[gmx-users] mdrun-gpu error
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 19 19:11:07 CET 2012
aiswarya pawar wrote:
> 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.
>
You're trying to solve multiple problems at once. You told Mark that the normal
mdrun executable (which works independently of any GPU components) also hangs,
so either your filesystem is faulty or your installation procedure produced
nonfunctional executables.
You're posting bits and pieces of information, which makes it incredibly hard
for anyone to help you. Let's recap and try again. Please provide:
1. The Gromacs version you're using
2. Description of the hardware (GPU and non-GPU components)
3. Installation procedure for Gromacs and any of the prerequisite software and
libraries that were required, including versions
4. The exact command(s) you're issuing, including the full script that is
causing a problem
-Justin
> Thanks
>
> On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll <szilard.pall at cbr.su.se
> <mailto: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 <mailto: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
> <http://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 <mailto: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 <mailto: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 <mailto: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 <mailto:Mark.Abraham at anu.edu.au>>
> >>> > wrote:
> >>> >>
> >>> >> On 19/01/2012 2:59 AM, aiswarya.pawar at gmail.com
> <mailto: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
> <mailto:szilard.pall at cbr.su.se>>
> >>> >> Sender: gmx-users-bounces at gromacs.org
> <mailto: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
> <mailto:gmx-users at gromacs.org>>
> >>> >> Reply-To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto: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 <mailto: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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> >>> >>
> >>> >>
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> >>> >
> >>> >
> >>> >
> >>> >
> >>> > --
> >>> > Aiswarya B Pawar
> >>> >
> >>> > Bioinformatics Dept,
> >>> > Indian Institute of Science
> >>> > Bangalore
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > --
> >>> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
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> >>
> >>
> >>
> >>
> >> --
> >> Aiswarya B Pawar
> >>
> >> Bioinformatics Dept,
> >> Indian Institute of Science
> >> Bangalore
> >>
> >>
> >
> >
> >
> > --
> > Aiswarya B Pawar
> >
> > Bioinformatics Dept,
> > Indian Institute of Science
> > Bangalore
> >
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
> --
> Aiswarya B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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