Re: [Condor-users] segmentation fault in vanilla universe

[Craig Struble <craig.struble@xxxxxxxxxxxxx>]

Hi Satyanarayan,

We ran into problems trying to run the Linux version of MATLAB through Condor. One of the things we needed to do in our script was to set the HOME environment variable (which, in general, is not set when running scripts non-interactively through Condor). You might try modifying your script to be:

#!/bin/bash

HOME=`pwd` ; export HOME

/usr/local/Matlab/bin/matlab -nojvm -nosplash -nodisplay < /usr/local/Matlab/bin/test_matlab.m
hostname

This will set the environment variable to Condor's execute directory and allow Matlab to temporarily create the configuration files it wants to create.

    Craig

On Dec 30, 2009, at 1:06 PM, satyanarayan rao wrote:

Respected Matt,

Thank you for responding.
Here the scenario is different. The node from where i am submitting the job is not having matlab installed, the path of the executable which is been used in the script is exist on grid1.iiitm.ac.in (/usr/local/Matlab/bin/matlab). And there is no error in execution of that command on grid1.iiitm.ac.in node, mean there is no problem from matlab side,

In concise, i have a script file that is suppose to run grid1.iiitm.ac.in.

Please suggest.

Thanks and Regards,
Satyanarayan Rao

2009/12/31 Matthew Farrellee <matt@xxxxxxxxxx>

You might try configuring grid1 to capture core files. Though if the bug is in matlab it might be tough to get fixed.

Best,


matt

On 12/30/2009 12:33 PM, satyanarayan rao wrote:
> Dear Hailong,
>
> The answer is no, the script is running fine on the node

> grid1.iiitm.ac.in <http://grid1.iiitm.ac.in>. The problem is something

> else which i am not able to recognise.
>
> Thanks and regards,
> Satyanarayan Rao
>
> On Wed, Dec 30, 2009 at 5:19 PM, hailong.yang1115

> <hailong.yang1115@xxxxxxxxx <mailto:hailong.yang1115@xxxxxxxxx>> wrote:
>
>     Hi Satyanarayan,
>
>     Have you tried to run the script file run_matlab.sh on the execute

>     machine *grid1.iiitm.ac.in* <http://grid1.iiitm.ac.in/>? Did it run

>     correctly? It seems the commands you wrote in the script file met
>     with segmentation faults.
>
>     -Hailong
>
>     2009-12-30
>     ------------------------------------------------------------------------
>     ***********************************************
>     * Hailong Yang, PhD. Candidate
>     * Sino-German Joint Software Institute,
>     * School of Computer Science&Engineering, Beihang University
>     * Phone: (86-010)82315908

>     * Email: hailong.yang1115@xxxxxxxxx <mailto:hailong.yang1115@xxxxxxxxx>

>     * Address: G413, New Main Building in Beihang University,
>     *              No.37 XueYuan Road,HaiDian District,
>     *              Beijing,P.R.China,100191
>     ***********************************************
>     ------------------------------------------------------------------------
>     *发件人：* satyanarayan rao
>     *发送时间：* 2009-12-30  19:13:23
>     *收件人：* Condor-Users Mail List
>     *抄送：*
>     *主题：* [Condor-users] segmentation fault in vanilla universe
>     Hello All,
>
>     I am having problem with running the matlab command using vanilla
>     universe.
>     I have matlab installed on two nodes, i am using only

>     one(*grid1.iiitm.ac.in <http://grid1.iiitm.ac.in>*) in submit by

>     putting it in requirement parameter.
>     The command which i am using is successfully running on the node,
>     but if i am submitting using vanilla universe it is giving error.
>     Process which i followed is following.
>
>     [grid-node@grid-server ~]$ cat run_matlab.sh
>     #!/bin/bash
>     /usr/local/Matlab/bin/matlab -nojvm -nosplash -nodisplay <
>     /usr/local/Matlab/bin/test_matlab.m
>     hostname
>     [grid-node@grid-server ~]$
>
>     [grid-node@grid-server ~]$ cat vanilla.submit
>
>                 Executable     = /home/grid-node/run_matlab.sh
>                 Universe       = vanilla
>                 Requirements   = (machine=="grid1.iiitm.ac.in

>     <http://grid1.iiitm.ac.in>")

>                 Error   = err.$(Process)
>                 Output  = out.$(Process)
>                  Log = foo.log
>                  transfer_executable = true
>                  should_transfer_files = YES
>                  when_to_transfer_output = ON_EXIT
>                  Queue 10
>
>     [grid-node@grid-server ~]$
>
>
>     [grid-node@grid-server ~]$ condor_status
>
>     Name               OpSys      Arch   State     Activity LoadAv Mem
>     ActvtyTime
>
>     slot1@anlab-node8. LINUX      INTEL  Unclaimed Idle     0.000   497
>     0+03:10:05
>     slot2@anlab-node8. LINUX      INTEL  Unclaimed Idle     0.000   497
>     0+15:03:00
>     slot1@grid-server. LINUX      INTEL  Unclaimed Idle     0.840  1006
>     0+03:15:07
>     slot2@grid-server. LINUX      INTEL  Unclaimed Idle     0.000  1006
>     0+15:15:31

>     grid1.iiitm.ac.in <http://grid1.iiitm.ac.in>  LINUX      INTEL

>     Unclaimed Idle     0.000   242  0+02:15:04
>
>                          Total Owner Claimed Unclaimed Matched
>     Preempting Backfill
>
>              INTEL/LINUX     5     0       0         5       0
>     0        0
>
>                    Total     5     0       0         5       0
>     0        0
>     [grid-node@grid-server ~]$
>
>
>     [grid-node@grid-server ~]$ condor_submit vanilla.submit
>     Submitting job(s)..........
>     Logging submit event(s)..........
>     10 job(s) submitted to cluster 1042.
>     [grid-node@grid-server ~]$
>
>     [grid-node@grid-server ~]$ cat out.1

>     grid1.iiitm.ac.in <http://grid1.iiitm.ac.in>

>     [grid-node@grid-server ~]$ cat err.1
>     /opt/condor-7.2.4/local.grid1/execute/dir_15382/condor_exec.exe:
>     line 2: 15385 Segmentation fault      /usr/local/Matlab/bin/matlab
>     -nojvm -nosplash -nodisplay </usr/local/Matlab/bin/test_matlab.m
>     [grid-node@grid-server ~]$
>
>     Any help will be greatly appreciated.
>
>     Thanks and Regards,
>     Satyanarayan Rao
>
>
>     --
>     Satyanarayan Rao
>     ABV-IIITM Gwalior
>     http://www.iiitm.ac.in
>     Ph: +91-9179346657
>
>
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>
>
>
> --
> Satyanarayan Rao
> ABV-IIITM Gwalior
> http://www.iiitm.ac.in
> Ph: +91-9179346657
>
>
>
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--
Satyanarayan Rao
ABV-IIITM Gwalior
http://www.iiitm.ac.in
Ph: +91-9179346657

<ATT00001.txt>

--

Craig A. Struble, Ph.D. | 369 Cudahy Hall  | Marquette University

Associate Professor of Computer Science    | (414)288-3783

Director, Master of Bioinformatics Program | (414)288-5472 (fax)

http://www.mscs.mu.edu/~cstruble | craig.struble@xxxxxxxxxxxxx