Introduction to Unix and SGE for beginners

How to use interactive sessions with qrsh

If you want to run an interactive session using software such as R or Matlab, you need to use qrsh to start an interactive session and similar to qsub you need to ask for specific resources. You may want to use screen command before you start your session so that after you logged out and if you left somethings running in your session you can re-attach your session. See [here] for screen usage tutorial. In addition, if your software needs X11 forwarding (for example you will need this for R plots) you need to ssh to login1 with -X option such as ssh username@login1 -X

Here is how you can start an R session using qrsh. The session directly starts R, and qrsh asks for 10G memory max and 5G memory should be available at the moment.

username@login1:~$ qrsh -V -l h_vmem=10G,mem_free=5G R

Alternatively, you can login to a suitable machine using qrsh and then start R. The qrsh reguests 3 slots and 5G per slot maximum memory (3*5=15G max memory).

username@login1:~ $  qrsh -now no -pe smp 3 -l  h_vmem=5G
local configuration login1.mdccluster not defined - using global configuration
aakalin@node023:~$ R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

A "particular" node can request by:

username@login1:~ $ qrsh -l h='node050' -now no ....
...
username@node050:~$