Matt,
I just found something else with your job script. You are defining the
LD_LIBRARY_PATH environment variable, and *then* loading the openmpi
environment module:
>>> #!/bin/bash
>>> export TMPDIR=$SCRATCH/abyss_tmp/
>>> LD_LIBRARY_PATH=/work/01301/mmacmane
>>>
On Apr 26, 2010, at 9:08 AM, Matthew MacManes wrote:
>>
>>> I am using SGE to submit jobs to one of the TeraGrid sites,
>>> specifically TACC-RANGER. The problem, is, that I am using a
>>> program that requires OpenMPI version 1.4.1, and the latest
>>> instal
My question about version wasn't "why can't you use 1.3?". It was "why do you
believe the problems you are seeing are caused by not finding the correct
version?".
It looks to me like everything is working correctly, but that communications
are blocked for some reason. That doesn't sound like a
Hi Ralph,
Its a no-go with the --enable-mpirun-prefix-by-default.
Version issue: The program I am trying to run (RAY:
http://sourceforge.net/apps/mediawiki/denovoassembler/index.php?title=Main_Page#Installation
) will not work with earlier versions of OpenMPI- this is confirmed both by
the autho
Matthew MacManes writes:
> I am using SGE to submit jobs to one of the TeraGrid sites,
> specifically TACC-RANGER.
It's more on-topic here than the SGE list, but you should still ask the
Ranger support people. People who don't know Ranger can't say if you
actually can use the TCP BTL on it, bu
ustre/work/saddepal/openmpi-1.4-BM
CC=icc FC=ifort
Rangam
From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of
Matthew MacManes [macma...@gmail.com]
Sent: Monday, April 26, 2010 10:37 AM
To: Open MPI Users
Subject: Re: [OMPI users] problem
When configuring OMPI. Your configure should look like this:
./configure --prefix= --enable-mpirun-prefix-by-default .
Just curious: what convinces you that you have a version mismatch? Connectivity
failures can occur for a variety of reasons - this looks more like you have
some kind of net
Hi Ralph,
Thanks! Do you mean to pass '--enable-mpirun-prefix-by-default' when
configuring OpenMPI, or when configuring the program I am trying to use.
Sorry if this should be obvious!
On Mon, Apr 26, 2010 at 08:13, Ralph Castain wrote:
> First, is the directory where you installed OMPI 1.4.1 v
Hi Rangam,
Thanks.. Just tried. Still the 'no route to host' issue..
Matt
_
Matthew MacManes
PhD Candidate
University of California- Berkeley
Museum of Vertebrate Zoology
Phone: 510-495-5833
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://ma
Hello Matthew,
Not sure it it helps but I am guessing that
module load openmpi (in bash script) is updating variables to RANGER openmpi
installation. Try removing this line in your script file and resubmit your job,
also
#$ -V in the submission script exports env variables from your current
First, is the directory where you installed OMPI 1.4.1 visible to all the
nodes? If not, then this won't work.
If it is, then try configuring with --enable-mpirun-prefix-by-default, and be
sure you specify a prefix that points to your installation.
On Apr 26, 2010, at 9:08 AM, Matthew MacManes
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