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Subject: Re: [OMPI users] qsub - mpirun problem
From: Zhiliang Hu (zhu_at_[hidden])
Date: 2008-09-29 17:30:53


At 02:15 PM 9/29/2008 -0700, you wrote:
>It sounds like you may not have setup paswordless ssh between all
>your nodes.
>
>Doug Reeder

That's not the case. paswordless ssh is set up and it works fine.
-- that's how I can do "mpirun -np 6 -machinefiles ......" fine.

Zhiliang

>On Sep 29, 2008, at 2:12 PM, Zhiliang Hu wrote:
>
>>At 10:45 PM 9/29/2008 +0200, you wrote:
>>>Am 29.09.2008 um 22:33 schrieb Zhiliang Hu:
>>>
>>>>At 07:37 PM 9/29/2008 +0200, Reuti wrote:
>>>>
>>>>>>"-l nodes=6:ppn=2" is all I have to specify the node requests:
>>>>>
>>>>>this might help: http://www.open-mpi.org/faq/?category=tm
>>>>
>>>>Essentially the examples given on this web is no difference from
>>>>what I did.
>>>>Only thing new is, I suppose "qsub -I " is for interactive mode.
>>>>When I did this:
>>>>
>>>> qsub -I -l nodes=7 mpiblastn.sh
>>>>
>>>>It hangs on "qsub: waiting for job 798.nagrp2.ansci.iastate.edu to
>>>>start".
>>>>
>>>>
>>>>>>UNIX_PROMPT> qsub -l nodes=6:ppn=2 /path/to/mpi_program
>>>>>>where "mpi_program" is a file with one line:
>>>>>>/path/to/mpirun -np 12 /path/to/my_program
>>>>>
>>>>>Can you please try this jobscript instead:
>>>>>
>>>>>#!/bin/sh
>>>>>set | grep PBS
>>>>>/path/to/mpirun /path/to/my_program
>>>>>
>>>>>All should be handled by Open MPI automatically. With the "set"
>>>>>bash
>>>>>command you will get a list with all defined variables for further
>>>>>analysis; and where you can check for the variables set by Torque.
>>>>>
>>>>>-- Reuti
>>>>
>>>>"set | grep PBS" part had nothing in output.
>>>
>>>Strange - you checked the .o end .e files of the job? - Reuti
>>
>>There is nothing in -o nor -e output. I had to kill the job.
>>I checked torque log, it shows (/var/spool/torque/server_logs):
>>
>>09/29/2008 15:52:16;0100;PBS_Server;Job;799.xxx.xxx.xxx;enqueuing
>>into default, state 1 hop 1
>>09/29/2008 15:52:16;0008;PBS_Server;Job;799.xxx.xxx.xxx;Job Queued
>>at request of zhu_at_xxx.xxx.xxx, owner = zhu_at_xxx.xxx.xxx, job name =
>>mpiblastn.sh, queue = default
>>09/29/2008 15:52:16;0040;PBS_Server;Svr;xxx.xxx.xxx;Scheduler sent
>>command new
>>09/29/2008 15:52:16;0008;PBS_Server;Job;799.xxx.xxx.xxx;Job
>>Modified at request of Scheduler_at_xxx.xxx.xxx
>>09/29/2008 15:52:27;0008;PBS_Server;Job;799.xxx.xxx.xxx;Job deleted
>>at request of zhu_at_xxx.xxx.xxx
>>09/29/2008 15:52:27;0100;PBS_Server;Job;799.xxx.xxx.xxx;dequeuing
>>from default, state EXITING
>>09/29/2008 15:52:27;0040;PBS_Server;Svr;xxx.xxx.xxx;Scheduler sent
>>command term
>>09/29/2008 15:52:47;0001;PBS_Server;Svr;PBS_Server;is_request, bad
>>attempt to connect from 172.16.100.1:1021 (address not trusted -
>>check entry in server_priv/nodes)
>>
>>where the server_priv/nodes has:
>>node001 np=4
>>node002 np=4
>>node003 np=4
>>node004 np=4
>>node005 np=4
>>node006 np=4
>>node007 np=4
>>
>>which was set up by the vender.
>>
>>What is "address not trusted"?
>>
>>Zhiliang
>>
>>
>>
>>
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>
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