Aw: Re: [gmx-users] GPU problem

[lloyd riggs]

 

Thanks, thats exact what I was looking for.

 

Stephan


Gesendet: Dienstag, 04. Juni 2013 um 22:28 Uhr
Von: "Justin Lemkul" 
An: "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] GPU problem



On 6/4/13 3:52 PM, lloyd riggs wrote:
> Dear All or anyone,
> A stupid question. Is there an script anyone knows of to convert a 53a6ff from
> .top redirects to the gromacs/top directory to something like a ligand .itp?
> This is usefull at the moment. Example:
> [bond]
> 6 7 2 gb_5
> to
> [bonds]
> ; ai aj fu c0, c1, ...
> 6 7 2 0.139 1080.0 0.139 1080.0 ; C CH
> for everything (a protein/DNA complex) inclusive of angles, dihedrials?
> Ive been playing with some of the gromacs user supplied files, but nothing yet.

Sounds like something grompp -pp should take care of.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] GPU problem

[Justin Lemkul]

On 6/4/13 3:52 PM, lloyd riggs wrote:

Dear All or anyone,
A stupid question.  Is there an script anyone knows of to convert a 53a6ff from
.top redirects to the gromacs/top directory to something like a ligand .itp?
This is usefull at the moment.  Example:
[bond]
 6 7 2gb_5
to
[bonds]
; ai  aj  fuc0, c1, ...
   6  7   20.139  1080.00.139  1080.0 ;   C  CH
for everything (a protein/DNA complex) inclusive of angles, dihedrials?
Ive been playing with some of the gromacs user supplied files, but nothing yet.


Sounds like something grompp -pp should take care of.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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RE:[gmx-users] GPU problem

[lloyd riggs]

 

Dear All or anyone,

 

A stupid question.  Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp?  This is usefull at the moment.  Example:

 

[bond]

    6 7 2    gb_5

 

to

 

[bonds]

; ai  aj  fu    c0, c1, ...

  6  7   2    0.139  1080.0    0.139  1080.0 ;   C  CH  

 

for everything (a protein/DNA complex) inclusive of angles, dihedrials?

 

Ive been playing with some of the gromacs user supplied files, but nothing yet.

 

Stephan Watkins
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Re: [gmx-users] GPU problem

[Szilárd Páll]

"-nt" is mostly a backward compatibility option and sets the total
number of threads (per rank). Instead, you should set both "-ntmpi"
(or -np with MPI) and "-ntomp". However, note that unless a single
mdrun uses *all* cores/hardware threads on a node, it won't pin the
threads to cores. Failing to pin threads will lead to considerable
performance degradation; just tried and depending on how (un)lucky the
thread placement and migration is, I get 1.5-2x performance
degradation with running two mdrun-s on a single dual-socket node
without pining threads.

My advise is (yet again) that you should check the
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
wiki page, in particular the section on how to run simulations. If
things are not, clear please ask for clarification - input and
constructive criticism should help us improve the wiki.

We have been patiently pointing everyone to the wiki, so asking
without reading up first is neither productive nor really fair.

Cheers,
--
Szilárd


On Tue, Jun 4, 2013 at 11:22 AM, Chandan Choudhury  wrote:
> Hi Albert,
>
> I think using -nt flag (-nt=16) with mdrun would solve your problem.
>
> Chandan
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Tue, Jun 4, 2013 at 12:56 PM, Albert  wrote:
>
>> Dear:
>>
>>  I've got four GPU in one workstation. I am trying to run two GPU job with
>> command:
>>
>> mdrun -s md.tpr -gpu_id 01
>> mdrun -s md.tpr -gpu_id 23
>>
>> there are 32 CPU in this workstation. I found that each job trying to use
>> the whole CPU, and there are 64 sub job when these two GPU mdrun submitted.
>>  Moreover, one of the job stopped after short of running, probably because
>> of the CPU issue.
>>
>> I am just wondering, how can we distribute CPU when we run two GPU job in
>> a single workstation?
>>
>> thank you very much
>>
>> best
>> Albert
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>>
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Re: [gmx-users] GPU problem

[Albert]

On 06/04/2013 11:22 AM, Chandan Choudhury wrote:

Hi Albert,

I think using -nt flag (-nt=16) with mdrun would solve your problem.

Chandan



thank you so much.

it works well now.

ALBERT
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Re: [gmx-users] GPU problem

[Chandan Choudhury]

Hi Albert,

I think using -nt flag (-nt=16) with mdrun would solve your problem.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Jun 4, 2013 at 12:56 PM, Albert  wrote:

> Dear:
>
>  I've got four GPU in one workstation. I am trying to run two GPU job with
> command:
>
> mdrun -s md.tpr -gpu_id 01
> mdrun -s md.tpr -gpu_id 23
>
> there are 32 CPU in this workstation. I found that each job trying to use
> the whole CPU, and there are 64 sub job when these two GPU mdrun submitted.
>  Moreover, one of the job stopped after short of running, probably because
> of the CPU issue.
>
> I am just wondering, how can we distribute CPU when we run two GPU job in
> a single workstation?
>
> thank you very much
>
> best
> Albert
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> http://www.gromacs.org/**Support/Mailing_Lists
>
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[gmx-users] GPU problem

[Albert]

Dear:

 I've got four GPU in one workstation. I am trying to run two GPU job 
with command:


mdrun -s md.tpr -gpu_id 01
mdrun -s md.tpr -gpu_id 23

there are 32 CPU in this workstation. I found that each job trying to 
use the whole CPU, and there are 64 sub job when these two GPU mdrun 
submitted.  Moreover, one of the job stopped after short of running, 
probably because of the CPU issue.


I am just wondering, how can we distribute CPU when we run two GPU job 
in a single workstation?


thank you very much

best
Albert
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