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using_perun [2017/06/02 09:14] – cgeb2001using_perun [2021/09/08 13:29] (current) – 134.190.232.139
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-**Accessing and Using Perun**+====== Accessing and Using Perun ====== 
  
 for an account contact  for an account contact 
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-**#!/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 The next two lines should be
  
  
-**#$ -S /bin/sh**+**#$ -S /bin/bash**
  
  
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 **qsub -q 144G-batch name_of_script** (nodes with 144 GB RAM, 24 slots per node (1)) **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 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))
  
  
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 This will list all the jobs currently being run on perun as well as who is logged in. To just see your jobs 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** **qstat | grep username**
 +
 +or 
 +
 +**watch qstat** (control c to exit).
 +
 +
  
  
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 If you do ls in the directory where you submitted the script myscript.x to the queue you will see that there is a file called something like this - myscript.x.e798764.  This is the error file associated with your submission and one is created every single time you submit something regardless of whether there are any errors. Usually this error file will be empty if the script/program runs successfully. However, sometimes it contains useful information generated by the script/program that has nothing to do with errors so once your process finishes you should check this file. The number after the e is the job_id of the process. If you do ls in the directory where you submitted the script myscript.x to the queue you will see that there is a file called something like this - myscript.x.e798764.  This is the error file associated with your submission and one is created every single time you submit something regardless of whether there are any errors. Usually this error file will be empty if the script/program runs successfully. However, sometimes it contains useful information generated by the script/program that has nothing to do with errors so once your process finishes you should check this file. The number after the e is the job_id of the process.
  
-You can have multiple perun sessions/terminals open at any one time. You can also remain logged in indefinitely. If you wish to exit you can close the terminal or else enter +You can have multiple perun sessions/terminals open at any one time. You can also remain logged in indefinitely. If you wish to exit you can close the terminal or else enter. 
 + 
 +**qalter -q [node you want, eg 256G-batch] [job ID number]** 
 + 
 +The command above can change the job's hard queue after submission (without killing it).
  
  
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 Finding the path of an installed program 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/
  
  
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  eg blastn -help  eg blastn -help
 4. 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. 4. 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.
- 
using_perun.1496405685.txt.gz · Last modified: by cgeb2001