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...@@ -1541,6 +1541,145 @@ You can load R with one of the modules: ...@@ -1541,6 +1541,145 @@ You can load R with one of the modules:
* statistical/R/4.0.0/gcc.8.3.1 * statistical/R/4.0.0/gcc.8.3.1
* statistical/RStudio/1.2.5033/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salloc: Job allocation 386499 has been revoked.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 #### 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. Unfornately, "R" is not very efficient when running on a HPC cluster. Basically every R instance is running on only 1 core.
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