Changes between Initial Version and Version 1 of cypress/R

Timestamp:

08/19/15 14:38:32 (9 years ago)

Author:

cmaggio

Comment:

—

cypress/R

@@ +1 @@
+[[PageOutline]]
+
+= Running R on Cypress = 
+
+== Python Modules ==
+As of August 18th, 2015 there is one version of R installed on Cypress in the module
+
+* R/3.1.2
+
+== Installing Packages ==
+
+
+== Running R Interactively ==
+
+Start an interactive session using idev
+
+{{{
+[tulaneID@cypress1 pp-1.6.4]$ idev 
+Requesting 1 node(s)  task(s) to normal queue of defq partition
+1 task(s)/node, 20 cpu(s)/task, 2 MIC device(s)/node
+Time: 0 (hr) 60 (min).
+Submitted batch job 52311
+Seems your requst is pending.
+JOBID=52311 begin on cypress01-035
+--> Creating interactive terminal session (login) on node cypress01-035.
+--> You have 0 (hr) 60 (min).
+[tulaneID@cypress01-035 pp-1.6.4]$ 
+}}}
+
+Load the R module
+
+{{{
+[tulaneID@cypress01-035 pp-1.6.4]$ module load R/3.1.2
+[tulaneID@cypress01-035 pp-1.6.4]$ module list
+Currently Loaded Modulefiles:
+  1) git/2.4.1           3) idev                5) R/3.1.2
+  2) slurm/14.03.0       4) bbcp/amd64_rhel60
+}}}
+
+Run R in the command line window
+
+{{{
+[tulaneID@cypress01-035 pp-1.6.4]$R
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> 
+
+}}}
+
+== Running a R script in Batch mode ==
+
+You can also submit your Python job to the batch nodes (compute nodes) on Cypress. Inside your SLURM script, include a command to load the desired Python module. Then invoke '''python''' on your python script.
+
+{{{#!bash
+#!/bin/bash
+#SBATCH --qos=workshop          # Quality of Service
+#SBATCH --partition=workshop    # Partition
+#SBATCH --job-name=R            # Job Name
+#SBATCH --time=00:01:00         # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI processes)
+#SBATCH --cpus-per-task=1       # Number of threads per task (OMP threads)
+
+module load R/3.1.2
+python myRscript.py
+}}}
+
+== Running a Parallel R Job ==
+