[gmx-developers] Problem with qmmm and mpi combo (4.0.5)

[Gerrit Groenhof]

Hi Ake,

I understand your frustrations, and I am sorry for that. As Christian  
writes, QMMM on multiple processors is not working with domain  
decomposition. For the linked gamess-uk (6.something version0,  
gamessuk and gromacs were using the same

MOst of the time one does a semi-empirical (mopac or dftb), or  
gaussian based QM/MM computation. Therefore, I have not yet worked on  
making the QM/MM interface work with the PD.

I do not know what type of application your users are planning to do,  
but if there is nothing special required from gamess-uk, the most  
convenient option might be to simply use gaussian, or orca, for which  
Christoph Riplinger wrote an interface that seems to work smoothly.


Hope this helps.

Gerrit




On 20 Nov 2009, at 18:34, Christian Seifert wrote:

> Hi!
>
> I never managed to run GMX with MPI when using QMMM. I tried it with  
> different
> versions (also GMX 3). As Berk wrote, most of the time (in my case  
> more than
> 95%) the QM program has to calculate. I guess that running the MM  
> part in QMMM
> with multiple CPU will be even slower compared to MM part of QMMM on  
> a single
> CPU (because of communication overhead).
> So my decision was:
> I do not compile GMX_qmmm with mpi.
>
> Greets,
> Christian
>
> Am Freitag, 20. November 2009 um 16:40 schrieb Ake Sandgren:
> Hi!
>
> When building gromacs 4.0.5 for qmmm and mpi something goes wrong
> (unless its in the input data of course :-)
>
> For the input data I'm using (from a user of ours) i have the  
> following
> problem:
> In qmmm.c update_QMMMrec the gmx_sumi in the parallel excecution part
> have inconsistent values in md->nr, i.e. not the same on process 0 and
> process 1. (Causing a problem in the Allreduce)
>
> Also fr->QMMMlist_sr.nri is different between processes.
>
> What might be the cause of this? Input data error or bug in the code?
>
> I've been trying to backtrace this but it's now friday afternoon and  
> i'm
> giving up :-(
>
> -- 
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
>
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>
> M.Sc. Christian Seifert
> Department of Biophysics
> University of Bochum
> ND 04/67
> 44780 Bochum
> Germany
> Tel: +49 (0)234 32 28363
> Fax: +49 (0)234 32 14626
> E-Mail: cseifert at bph.rub.de
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--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/