home.md

@@ -1541,6 +1541,145 @@ You can load R with one of the modules:
 * statistical/R/4.0.0/gcc.8.3.1
 * statistical/RStudio/1.2.5033/gcc-8.3.1
 
+#### Running R interactively
+
+```
+[username@res-hpc-lo01 ~]$ salloc -N1 -n1
+salloc: Pending job allocation 386499
+salloc: job 386499 queued and waiting for resources
+salloc: job 386499 has been allocated resources
+salloc: Granted job allocation 386499
+salloc: Waiting for resource configuration
+salloc: Nodes res-hpc-exe017 are ready for job
+
+[username@res-hpc-exe017 ~]$ module add statistical/R/4.0.0/gcc.8.3.1
+[username@res-hpc-exe017 ~]$ R
+
+R version 4.0.0 (2020-04-24) -- "Arbor Day"
+...
+Type 'q()' to quit R.
+
+> q()
+Save workspace image? [y/n/c]: n
+
+[username@res-hpc-exe017 ~]$ exit
+exit
+salloc: Relinquishing job allocation 386499
+salloc: Job allocation 386499 has been revoked.
+```
+
+#### Running a R script in batch mode
+
+HelloWorld.R
+```
+print ("Hello world!")
+```
+
+myscript.sh
+```
+#!/bin/bash
+
+#SBATCH --job-name=HelloWord            # Job name
+#SBATCH --output=slurm.out              # Output file name
+#SBATCH --error=slurm.err               # Error file name
+#SBATCH --partition=short               # Partition
+#SBATCH --time=00:05:00                 # Time limit 
+#SBATCH --nodes=1                       # Number of nodes
+#SBATCH --ntasks-per-node=1             # MPI processes per node
+
+module purge
+module add statistical/R/4.0.0/gcc.8.3.1
+
+Rscript --vanilla HelloWorld.R
+```
+
+* sbatch myscript.sh
+Submitted batch job 386860
+
+[username@res-hpc-lo01 R]$ cat slurm.out 
+[1] "Hello world!"
+
+
+driver.R
+```
+x <- rnorm(50)
+cat("My sample from N(0,1) is:\n")
+print(x)
+```
+
+run.slurm
+```
+#!/bin/bash
+
+#SBATCH --job-name=serialR              # Job name
+#SBATCH --output=slurm.out              # Output file name
+#SBATCH --error=slurm.err               # Error file name
+#SBATCH --partition=short               # Partition
+#SBATCH --time=00:05:00                 # Time limit 
+#SBATCH --nodes=1                       # Number of nodes
+#SBATCH --ntasks-per-node=1             # MPI processes per node
+
+module purge
+module add statistical/R/4.0.0/gcc.8.3.1
+
+Rscript driver.R
+```
+
+```
+[username@res-hpc-lo01 R]$ sbatch run.slurm 
+Submitted batch job 386568
+
+[username@res-hpc-lo01 R]$ ls -l
+total 78
+-rw-r--r-- 1 username Domain Users  59 Jun  5 11:42 driver.R
+-rw-r--r-- 1 username Domain Users 483 Jun  5 11:42 run.slurm
+-rw-r--r-- 1 username Domain Users   0 Jun  5 11:43 slurm.err
+-rw-r--r-- 1 username Domain Users 671 Jun  5 11:43 slurm.out
+
+[username@res-hpc-lo01 R]$ cat slurm.out 
+My sample from N(0,1) is:
+ [1]  0.32241013 -0.78250675 -0.28872991  0.12559634 -0.29176358  0.57962942
+ [7] -0.38277807 -0.21266343  0.86537064  1.06636737  0.96487417  0.31699518
+[13]  0.38003556  0.78275327 -0.85745177 -1.47682958 -0.16192662  0.09207091
+[19] -0.64508782  1.01504976 -0.07736039 -1.08819811  1.17762738 -0.22819258
+[25]  0.79564029  1.36863520 -0.63137494 -0.58452239 -0.96832479 -1.56506037
+[31]  1.68344229  1.03967058 -0.20854621  1.39479829 -0.95509839  0.80826154
+[37] -0.89781029  0.99954821 -1.25047597 -1.11034908 -1.10759254  1.32150663
+[43] -0.04589279 -0.62886137  0.63947415  0.18295622  0.63929410  0.16774740
+[49]  0.92311091 -0.13370228
+```
+
+```
+[username@res-hpc-lo01 R]$ scontrol show job 386568
+JobId=386568 JobName=serialR
+   UserId=username(225812) GroupId=Domain Users(513) MCS_label=N/A
+   Priority=449759 Nice=0 Account=dnst-ict QOS=normal
+   JobState=COMPLETED Reason=None Dependency=(null)
+   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
+   RunTime=00:00:02 TimeLimit=00:05:00 TimeMin=N/A
+   SubmitTime=2020-06-05T11:43:02 EligibleTime=2020-06-05T11:43:02
+   AccrueTime=2020-06-05T11:43:02
+   StartTime=2020-06-05T11:43:02 EndTime=2020-06-05T11:43:04 Deadline=N/A
+   SuspendTime=None SecsPreSuspend=0 LastSchedEval=2020-06-05T11:43:02
+   Partition=short AllocNode:Sid=res-hpc-ma01:27472
+   ReqNodeList=(null) ExcNodeList=(null)
+   NodeList=res-hpc-gpu01
+   BatchHost=res-hpc-gpu01
+   NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
+   TRES=cpu=1,mem=2G,node=1,billing=1
+   Socks/Node=* NtasksPerN:B:S:C=1:0:*:* CoreSpec=*
+   MinCPUsNode=1 MinMemoryCPU=2G MinTmpDiskNode=0
+   Features=(null) DelayBoot=00:00:00
+   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
+   Command=/home/username/R/run.slurm
+   WorkDir=/home/username/R
+   StdErr=/home/username/R/slurm.err
+   StdIn=/dev/null
+   StdOut=/home/username/R/slurm.out
+   Power=
+   MailUser=(null) MailType=NONE
+```
+
 #### Running R parallel
 
 Unfornately, "R" is not very efficient when running on a HPC cluster. Basically every R instance is running on only 1 core.