Myunggi Yi wrote:
I have tested with 8, 16, 24 and 32 cpus.
Only parallel with 8 and 16 cpus works, and the other cases (24 and
32) are even much slower than 8 cpus' case.
Any idea about this?
larger systems
check mailing list
use 16 cpus until gmx 4
On Nov 24, 2007 11:42 AM, David van der Spoel <[EMAIL PROTECTED]> wrote:
Myunggi Yi wrote:
Thank you for the answer.
I compiled gmx with gcc and gnu onpempi.
I have seen very good performance with 16 cpus (about 12,000 atoms).
+++++++++++++++++++++++++++++++++++
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 50.828 19.920 14.648 1.638
Total Scaling: 95% of max performance
+++++++++++++++++++++++++++++++++++
Now I just submit a job with 32 cpus (about 48,000 atoms).
It looks very very slow.
Would you recommend the optimal numer of cpus?
No. You have to test for yourself (as you are doing right now).
It is very dependent on simulation size, network etc.
On Nov 24, 2007 10:53 AM, David van der Spoel <[EMAIL PROTECTED]> wrote:
Myunggi Yi wrote:
Sorry. Here is more information.
GNU C/C++ 3.4.6
Intel C/C++ 10.0.026
and
OpenMPI GNU 1.2.4
OpenMPI Intel 1.2.4
Everything will probably be easier with the gcc compiler, and the
performance difference is negligible for gromacs.
On Nov 24, 2007 10:31 AM, Myunggi Yi <[EMAIL PROTECTED]> wrote:
Dear gromacs users,
I'm a beginner.
I'm trying to compile gromacs 3.3.1 or 3.3.2 on the following linux
cluster (centOS).
Dual, Dual-Core 2220 2.8 GHz Opterons, 2 GB RAM per core, 64-bit.
I will use 16 to 32 (64) cpus for the parallel simulations.
I tested mpich2, but there is a problem with infiniband communications.
I have intel and GNU compilers and openMPI.
Which option will give me the best performance?
Have a nice weekend.
--
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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