[gmx-users] mdrun-gpu error
aiswarya pawar
aiswarya.pawar at gmail.com
Fri Jan 20 05:59:35 CET 2012
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
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'
in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory
On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul <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**>> 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<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<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<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<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 <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**>>
>> >>> >> Sender: gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces@**gromacs.org<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<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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>> <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>
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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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>> posting!
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>> >.
>>
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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
>> <mailto:gmx-users at gromacs.org>
>>
>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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>> >.
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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>
--
Aiswarya B Pawar
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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