.com
 #PBS -m abe
-# make sure appropriate R module is available
-source /etc/profile.d/modules.sh
-MODULEPATH=/opt/gridware/bioinformatics/modules:${MODULEPATH}
 # Add R module (includes appropriate openMPI and gcc modules)
-module add R/3.1.3
+module add chpc/R/3.2.3-gcc5.1.0
 # explicitly calculate number of processes.
@@ Line 52: / Line 36: @@
 # make sure we're in the correct working directory.
-cd /export/home/username/scratch5/my_R_data
+cd /mnt/lustre/users/USERNAME/my_R_data
-mpirun -np $nproc -machinefile $PBS_NODEFILE  R --slave -f /export/home/username/scratch5/my_R_data/myScRipt.r
+mpirun -np $nproc -machinefile $PBS_NODEFILE  R --slave -f myScRipt.r
 </file>
 **Notes:**
-  * Replace ''username'' with **your** user name.
+  * Replace ''USERNAME'' with **your** user name.
+  * Replace ''SHORTNAME'' with **your research programme's** short name.
   * Replace ''myemailaddress@someplace.com'' with **your** email address.
-  * And replace ''my_R_data'' with your program's //working directory// (which **must** be on ''scratch'').
+  * 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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