[gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Jones de Andrade wrote:

<snip>

> Using just the "simple" tests now to try to find out where is the error. 
> Since the error goes everywhere, it just simplify things.
> It outputs everything ok with the serial part, but it all gets really 
> messy in the mpi section.
> 
> In version 4.0.4, it's complaining that the grompp is not understanding 
> the "-np" flag (Invalid command line argument). Then, it doesn't even 
> create a mdrun.out file. I tried to google this error, but basically 
> nothing was found. It also can't be a mixing of compilations, since 
> everything is done in completelly different and independent directories.
> 

This has been discussed several times on the list.  The -np flag is no longer 
necessary with grompp.  You don't get an mdrun.out because the .tpr file is 
likely never created, since grompp fails.

> Version 3.3.3 on the other hand already failed in so many different 
> places that I'm really thinking IF I'll make it available in the new 
> cluster. :P
> 

What messages are you getting from 3.3.3?  I thought you said the 3.3.x series 
worked fine.

-Justin

> This has to be any sort of pretty stupid mistake so. But I'm clueless 
> this time. :( Any ideas?
> 
> Thanks a lot in advance! :)
> 
> Jones
> 
> On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Jones de Andrade wrote:
> 
>         Hi everyone.
> 
>         Well, lets go straight to the point: last time I've installed
>         gromacs, it was still 3.3.x and there was no testbed available
>         yet. I've done some tests of my own and everything gone fine.
> 
>         I'm doing some new installations now, both gmx3.3.3 and
>         gmx4.0.4. They weem to work pretty well in serial, but
>         absolutelly not with mpi. A whole "plethora" of different errors
>         appear.
> 
>         Before bothering the list with error messages, my question is:
>         someone has successfully used it with OpenMPI or MPIch? Before
>         questions arise, I have different test users for each, and
>         absolutelly independent compilations.
> 
> 
>     Every installation (serial and MPI) that I have installed worked
>     flawlessly. Our cluster uses mpich, and our local machines
>     (dual-core) use OpenMPI.
> 
>     Can you provide some of the error messages?  Are the reported from
>     Gromacs, or from the MPI implementations?
> 
>     -Justin
> 
>         Thanks a lot for any answer in advance.
> 
>         Sincerally yours,
> 
>         Jones
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================