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Re: [ESPResSo-users] Using Espresso with Sun Grid Engine


From: Axel Arnold
Subject: Re: [ESPResSo-users] Using Espresso with Sun Grid Engine
Date: Thu, 26 Jan 2012 14:41:13 +0100
User-agent: KMail/1.13.5 (Linux/2.6.34.10-0.4-desktop; KDE/4.4.4; x86_64; ; )

On Thursday 26 January 2012 14:18:34 Markus Gusenbauer wrote:
> Hi everyone,
> 
> has anyone of you experience with using a grid engine. I am trying to
> start the program like this
> 
> qsub -N test -l h_vmem=2G -cwd ESPRESSO SCRIPT
> 
> Here is the error I get:
> 
> Tcl_InitNotifier: unable to start notifier thread
> /opt/sge/default/spool/simnode19/job_scripts/6439: line 12: 28670
> Aborted                 (core dumped) $ESPRESSO_HOME/$ESPRESSO test
> 
> My first thought was to use the argument -pe (parallel environment), but
> I failed to run the program.

Hi,

from what it looks like, SGE doesn't allow to start threads, but you have a 
thread-enabled Tcl. Not allowing threads to start  is a bad habit of quite 
some queueing systems,  so you will need to find a non-threaded Tcl or compile 
it yourself (by default Tcl is not thread-enabled). Note that this also means 
that you cannot use pipes, for example to read compressed data.

Regards,
Axel

-- 
JP Dr. Axel Arnold
ICP, Universit├Ąt Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609



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