[gmx-developers] git gromacs and -dlb

[Carsten Kutzner]

Done.

C.


On Jun 29, 2010, at 3:46 PM, hess at sbc.su.se wrote:

> Please file a bugzilla.
> 
> Thanks,
> 
> Berk
> 
>> On Jun 29, 2010, at 3:53 AM, Roland Schulz wrote:
>> 
>>> 
>>> 
>>> On Mon, Jun 28, 2010 at 4:32 AM, Carsten Kutzner <ckutzne at gwdg.de>
>>> wrote:
>>> On Jun 28, 2010, at 10:23 AM, hess at sbc.su.se wrote:
>>> 
>>>> Hi,
>>>> 
>>>> But does dlb get turned on at some point without -dlb?
>>>> 
>>> Apparently not, at least not in the runs I just looked at.
>>> 
>>> Does it crash immediately or after many steps?
>>> If it is the later one:  often it is possible to make it reproducible
>>> crash by setting GMX_DLB_FLOP to 1.
>>> 
>> Hi,
>> it crashes immediately and reproducibly in step 0, with various tpr files
>> that all work
>> in 4.0.x, for different architectures/MPI libs. It's not a real problem,
>> because I can as well
>> leave the -dlb flag away, but since this worked in 4.0.x, I guess it
>> should still work now.
>> 
>> Carsten
>> 
>>> Roland
>>> 
>>> 
>>> Carsten
>>> 
>>>> Berk
>>>> 
>>>>> Hi,
>>>>> 
>>>>> there appears to be an issue with the -dlb flag when turned on
>>>>> from the very beginning in mdrun. For at least two different
>>>>> MD systems (incl. dppc with PME) I get errors like
>>>>> 
>>>>> Fatal error:
>>>>> 248 particles communicated to PME node 3 are more than 2/3 times the
>>>>> cut-off out of the domain decomposition cell of their charge group in
>>>>> dimension y.
>>>>> 
>>>>> when started with
>>>>> mpirun -np 4 mdrun -s ../tpr/ap_1ps.tpr -dlb yes.
>>>>> 
>>>>> With -dlb no everything works fine.
>>>>> 
>>>>> Carsten
>>>>> 
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
> 
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne