AW: Two GPU-based workstation

From: Norman Geist (
Date: Mon Nov 11 2013 - 03:23:53 CST

The error you see has nothing to do with pme. If you search around the mailing list you will notice that it is about the box dimensions itself. When namd starts, it defines a patch grid to depart the work for the parallel execution. This patch grid cannot be reinitialized while the simulation is running. This means, that if the box fox example shrinks heavily due a barostat and bad initial solvent density, the cell becomes too small for this initial patch grid as single patches will get empty. If the error occurs right from the start, this indicates wrong settings of the periodic box. If it occurs during the simulation cause of using a barostat, you might want to just restart which will reinitialize the patch grid to the new cell dimensions, or use margin to add some additional space to the patchgrids. The latter will come with a slowdown of the simulation and should therefore be used only while the barostat is active and the value be chosen wisely.


Norman Geist.


Von: James Starlight []
Gesendet: Montag, 11. November 2013 09:49
An: Norman Geist; Namd Mailing List
Betreff: Re: namd-l: Two GPU-based workstation


2) about cores

so If my physical number is 6 ( I dont really know why debian recognize 12 cores)

I should use +p6 +ppn3 +devices 0,1 do adjust each 3 cores for each gpu shouldn't it ?


2013/11/11 James Starlight <>



pmegridspacing 1;
fullElectFrequency 2;

instead of

PMEGridSizeX $fftx; # should be close to the cell size
PMEGridSizeY $ffty; # corresponds to the charmm input fftx/y/z
PMEGridSizeZ $fftz;
pmegridspacing 1;

have crashed my simulation at the beginning

namd2 +idlepoll +p12 +ppn6 +devices 0,1 ./aMD.conf >> b2ar_p0gDiheBoostlog_20000
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

 (this time I've start from the checkpoint of the previous run, performed with the defined XYZ of the PME. Does it means that I should to begin simulation from the beginning of the equilibration phase with fullElectFrequency >1 or there are alternative solutions?




2013/11/11 Norman Geist <>

Why not simply setting „pmegridspacing 1“?


I usually use numcpus/numgpus for each gpu. And really believe me, you only got 6 cores not 12. And running 2 simulations on only one cpu socket is inefficient.


Norman Geist.


Von: [] Im Auftrag von James Starlight

Gesendet: Samstag, 9. November 2013 15:53

An: Namd Mailing List

Betreff: Re: namd-l: Two GPU-based workstation


by the way increasing of the fullElectFrequency > 1 has end simulation with the errors about unproperly set XYZ of the PME boundaries ( with fullElectFrequency 1 I use 80 80 120 simulating membrane protein and have not any errors. How could I change pme options ?

also my question is the optimal balancing of the number of CPUs for each GPU. Is there some impirical relationships showing what amount of CPUs is needed for each GPU ?

assuming that I obtained best performance using
 namd2 +idlepoll +p12 +devices 0 ./aMD.conf

I'd like to share some CPUs between both available GPUs for the 2 parallel simulations.



2013/11/8 James Starlight <>

Could fullelectfrequency 4 increase performance exactly dual-gpu regime ?

In case of running two simulations will it be enough to provide each gpu with the 6 cores ? ( I suppose that I have not obtain good performance in 2 gpu regime exactly due to small number of cores for each gpu)



2013/11/7 Ajasja Ljubetič <>

On 7 November 2013 06:32, James Starlight <> wrote:

I've gone to conclusion that using 2 GPUs simultaneously gave me the same performance as 1 GPU like


Yes, this is expected, for such small systems there is too little work at each step to scale efficiently. You can however run one (or two or three) independent simulations on each GPU.








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