[gmx-users] mdrun-gpu error

[aiswarya pawar]

Has the tesla card got to do anything with the error. Am using Nvidia Tesla
S1070 1U server.


On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> And sorting out where the /bin/cat error comes from because that is
> surely not a Gromacs message!
>
> Cheers,
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
> >
> > Mark,
> >
> > THe normal mdrun also hangs thus not generating any output.
> >
> >
> > OK. It's your problem to solve... keep simplifying stuff until you can
> > isolate a small number of possible causes. Top of the list is file system
> > availability.
> >
> > Mark
> >
> >
> >
> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
> > wrote:
> >>
> >> On 19/01/2012 2:59 AM, aiswarya.pawar at gmail.com wrote:
> >>
> >> Hi,
> >>
> >> Its going into the running mode but gets hang there for long hours which
> >> generating any data in the output file. And am not able to figure out
> the
> >> error file_doc. Please anyone knows what's going wrong.
> >>
> >>
> >> No, but you should start trying to simplify what you're doing to see
> where
> >> the problem lies. Does normal mdrun work?
> >>
> >> Mark
> >>
> >>
> >> Thanks
> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
> for
> >> it!
> >>
> >> -----Original Message-----
> >> From: Szilárd Páll <szilard.pall at cbr.su.se>
> >> Sender: gmx-users-bounces at gromacs.org
> >> Date: Wed, 18 Jan 2012 14:47:59
> >> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> >> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Subject: Re: [gmx-users] mdrun-gpu error
> >>
> >> Hi,
> >>
> >> Most of those are just warnings, the only error I see there comes from
> >> the shell, probably an error in your script.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
> >> <aiswarya.pawar at gmail.com> wrote:
> >>
> >> Hi users,
> >>
> >> Am running mdrun on gpu . I receive an error such as=
> >>
> >> WARNING: This run will generate roughly 38570 Mb of data
> >>
> >>
> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> >> integrator.
> >>
> >>
> >> WARNING: OpenMM supports only Andersen thermostat with the
> >> md/md-vv/md-vv-avek integrators.
> >>
> >>
> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
> coupling.
> >>
> >>
> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
> and
> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> >> option.
> >>
> >> /bin/cat: file_loc: No such file or directory
> >>
> >>
> >> and the job is running but the nothing written into .xtc, .trr, .edr
> files
> >> .
> >> What could have gone wrong?
> >>
> >> --
> >> Aiswarya  B Pawar
> >>
> >> Bioinformatics Dept,
> >> Indian Institute of Science
> >> Bangalore
> >>
> >>
> >>
> >> --
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> >>
> >>
> >>
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> >
> >
> >
> > --
> > Aiswarya  B Pawar
> >
> > Bioinformatics Dept,
> > Indian Institute of Science
> > Bangalore
> >
> >
> >
> >
> >
> >
> > --
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-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
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