[gmx-users] GROMACS on glacier.westgrid.ca

[p.yamin at fz-juelich.de]

It seems like your nodes cannot communicate.
you might want to check your job-submitting script: does it call mdrun correctly? cpu/time allocation? try to see if mpi is installed correctly by submitting any other mpi-enabled code.


Peyman Yamin
Institut fuer Strukturbiologie und Biophysik (ISB)
ISB-3: Strukturbiochemie
Forschungszentrum Juelich
D-52425 Juelich 
Tel:	(49)-2461-61-2875  
Fax:	(49)-2461-61-2023
mailto: p.yamin[at]fz-juelich.de 

----- Original Message -----
From: Paymon Pirzadeh <ppirzade at ucalgary.ca>
Date: Thursday, May 28, 2009 6:35 pm
Subject: [gmx-users] GROMACS on glacier.westgrid.ca

> Hello all,
> A follow up from my previous problems on running the gromacs on 
> glacierturned out that I had problems in installation. The guide in 
> the manual
> was not clear enough. So, I installed the code fine this time, so, 
> I get
> errors from 4.0.4 version. 
> I ran the code interactively on the master node and everything went
> smooth and fine without any problems. But as soon as I started running
> it in parallel through que line, job gets killed. Following are the
> messages I received:
> 
> PBS Job Id: 4686006.teva.westgrid.ubc
> > >> Job Name:   sixsite-test
> > >> Exec host:  ice1_2/1+ice1_2/0+ice1_1/1+ice1_1/0
> > >> Aborted by PBS Server
> > >> Job cannot be executed
> 
> The error messages I receive in error file:
> > >> Killed by signal 2.^M
> > >> Killed by signal 2.^M
> > >> Killed by signal 2.^M
> 
> Running on 4 processors.
> > >> Starting run at: Mon May 25 20:29:34 PDT 2009
> > >> p2_11876:  p4_error: Timeout in establishing connection to remote
> > >> process: 0
> > >> p0_4273:  p4_error: net_recv read:  probable EOF on socket: 1
> > >> Job finished at: Mon May 25 20:34:40 PDT 2009
> 
> All the clues show that the program had started working, initial
> conditions were reviewed by the code, but suddenly everything 
> crashed. I
> really do not know where the error originates from!!! This is while my
> friend has compiled the code in the same way as I did, and she is
> running fine on another cluster.
> Regards,
> 
> Payman
> 
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