Re: [gmx-users] Simulation on multi nodes performance

[Mark Abraham]

Hi,

There's some useful background at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html

Whether you want mpirun -np X mdrun_mpi or mpirun -np X gmx_mpi mdrun
depends whether GROMACS was configured to build only mdrun.

Otherwise, the logfile is indeed your friend - so that you can see whether
mdrun agreed with what you thought the hardware was, and in the performance
report at the end to see what took lots of time.

Mark

On Mon, Nov 27, 2017 at 7:21 AM Ali Ahmed  wrote:

> Hello GMX users
>
> I'm trying to do simulations on multi nodes so I used  8 nodes (128
> processors). AS I see there is no difference between 1 node and 8 nodes.
>
> I used these commands:
>
> ---
>
> load apps/gromacs-2016
>
> load apps/openmpi-2.1.1
>
> gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr
>
> mpirun -np 128 mdrun_mpi -v -deffnm EMZ
>
> 
>
> I'm kind of confused about the right commands
>
> Any comment will be helpful
>
> Thanks in advance
>
> Ali
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Re: [gmx-users] Simulation on multi nodes performance

[Alexandr Nasedkin]

On 27/11/2017 07:21, Ali Ahmed wrote:Hello GMX users

I'm trying to do simulations on multi nodes so I used  8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.
Check the log file showing how many nodes you use, look for a line as in 
template:

Running on 2 nodes with total 40 cores, 40 logical cores


I used these commands:

---

load apps/gromacs-2016

load apps/openmpi-2.1.1

gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr

mpirun -np 128 mdrun_mpi -v -deffnm EMZ



I'm kind of confused about the right commands
I use gmx mdrun_mpi instead of mdrun_mpi: all depends on how your 
gromacs is installed.


Any comment will be helpful

Thanks in advance

Ali

-Alex

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[gmx-users] Simulation on multi nodes performance

[Ali Ahmed]

Hello GMX users

I'm trying to do simulations on multi nodes so I used  8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.

I used these commands:

---

load apps/gromacs-2016

load apps/openmpi-2.1.1

gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr

mpirun -np 128 mdrun_mpi -v -deffnm EMZ



I'm kind of confused about the right commands

Any comment will be helpful

Thanks in advance

Ali
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