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 <jalem...@vt.edu
<mailto:jalem...@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.p...@cbr.su.se <mailto:szilard.p...@cbr.su.se>
<mailto:szilard.p...@cbr.su.se
<mailto:szilard.p...@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.pa...@gmail.com <mailto:aiswarya.pa...@gmail.com>
<mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@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.pa...@gmail.com <mailto:aiswarya.pa...@gmail.com>
<mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@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.p...@cbr.su.se <mailto:szilard.p...@cbr.su.se>
<mailto:szilard.p...@cbr.su.se <mailto:szilard.p...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>
>>> > wrote:
>>> >>
>>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com>
<mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@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.p...@cbr.su.se
<mailto:szilard.p...@cbr.su.se>
<mailto:szilard.p...@cbr.su.se
<mailto:szilard.p...@cbr.su.se>__>>
>>> >> Sender: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
<mailto:gmx-users-bounces@__gromacs.org
<mailto:gmx-users-boun...@gromacs.org>>
>>> >> Date: Wed, 18 Jan 2012 14:47:59
>>> >> To: Discussion list for GROMACS
users<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>__>
>>> >> Reply-To: Discussion list for GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@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.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com>
<mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@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@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
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>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > Aiswarya B Pawar
>>> >
>>> > Bioinformatics Dept,
>>> > Indian Institute of Science
>>> > Bangalore
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@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@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>
==============================__==========
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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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