Differences

This shows you the differences between two versions of the page.

--- using_perun [2017/07/24 11:15] – cgeb2001
+++ using_perun [2021/09/08 13:29] (current) – 134.190.232.139
@@ Line 86: / Line 86: @@
-**#!/bin/sh**
+**#!/bin/bash**
-at the very top. This tells the UNIX system what type of shell to use (this one is the bourne shell). You could use other UNIX shells like csh or tcsh if you wanted to.
+at the very top. This tells the UNIX system what type of shell to use (this one is the Bourne-Again shell). You could use other UNIX shells like csh or tcsh if you wanted to.
 The next two lines should be
-**#$ -S /bin/sh**
+**#$ -S /bin/bash**
@@ Line 139: / Line 139: @@
 **qsub -q 144G-batch name_of_script** (nodes with 144 GB RAM, 24 slots per node (1))
 **qsub -q 16G-batch name_of_script** (nodes with 16 GB RAM, 8 slots per node (12))
-**qsub -q 256G0batch name_of _script**  (nodes with 256 GB RAM, 48 slots per node (2))
+**qsub -q 256G-batch name_of _script**  (nodes with 256 GB RAM, 48 slots per node (2))
@@ Line 154: / Line 154: @@
 This will list all the jobs currently being run on perun as well as who is logged in. To just see your jobs
+you would normally do qstat -u username but for some reason that doesn't work on perun so do
 **qstat | grep username**
+or
+**watch qstat** (control c to exit).
@@ Line 190: / Line 197: @@
 Finding the path of an installed program
-Most programs are installed in common, standard places on UNIX systems. On perun many of the programs/packages are installed in /opt/perun/ or /opt/perun/bin/
+Most programs are installed in common, standard places on UNIX systems. On perun many of the programs/packages are installed in /opt/perun/ or /opt/perun/bin/ or /scratch2/software/
@@ Line 239: / Line 246: @@
 		eg blastn -help
 . If all else fails you can try and read the program code (if it is in perl or python as opposed to  C or C++) and try and figure out what the authors want.