[gmx-users] mdrun-gpu error

Thu Jan 19 18:42:49 CET 2012

Szilárd,

I did a memory test run yesterday and it went fine but today received an
error. So you mean to say the tesla card version nothing to do with this
right.

Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> That's a generic GPU kernel launch failure which can mean anything,
> from faulty hardware to bad driver to messed up installation.
>
> Does the memory test run? Try to compile/install again and see if it works.
>
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
> <aiswarya.pawar at gmail.com> wrote:
> > when i tired running it again, i got an error as
> >
> > Cuda error in file
> >
> '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
> bbsort.cu'
> > in line 176 : unspecified launch failure.
> >
> > /bin/cat: file_loc: No such file or directory
> >
> >
> > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar <
> aiswarya.pawar at gmail.com>
> > wrote:
> >>
> >> 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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> >>> >
> >>> >
> >>> >
> >>> > --
> >>> > Aiswarya  B Pawar
> >>> >
> >>> > Bioinformatics Dept,
> >>> > Indian Institute of Science
> >>> > Bangalore
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > --
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> >>
> >>
> >>
> >>
> >> --
> >> Aiswarya  B Pawar
> >>
> >> Bioinformatics Dept,
> >> Indian Institute of Science
> >> Bangalore
> >>
> >>
> >
> >
> >
> > --
> > 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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