[torqueusers] Problem with pbsdsh

Abraham Zamudio abraham.zamudio at gmail.com
Tue Oct 25 09:51:45 MDT 2011


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.
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