[gmx-users] mdrun-gpu error
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 20 13:28:55 CET 2012
aiswarya pawar wrote:
> Justin,
>
> Sorry for not giving the correct information.
>
> Gromacs version 4.5.5
> Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor)
> Cuda version 3.1
> CMake 2.8
>
> I installed the OpenMM from the source using commands=
>
> ccmake -i .
> make
> make test
> make install
>
> everything went fine and set the paths
>
> export OPENMM_ROOT_DIR=path_to_custom_openmm_installation
> cmake -DGMX_OPENMM=ON
>
The "path_to_custom_openmm_installation" is a hint for you to specify a real
path. If you used it, and somehow magically the installation finished with no
errors, I'd be amazed. Otherwise, please provide your real commands here,
rather than the copy/pasted generic framework.
> then
> make
> make install
>
> The submission script used is=
>
> #!/bin/csh
> #PBS -l gpu=1
> #PBS -l ncpus=1
> #PBS -o /global/utemp/cuda-out2.out
> #PBS -e /global/utemp/cuda-err2.out
> /home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device
> "OpenMM:platform=Cuda,DeviceID=0,Memtest=15,//,force-device=yes" -v
> -deffnm /global/utemp/md
>
> for this i receive an error such as
> Cuda error in file
> '/home/staff/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
>
>
This sounds more like an environmental problem, rather than something to do with
Gromacs.
You previously stated that the normal, non-GPU mdrun executable was hanging.
Start there. If your Gromacs installation is nonfunctional, sort that out first
before adding a layer of complexity with GPU settings.
-Justin
>
>
> On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>
> <mailto: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>
> <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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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 BlackBerryŽ 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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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
> >>> >>
> >>> >>
> >>> >>
> >>> >> --
> >>> >> 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
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > --
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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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>
> --
> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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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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