Re: mdrun -nt

[Valentina]

Hello!

Firstly - you want 8 threads?

This is from my settings.xml:

<cg>

  <inverse> 

    <gromacs>

      <mdrun>

        <command> mpirun -np 8 mdrun_s_mpi </command>  

      </mdrun>

    </gromacs>

  </inverse>

</cg>

So yours seems fine, just check you have correct number of spaces before <mdrun> , all of the options are included in right place and options closed </mdrun>

It is hard to tell without knowing the error/ seeing the .xml

V

On Monday, July 23, 2012 5:47:58 PM UTC+1, Soree Kim wrote:

Hi, I am working on CG simulations with VOTCA.

I have a question about settings.xml options.

I want to use "mdrun -nt" option, but I don't know where to put it.

I have tried <mdrun><command> -nt 8 </command></mdrun> and

<mdrun><opts> -nt 8 </opts></mdrun>. 

However, it doesn't work.

Please, tell me what is the problem.

Thank you.

Best,

Soree Kim

[Christoph Junghans]

Hi,

which version of votca are you using?

2012/7/23 Soree Kim <ksr...@gmail.com>:

> Hi, I am working on CG simulations with VOTCA.
>
> I have a question about settings.xml options.
>
> I want to use "mdrun -nt" option, but I don't know where to put it.
>
> I have tried <mdrun><command> -nt 8 </command></mdrun> and
> <mdrun><opts> -nt 8 </opts></mdrun>.

The according xml option is:
"cg.inverse.gromacs.mdrun.opts", so
<cg>
<inverse>
<gromacs>
<mdrun>
<opts> -nt 4 </opts>
</mdrun>
</gromacs>
</inverse>
</cg>

In most case that should not be needed at all, as mdrun detects the
number of cpus automatically.
(-nt 0 is the default)

Christoph

>
> However, it doesn't work.
>
> Please, tell me what is the problem.
>
> Thank you.
>
> Best,
> Soree Kim
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Christoph Junghans]

2012/7/23 Valentina <valentina...@yahoo.co.uk>:

> Hello!
>
> Firstly - you want 8 threads?
> This is from my settings.xml:
>
> <cg>
>
> <inverse>
>
> <gromacs>
>
> <mdrun>
>
> <command> mpirun -np 8 mdrun_s_mpi </command>
>
> </mdrun>
>
> </gromacs>
>
> </inverse>
>
> </cg>

Thanks, Valentina.

This is the other option to run mdrun in parallel.

@Soreen Kim: You first have to decide if you want to use MPI
(distribution and shared memory) or threads (shared memory only) and
then use one of the two solutions.

Christoph

>
>
> So yours seems fine, just check you have correct number of spaces before
> <mdrun> , all of the options are included in right place and options closed
> </mdrun>
>
>
> It is hard to tell without knowing the error/ seeing the .xml
>
>
> V
>
>
>
> On Monday, July 23, 2012 5:47:58 PM UTC+1, Soree Kim wrote:
>>
>> Hi, I am working on CG simulations with VOTCA.
>>
>> I have a question about settings.xml options.
>>
>> I want to use "mdrun -nt" option, but I don't know where to put it.
>>
>> I have tried <mdrun><command> -nt 8 </command></mdrun> and
>> <mdrun><opts> -nt 8 </opts></mdrun>.
>>
>> However, it doesn't work.
>>
>> Please, tell me what is the problem.
>>
>> Thank you.
>>
>> Best,
>> Soree Kim
>

> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To view this discussion on the web visit

> https://groups.google.com/d/msg/votca/-/3UpsrDBvbQwJ.

[Soree Kim]

I tried to use threads.

My problem was that I didn't put the options in right place.. And now, it is solved.

Thank you!

Soree Kim

2012년 7월 24일 화요일 오전 2시 14분 26초 UTC+9, Christoph Junghans 님의 말:

> votca+unsubscribe@googlegroups.com.

[abrukhno]

Here is Christoph's response for those interested:
=====
Concerning your question:
1.) set cg.inverse.dlpoly.command to something like "mpirun -np 8
DLPOLY.Z" to make dlpoly run using mpi
2.) do NOT run csg_inverse using mpirun in the queueing script
3.) use csg_inverse --wall-time $((24*3600)) to give the wall clock
time (in sec) to csg_inverse. csg_inverse will stop if it cannot make
another iteration step.
4.) if you want automatic resubmission add a line like
[[ $? -eq 0 && ! -f done ]] && qsub $QSCRIPT
to the end of your submit script.

Christoph
=====