[gmx-users] parallel processing

[abhisek Mondal]

Hello Mark,

I had gone through the page. Not finding any solution there.

My architecture is:
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                16
On-line CPU(s) list:   0-15
Thread(s) per core:    1
Core(s) per socket:    8
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 45
Stepping:              7
CPU MHz:               2593.616
BogoMIPS:              5186.82
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              20480K
NUMA node0 CPU(s):     0-7
NUMA node1 CPU(s):     8-15


When i put "mpirun -np 64 gmx_mpi mdrun  -v -deffnm npt" it just runs on a
single node using 64 threads (16 availavle for a single node normally).

How am I supposed to do node distribution efficiently ? I'm trying to run
the job using 4 nodes and 16 threads.
A little suggestion would be highly appreciated.



On Fri, Dec 2, 2016 at 4:55 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Please check out
> http://manual.gromacs.org/documentation/2016.1/user-
> guide/mdrun-performance.html.
> Your first sample command is woefully inefficient, but for em this likely
> doesn't matter.
>
> Mark
>
> On Fri, 2 Dec 2016 09:01 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
>
> > But if I want to run the same job in 4 nodes (available cores= 4*16) then
> > how would this work ?
> >
> > On Fri, Dec 2, 2016 at 2:20 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> >
> > > Hi Abhisek,
> > >
> > > You would need to use another version of gromacs with mpi rather than
> > > thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
> > > could then use the following command
> > >
> > > mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
> > >
> > > I'm not sure why you are specifying -npme 0 but would suggest you don't
> > do
> > > this and instead let the number of separate pme ranks be set
> > > automatically.
> > >
> > > Best wishes
> > > James
> > >
> > > > Hi,
> > > >
> > > > I'm running gromacs on a cluster configuration as follows:
> > > > 1 node = 16 cores
> > > >
> > > > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme
> 0
> > -v
> > > > -deffnm em" command.
> > > >
> > > > How can I be able to run on multiple node (I have 20 nodes
> available) ?
> > > > "-nt" is not doing good here.
> > > >
> > > >
> > > >
> > > > --
> > > > Abhisek Mondal
> > > >
> > > > *Research Fellow*
> > > >
> > > > *Structural Biology and Bioinformatics Division*
> > > > *CSIR-Indian Institute of Chemical Biology*
> > > >
> > > > *Kolkata 700032*
> > > >
> > > > *INDIA*
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> > --
> > Abhisek Mondal
> >
> > *Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
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-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*