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

[Paymon Pirzadeh]

I am running other softwares in parallel on glacier. GROMACS has shown
such problem up to now!

On Thu, 2009-05-28 at 21:52 +0200, p.yamin at fz-juelich.de wrote:
> 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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> 
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