On 21/02/2012 8:11 AM, Floris Buelens wrote:
Poor scaling with MPI on many-core machines can also be due uneven job
distributions across cores or jobs being wastefully swapped between
cores. You might be able to fix this with some esoteric configuration
options of mpirun (--bind-to-core worked for me with openMPI), but the
surest option is to switch to gromacs 4.5 and run using thread-level
parallelisation, bypassing MPI entirely.
That can avoid problems arising from MPI performance, but not those
arising from PP-vs-PME load balance, or intra-PP load balance. The end
of the .log files will suggest if these latter effects are strong
contributors. Carsten's suggested solution is one good one.
Mark
------------------------------------------------------------------------
*From:* Sara Campos <[email protected]>
*To:* [email protected]
*Sent:* Monday, 20 February 2012, 17:12
*Subject:* [gmx-users] Scaling/performance on Gromacs 4
Dear GROMACS users
My group has had access to a quad processor, 64 core machine (4 x
Opteron 6274 @ 2.2 GHz with 16 cores)
and I made some performance tests, using the following specifications:
System size: 299787 atoms
Number of MD steps: 1500
Electrostatics treatment: PME
Gromacs version: 4.0.4
MPI: LAM
Command ran: mpirun -ssi rpi tcp C mdrun_mpi ...
#CPUS Time (s) Steps/s
64 195.000 7.69
32 192.000 7.81
16 275.000 5.45
8 381.000 3.94
4 751.000 2.00
2 1001.000 1.50
1 2352.000 0.64
The scaling is not good. But the weirdest is the 64 processors performing
the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper
on JCTC
and I do not understand why this is happening. Can anyone help?
Thanks in advance,
Sara
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
