[gmx-users] mdrun-gpu error

[Mark Abraham]

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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>
>
> -- 
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>

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