Hi Ross,
I am running the example of tutorial B3. I tried to run on a single node. The attached file is the information of the server by type 'cat /proc/cpuinfo'. Thanks.
Aimin
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Monday, August 01, 2011 5:25 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] About running sander parallel
Hi Aimin
> I have tried the following:
>
> cd $AMBERHOME/test
> unset DO_PARALLEL
> unset TESTsander
> export DO_PARALLEL='mpirun -np 4'
> make test.parallel
>
> And attached is the files created by running above commands. However,
> when I ran sander parallel as follows:
Your test cases look good now so it looks like things are running in
parallel properly.
> mpirun -np 4 $AMBERHOME/bin/sander.MPI -O -i....
>
> I found that the time to finish the job is the same as using single
> cpu. What can I do? Thank you.
What are the details of what you are trying to simulate? - How many atoms,
what input options, PME or GB etc?
Also what are the details regarding your hardware, are you trying to run on
a single node here? What does 'cat /proc/cpuinfo' give you. If you are
trying to run on multiple nodes what is the interconnect between nodes? Are
you certain the MPI tasks are being handed out to the correct nodes etc etc.
Performance in parallel is VERY problem and hardware specific, thus we need
a lot more information before we will be able to help.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Aug 01 2011 - 18:30:02 PDT
