Re: [gmx-users] problem with MPI,thread and number of CPU

[Mark Abraham]

Hi,

On Mon, May 16, 2016 at 9:13 PM  wrote:

>
>
> 
> p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }
>
>
> Dear Gromacs users
>
>
> During simulating DPPC membrane I confront with several Problems. I
> intend to express them here and I really appreciate it if you help me.
> Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC
> molecules. the trend ( I mean the way it increase or decrease) of
> Pressure xx is important to me. as one can expect, due to the size of my
> system ( number of atom) the result is so erratic  ( about 200bar).
> so I enlarge the system in X-direction considering consistent trend for
> both system. so I replicated system in X-direction, minimized it and do
> an NPT on it.
>

A common mistake here is to concatenate boxes without leaving a suitable
spacing between them, because atoms whose centers are close to the old
edges of the box can now be too close to their new neighbours.


> during NPT, my working job blew up with this error :
>
>
> An atom moved too far between two domain decomposition steps
>
>
> does this error relate to the number of cpu-cores, because when I
> decrease number of the cores from 16 to 8 using -nb 8, I dont see
> this error again, but there is no progress in the number of steps !!!
>

Different parallelism leads to different forces, and (in this case)
different ways for the simulation to blow up, particularly if my guess is
correct.


> also I have question about MPI. In my laptop when I simulate a box
> ( 128
> DPPC with 2000 W), the system runs with :
>
>
> Using 1 MPI thread
>
> Using 4 OpenMP threads
>
>
> when I do the same, in High performance Computer of the
> university, Its
> output is totally different which also uses automatically :
>
>
> Using 24 MPI threads
>
> Using 1 OpenMP thread per tMPI thread
>
>
> but when I used -ntmpi 1 to change MPI threads to 1, it gave the
> same
> answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I
> should notice that I now what is the meaning of MPI and thread, but
> dont now what is the optimum number 
>

It varies. mdrun has some heuristics that consider the kind of processor,
the number of cores, the number of atoms, the presence of GPUs, the value
of environment variables like OMP_NUM_THREADS...

Mark


>
> best  regards
>
>
> Ali
>
>
> ==
>
>
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
>
>
> Department of Mechanical Engineering
>
>
> Sharif University of Technology, Tehran, Iran
>
>
>
>
>
>
>
>
>
>
>
>
>
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[gmx-users] problem with MPI,thread and number of CPU

[khourshaeishargh]

p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Gromacs users


During simulating DPPC membrane I confront with several Problems. I
intend to express them here and I really appreciate it if you help me.
Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC
molecules. the trend ( I mean the way it increase or decrease) of
Pressure xx is important to me. as one can expect, due to the size of my
system ( number of atom) the result is so erratic� ( about 200bar).
so I enlarge the system in X-direction considering consistent trend for
both system. so I replicated system in X-direction, minimized it and do
an NPT on it.


during NPT, my working job blew up with this error :


An atom moved too far between two domain decomposition steps


does this error relate to the number of cpu-cores, because when I
decrease number of the cores from 16 to 8 using -nb 8, I dont see
this error again, but there is no progress in the number of steps !!!


also I have question about MPI. In my laptop when I simulate a box ( 128
DPPC with 2000 W), the system runs with :


Using 1 MPI thread

Using 4 OpenMP threads


when I do the same, in High performance Computer of the university, Its
output is totally different which also uses automatically :


Using 24 MPI threads

Using 1 OpenMP thread per tMPI thread


but when I used -ntmpi 1 to change MPI threads to 1, it gave the same
answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I
should notice that I now what is the meaning of MPI and thread, but
dont now what is the optimum number 


best� regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran




�




�

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