[GE users] MVAPICH 0.9.9 and SGE 6.2u1

rgigon rgigon at slb.com
Mon Aug 3 22:36:30 BST 2009


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Hi Reuti,

Thanks so much for your response.

Can you point me to the correct HOWTO on how to apply this patch?  The HOWTO I used was:  http://gridengine.sunsource.net/howto/mvapich/MVAPICH_Integration.html  which did not mention a patch or recompiling MVAPICH.

I found the patch you mentioned below attached to a message thread, but upon examination it looks like it is specific to mvapich-0.9.5.117.  I'm using mvapich-0.9.9.  Do I just need to edit the file to reflect the directory names for 0.9.9 or is there a different patch required.

Many thanks for your help!

Best regards,
Roberta

---------------------------------------------------------------------------------------------
Roberta M. Gigon
Schlumberger-Doll Research
One Hampshire Street, MD-B253
Cambridge, MA 02139
617.768.2099 - phone
617.768.2381 - fax

This message is considered Schlumberger CONFIDENTIAL.  Please treat the information contained herein accordingly.

-----Original Message-----
From: reuti [mailto:reuti at staff.uni-marburg.de]
Sent: Saturday, August 01, 2009 5:09 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] MVAPICH 0.9.9 and SGE 6.2u1

Hi,

Am 29.07.2009 um 18:32 schrieb rgigon:

> Hi there,
> I?m trying to achieve tight integration between MVAPICH 0.9.9 and
> SGE 6.2u1
> I followed the directions in the HOWTO and am able to submit jobs,
> but when I use qdel, it still does not kill all the processes.
>
> Results from ps on master:
>
> 6553  4370  6553  \_ sge_shepherd-1302 -bg
>  6578  6553  6578      \_ -bash /opt/sge/default/spool/fire7/
> job_scripts/1302
>  6669  6578  6578          \_ /usr/local/mpi/intel/mvapich-0.9.9/
> bin/mpirun_rsh -rsh -np 4 -hostfile /tmp/1302.1.normal.q/machines ./
> testtight.x
>  6670  6669  6578              \_ /usr/bin/rsh fire7 cd /people4/
> jliu17/roberta/source; /usr/bin/env LD_LIBRARY_PATH=/usr/local/mpi/
> intel/mvapich-0.9.9/lib/shared:/usr/local/mpi/intel/mvapich-0.9.9/
> lib:/usr/local/mpi/intel/mvapich-0.9.9/lib/shared: MPIRUN_MPD=0
> MPIRUN_HOST=fire7 MPIRUN_PORT=60546 MPIRUN_RANK=0 MPIRUN_NPROCS=4
> MPIRUN_ID=6669    NOT_USE_TOTALVIEW=1  ./testtight.x
>  6678  6670  6578              |   \_ [rsh] <defunct>
>  6671  6669  6578              \_ /usr/bin/rsh fire7 cd /people4/
> jliu17/roberta/source; /usr/bin/env LD_LIBRARY_PATH=/usr/local/mpi/
> intel/mvapich-0.9.9/lib/shared:/usr/local/mpi/intel/mvapich-0.9.9/
> lib:/usr/local/mpi/intel/mvapich-0.9.9/lib/shared: MPIRUN_MPD=0
> MPIRUN_HOST=fire7 MPIRUN_PORT=60546 MPIRUN_RANK=1 MPIRUN_NPROCS=4
> MPIRUN_ID=6669    NOT_USE_TOTALVIEW=1  ./testtight.x
>  6680  6671  6578              |   \_ [rsh] <defunct>
>  6672  6669  6578              \_ /usr/bin/rsh fire8 cd /people4/
> jliu17/roberta/source; /usr/bin/env LD_LIBRARY_PATH=/usr/local/mpi/
> intel/mvapich-0.9.9/lib/shared:/usr/local/mpi/intel/mvapich-0.9.9/
> lib:/usr/local/mpi/intel/mvapich-0.9.9/lib/shared: MPIRUN_MPD=0
> MPIRUN_HOST=fire7 MPIRUN_PORT=60546 MPIRUN_RANK=2 MPIRUN_NPROCS=4
> MPIRUN_ID=6669    NOT_USE_TOTALVIEW=1  ./testtight.x
>  6676  6672  6578              |   \_ [rsh] <defunct>
>  6673  6669  6578              \_ /usr/bin/rsh fire8 cd /people4/
> jliu17/roberta/source; /usr/bin/env LD_LIBRARY_PATH=/usr/local/mpi/
> intel/mvapich-0.9.9/lib/shared:/usr/local/mpi/intel/mvapich-0.9.9/
> lib:/usr/local/mpi/intel/mvapich-0.9.9/lib/shared: MPIRUN_MPD=0
> MPIRUN_HOST=fire7 MPIRUN_PORT=60546 MPIRUN_RANK=3 MPIRUN_NPROCS=4
> MPIRUN_ID=6669    NOT_USE_TOTALVIEW=1  ./testtight.x
>  6683  6673  6578                  \_ [rsh] <defunct>

a Tight Integration needs "rsh" compiled in, not an absolute path
like "/usr/bin/rsh" which shows up above. Did you also recompile
MVAPICH after applying the "mvapich-rsh.patch" from the HowTo archive?

-- Reuti


> Your thoughts are greatly appreciated.
>
> Best regards,
> Roberta
>
> ----------------------------------------------------------------------
> -----------------------
> Roberta M. Gigon
> Schlumberger-Doll Research
> One Hampshire Street, MD-B253
> Cambridge, MA 02139
> 617.768.2099 - phone
> 617.768.2381 - fax
>
> This message is considered Schlumberger CONFIDENTIAL.  Please treat
> the information contained herein accordingly.
>

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