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Old 10-03-2013, 07:16 AM   #1
hoi
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Registered: Jun 2013
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Unhappy submit job in cluster


I have a cluster which has 128 processor. I submit a job using below command

qsub script_file

my script file:

#!/bin/bash
#PBS -l nodes=2 : ppn=16
#PBS -l walltime=00:10:00:00
#PBS -o out.log
#PBS -e err.log
cat $PBS_NODEFILE
cd /home/my_name/content_of_input_file_folder
echo $PBS_WORK

mpirun -machinefile $PBS_NODEFILE -np 32 /opt/my_code/execution_file

echo "Done!!!!"


##qsub -l select=2:ncpus=12 submit.sh




Initially it shows running but there is no output file and after 3 sec it is stopped. I thing my script file is not correct. Please any suggestion...

Last edited by hoi; 10-03-2013 at 07:21 AM.
 
Old 10-03-2013, 07:36 AM   #2
colucix
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Location: Bologna
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The only thing I don't understand is the format of walltime with 4 fields instead of 3. Maybe you can try to set it in seconds which is another accepted format. Any clue from err.log or err.out?
 
Old 10-03-2013, 07:57 AM   #3
hoi
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Quote:
Originally Posted by colucix View Post
The only thing I don't understand is the format of walltime with 4 fields instead of 3. Maybe you can try to set it in seconds which is another accepted format. Any clue from err.log or err.out?
This two files are not generating.
 
Old 10-03-2013, 11:56 AM   #4
colucix
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Have you tried to change the walltime option to the number of seconds, e.g.
Code:
#PBS -l walltime=36000
for 10 hours. Anyway, the output and error files should be generated vene if they are empty (this is the normal behaviour). Try to look if they was undelivered: if this is the case you can find them under /var/lib/torque/undelivered or /var/spool/torque/undelivered (again the default, unless otherwise ordered by the sys admin).
 
Old 10-03-2013, 12:32 PM   #5
hoi
LQ Newbie
 
Registered: Jun 2013
Posts: 29

Original Poster
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Quote:
Originally Posted by colucix View Post
Have you tried to change the walltime option to the number of seconds, e.g.
Code:
#PBS -l walltime=36000
for 10 hours. Anyway, the output and error files should be generated vene if they are empty (this is the normal behaviour). Try to look if they was undelivered: if this is the case you can find them under /var/lib/torque/undelivered or /var/spool/torque/undelivered (again the default, unless otherwise ordered by the sys admin).
I have checked with "#PBS -l walltime=36000". I didn't get any output file again. Also I have looked /var/spool/torque/undelivered, nothing is there.
 
  


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bash scripting, clustering, queue, shell script


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