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pbs-dummies [2011/08/25 16:24]
damir
pbs-dummies [2015/11/16 10:33] (current)
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 ===== for Dummies ===== ===== for Dummies =====
  
-**1st thing you need to know:** Using a pbs script it's like if you're typing the commands from a shell. Therefore if after the login you need to change directory to launch the job from the shell, you'll need to do it even from the script.\\+**1st thing you need to know:** Using a pbs script it's like if you're typing the commands from a shell. Therefore ​you must include in the script all the command that you wuold use on the shell before/​after running your program (if after the login you need to change directory to launch the job, you'll need to do it even from the batch script).\\
 \\ \\
 Every instruction line for the queue manager start with #PBS, so\\ Every instruction line for the queue manager start with #PBS, so\\
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 The mandatory directives that you must **always** include in the scripts are: The mandatory directives that you must **always** include in the scripts are:
-  - Your email address. the official epfl address or something else, but must be a valid (worldwide) email address. This address mus be always present, no matter if you instruct the system to send or not the email messages.+  - Your email address. the official epfl address or something else, but must be a valid (worldwide) email address. ​**This address mus be always present, no matter if you instruct the system to send or not the email messages**.
   - How much time your job must run (if the job runs over this limit the cluster manager will kill it). the minimum is 1 minute and there'​s no maximum limit.   - How much time your job must run (if the job runs over this limit the cluster manager will kill it). the minimum is 1 minute and there'​s no maximum limit.
-  - How much memory (RAM) your job will use. Please remember that if your job use more memory than the limit you put here the cluster manager will kill the job. the minimum is 512 Mbyte, currently (as for Dec 2010) the maximum is ~64 Gbyte.+  - How much memory (RAM) your job will use. Please remember that if your job use more memory than the limit you put here the cluster manager will kill the job. the minimum is 512 Mbyte, currently (as for Jul 2015) the maximum is 64 Gbyte
 +  - How many cores/cpu must be reserved for your job. If you don't include this parameter only one core/cpu will be assigned to your job and you cannot run more than a single threaded job.
  
 The beginning of your script will be: The beginning of your script will be:
 <​code>​ <​code>​
 # you email address # you email address
-#PBS -M <my email address that everyone can use to send email messages to me>+#PBS -M <my email address that everyone, around the world, ​can use to send email messages to me>
 # how much time this process must run (hours:​minutes:​seconds)?​ 4 hours for this example # how much time this process must run (hours:​minutes:​seconds)?​ 4 hours for this example
 #PBS -l cput=04:​00:​00 #PBS -l cput=04:​00:​00
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 #PBS -l mem=1024mb #PBS -l mem=1024mb
 </​code>​ </​code>​
 +If your job is running a simulation that is multithreaded,​ you can use more than one cpu/core by indicating the number of cores you want with:
 +<​code>​
 +#Numer of cores needed by the application (8 in this example)
 +#PBS -l ppn=8
 +</​code>​
 +
  
 After this //prolog// you can add directives for instructing the system about the messages you After this //prolog// you can add directives for instructing the system about the messages you
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 </​code>​ </​code>​
  
-And then you want to assign a name to your job, so you will know what the cluster is doing for you when you look at the list of running jobs (using the command ''​qstat -an1''​).+And then you might want to assign a name to your job, so you will know what the cluster is doing for you when you look at the list of running jobs (using the command ''​qstat -an1''​).
  
 <​code>​ <​code>​
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 #PBS -l cput=04:​00:​00 #PBS -l cput=04:​00:​00
 #PBS -l mem=1024mb #PBS -l mem=1024mb
 +#PBS -l ppn=8
 # you want to receive an email messages when your job is started and when it's # you want to receive an email messages when your job is started and when it's
 finished (or blocked) finished (or blocked)
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 </​note>​ </​note>​
  
-After all this work, you just need to relax and wait until you receive the email messages from the queuing manager. At this point you return to the directory where the output files are saved and check the results.\\+After all this work, you just need to relax and wait until you receive the email messages from the queuing manager ​telling you about success or failure. At this point you return to the directory where the output files are saved and check the results.\\
 If you browse the the documentation we have on [[sge|Batch Queuing System]] you'll find examples on how to use Matlab or Mathematica and some explanation about the directives and the commands available for the queuing system. If you browse the the documentation we have on [[sge|Batch Queuing System]] you'll find examples on how to use Matlab or Mathematica and some explanation about the directives and the commands available for the queuing system.
  
pbs-dummies.txt · Last modified: 2015/11/16 10:33 (external edit)