[gmx-users] mdrun-gpu error

Szilárd Páll szilard.pall at cbr.su.se
Thu Jan 19 16:07:58 CET 2012


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
>
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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