Re: [gmx-users] parallel simulation in dual core PC

[Mark Abraham]

On 22/04/2010 3:12 AM, Arden Perkins wrote:

Did you preprocess the .tpr file for 2 cores with grompp?


This was only necessary for GROMACS 3.


Also, I
believe you have to have an additional -np 2 after the mdrun_mpi


This was only necessary with early versions of MPI libraries.


command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr
-g 200ns.log
-c 200ns.gro -np 2
-- at least this is what I understand from what my prof told me. We just
started running parallel simulations for an undergraduate research
project and I believe that is how we input commands. I'm sure the
gromacs experts will correct me if I'm wrong.


:-)

Mark


Good luck!
Arden
On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin mailto:jian...@phys.sinica.edu.tw>> wrote:

Hi,

I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type "lamboot" first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g
200ns.log
-c 200ns.gro.
When the simulation starts, I use the commend, "top", to check the
utility
of CPU.
I found there is only one core which is used by GROMACS.
And the utility of this core is separated to 52% and 48% for two
mdrun_mpi
jobs.
How can I do for that?
Any and all assistance is greatly appreciated.

Hsin-Lin

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Re: [gmx-users] parallel simulation in dual core PC

[Justin A. Lemkul]

Arden Perkins wrote:
Did you preprocess the .tpr file for 2 cores with grompp? Also, I 
believe you have to have an additional -np 2 after the mdrun_mpi 
command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr 
-g 200ns.log

-c 200ns.gro -np 2
-- at least this is what I understand from what my prof told me. We just 
started running parallel simulations for an undergraduate research 
project and I believe that is how we input commands. I'm sure the 
gromacs experts will correct me if I'm wrong.
 


Since this is Gromacs 4.0.5, there is no differentiation when running grompp 
regarding the number of processors, so there is no -np flag for grompp.


There is also no need for mdrun_mpi -np; the number of nodes is taken from 
mpirun -np.


In addition, if all the output files are named 200ns.*, then you can save 
yourself some typing:


mpirun -np 2 mdrun_mpi -deffnm 200ns

-Justin


Good luck!
 
Arden
On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin > wrote:


Hi,

I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type "lamboot" first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g
200ns.log
-c 200ns.gro.
When the simulation starts, I use the commend, "top", to check the
utility
of CPU.
I found there is only one core which is used by GROMACS.
And the utility of this core is separated to 52% and 48% for two
mdrun_mpi
jobs.
How can I do for that?
Any and all assistance is greatly appreciated.

Hsin-Lin

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] parallel simulation in dual core PC

[Arden Perkins]

Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe
you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np
2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c 200ns.gro -np 2
-- at least this is what I understand from what my prof told me. We just
started running parallel simulations for an undergraduate research project
and I believe that is how we input commands. I'm sure the gromacs experts
will correct me if I'm wrong.

Good luck!

Arden
On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin wrote:

> Hi,
>
> I want to use my dual core PC to do the simulation.
> The version of GROMACS installed is version 4.0.5.
> According the message post by others on mailing list before.
> I type "lamboot" first, and type the commend:
> mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
> -c 200ns.gro.
> When the simulation starts, I use the commend, "top", to check the utility
> of CPU.
> I found there is only one core which is used by GROMACS.
> And the utility of this core is separated to 52% and 48% for two mdrun_mpi
> jobs.
> How can I do for that?
> Any and all assistance is greatly appreciated.
>
> Hsin-Lin
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] parallel simulation in dual core PC

[Mark Abraham]

On 21/04/2010 11:29 PM, Hsin-Lin wrote:

Hi,

I compare the run times.
The calculation of two processors is faster than one.
And I saw the utility of the two cores large than 85% separately.
I can sure it's exactly parallel simulation in my PC now.

Another question is:
someone told me the interconnect, 1G Ethernet, of the machine in our lab. is
too slow to do parallel simulation.
What the effect should be in this kind of slow Ethernet environment?


GROMACS will run very slowly, because it needs low latency 
communication. Gigabit ethernet is too slow here. See papers by Carsten 
Kutzner, for example.


Mark


Is it why the utility of CPU are always less than 35% when I submit the same
job to the machine in our lab.?

Hsin-Lin

Hi,

I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type "lamboot" first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c 200ns.gro.
When the simulation starts, I use the commend, "top", to check the utility
of CPU.
I found there is only one core which is used by GROMACS.
And the utility of this core is separated to 52% and 48% for two mdrun_mpi
jobs.


Depending what is being measured by what, this could be a correct
result. We can't really tell because we don't know how you've set up
LAM, or how your top works.

Do a short test calculation with one and two processors and compare the
run times.

Mark


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Re: [gmx-users] parallel simulation in dual core PC

[Mark Abraham]

On 21/04/2010 12:55 AM, Hsin-Lin wrote:

Hi,

I want to use my dual core PC to do the simulation.
The version of GROMACS installed is version 4.0.5.
According the message post by others on mailing list before.
I type "lamboot" first, and type the commend:
mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c 200ns.gro.
When the simulation starts, I use the commend, "top", to check the utility
of CPU.
I found there is only one core which is used by GROMACS.
And the utility of this core is separated to 52% and 48% for two mdrun_mpi
jobs.


Depending what is being measured by what, this could be a correct 
result. We can't really tell because we don't know how you've set up 
LAM, or how your top works.


Do a short test calculation with one and two processors and compare the 
run times.


Mark
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