[torqueusers] Problem with pbsdsh

Abraham Zamudio abraham.zamudio at gmail.com
Tue Oct 25 09:58:01 MDT 2011


The ID of this job is 240 , and the log of torque :

cat /var/spool/torque/server_logs/20111025 | grep 240
10/25/2011 10:47:04;0100;PBS_Server;Job;240.master;enqueuing into batch,
state 1 hop 1
10/25/2011 10:47:04;0008;PBS_Server;Job;240.master;Job Queued at request of
mpiX at master, owner = mpiX at master, job name = matrix2, queue = batch
10/25/2011 10:47:05;0008;PBS_Server;Job;240.master;Job Run at request of
root at master
10/25/2011 10:47:05;000d;PBS_Server;Job;240.master;Not sending email: User
does not want mail of this type.
10/25/2011 10:47:05;000d;PBS_Server;Job;240.master;Not sending email: User
does not want mail of this type.
10/25/2011 10:47:05;0010;PBS_Server;Job;240.master;Exit_status=0
resources_used.cput=00:00:00 resources_used.mem=3096kb
resources_used.vmem=225088kb resources_used.walltime=00:00:00
10/25/2011 10:47:05;0100;PBS_Server;Job;240.master;dequeuing from batch,
state COMPLETE



On Tue, Oct 25, 2011 at 10:51 AM, Abraham Zamudio <abraham.zamudio at gmail.com
> wrote:

> Dr. Cole ,
>
> Now , i have the following problem :
>
> PBS: /jro_cluster/mpiX/Matrix/script1: Permission denied
> pbsdsh: error 17000 on spawn
> PBS: /jro_cluster/mpiX/Matrix/script1: Permission denied
> pbsdsh: error 17000 on spawn
> PBS: /jro_cluster/mpiX/Matrix/script1: Permission denied
> pbsdsh: error 17000 on spawn
> PBS: /jro_cluster/mpiX/Matrix/script1: Permission denied
> pbsdsh: error 17000 on spawn
>
> I do not undestand because i have no permissions .
>
> My qsub file :
>
> #PBS -S /bin/bash
> #PBS -V
> #PBS -N matrix2
> #PBS -q batch
> #PBS -l nodes=quad4:ppn=4
> #####    #PBS -j oe
> #PBS -e matrix_$PBS_JOBID.err
> #PBS -o matrix_$PBS_JOBID.out
>
> pbsdsh $PBS_O_WORKDIR/script1
>
>
> And the script1 file :
>
> #!/bin/bash
>
> $PBS_O_WORKDIR/matrix2 $PBS_O_WORKDIR/matrix_$PBS_VNODENUM.dat
>
>
>
>
> On Tue, Oct 25, 2011 at 10:16 AM, Coyle, James J [ITACD] <jjc at iastate.edu>wrote:
>
>> Abraham,****
>>
>> ** **
>>
>> I think   $PBS_VNODENUM  only gets a number inside a copy of****
>>
>> a script launched by pbsdsh.****
>>
>> ** **
>>
>> This is similar to the value of ****
>>
>>   n ****
>>
>> outside of the loop ****
>>
>>   for(n=0;n<4;n++){****
>>
>> }****
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>>   Try launching a script which uses  ****
>>
>> matrix_$PBS_VNODENUM.dat****
>>
>> ** **
>>
>> internally.****
>>
>> ** **
>>
>> ** **
>>
>> E.g.****
>>
>> ** **
>>
>> script1 is executable in $PBS_O_WORKDIR  and contains:****
>>
>> ** **
>>
>> #!/bin/bash****
>>
>> ** **
>>
>> ./ matrix2     matrix_$PBS_VNODENUM.dat****
>>
>> ** **
>>
>> and change the  pbsdsh command in your script to the two lines:****
>>
>> ** **
>>
>> cd $PBS_O_WORKDIR****
>>
>> pbsdsh  script1****
>>
>> ** **
>>
>> ** **
>>
>> James Coyle, PhD****
>>
>> High Performance Computing Group        ****
>>
>>  Iowa State Univ.          ****
>>
>> web: http://jjc.public.iastate.edu/<http://www.public.iastate.edu/%7Ejjc>
>> ****
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>> ** **
>>
>> *From:* torqueusers-bounces at supercluster.org [mailto:
>> torqueusers-bounces at supercluster.org] *On Behalf Of *Abraham Zamudio
>> *Sent:* Monday, October 24, 2011 4:14 PM
>> *To:* Torque Users Mailing List; David Beer; Ken Nielson; tbaer at utk.edu
>> *Subject:* [torqueusers] Problem with pbsdsh****
>>
>> ** **
>>
>> Hi people ,
>>
>> I have a following problem . I am trying run various copies of the
>> following code :
>>
>> #include <stdio.h>
>> #include <gsl/gsl_matrix.h>
>> #include <stdlib.h>
>> #include <unistd.h>
>> #include <sys/time.h>
>>
>> int main (int argc, char **argv)
>> {
>> int i,j;
>> int n,m;
>>
>> n=10000;
>> m=10000;
>>
>> gsl_matrix * A = gsl_matrix_alloc(n,m);
>>
>> struct timeval tval;
>> gettimeofday(&tval, 0);
>> long int NN = (tval.tv_sec ^ tval.tv_usec) ^ getpid() ;
>> srand(NN);
>>
>>
>> for (i = 0; i < n; i++)
>>     for (j = 0; j < m; j++)
>>         gsl_matrix_set (A, i, j, rand());
>>
>> FILE * f = fopen(argv[1],"wb");
>> gsl_matrix_fwrite (f, A);
>>
>> fclose (f);
>> gsl_matrix_free (A);
>>
>> return 0;
>>      }
>>
>>
>> The compilation is with :
>>
>> gcc -I/usr/include/gsl -Wall -pedantic -ggdb -std=c99 -lgsl -lgslcblas -o
>> matrix matrix.c
>>
>> Basically what i want is to generate an output file
>> (matrix_$PBS_VNODENUM.dat) for each  processor .
>>
>> My qsub file :
>>
>> #PBS -S /bin/bash
>> #PBS -V
>> #PBS -N matrix2
>> #PBS -q batch
>> #PBS -l nodes=quad4:ppn=4
>> #####    #PBS -j oe
>> #PBS -e matrix_$PBS_JOBID.err
>> #PBS -o matrix_$PBS_JOBID.out
>>
>> pbsdsh -v $PBS_O_WORKDIR/matrix2 $PBS_O_WORKDIR/matrix_$PBS_VNODENUM.dat
>>
>> The problem is that only stores an output file (matrix_0.dat) . I'm
>> looking for some advice .
>>
>>
>> --
>> Abraham Zamudio Ch.****
>>
>> _______________________________________________
>> torqueusers mailing list
>> torqueusers at supercluster.org
>> http://www.supercluster.org/mailman/listinfo/torqueusers
>>
>>
>
>
> --
> Abraham Zamudio Ch.
>
>


-- 
Abraham Zamudio Ch.
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