Dear Amber users,
I just installed Amber11 on our new cluster computer, and ran some test
cases on it.
Each node has 48 cores, and all nodes are connected with QDR infiniband.
I built parallel version of sander with both mvapich2-1.5 and
openmpi-1.4.3. The
performance of the program is quite strange:
Here is a case using 1 core, it took about 1 hr and 24 min:
| Job began at 10:00:53.602 on 07/27/2011
| Setup done at 10:00:54.844 on 07/27/2011
| Run done at 11:23:48.604 on 07/27/2011
And the case using 48 core (one computing node), it took about 9 min 40s
| Job began at 20:32:36.572 on 07/28/2011
| Setup done at 20:32:38.436 on 07/28/2011
| Run done at 20:41:17.902 on 07/28/2011
It is nice.
However, the case using 192 cores (4 computing nodes), it took about 12
min. !
| Job began at 20:20:14.506 on 07/28/2011
| Setup done at 20:20:17.208 on 07/28/2011
| Run done at 20:31:26.587 on 07/28/2011
Something is wrong when using more than one computing node, I
followed the installation
guide and compile the program using both intel and gcc compiler with MKL
lilbrary. I always
got the similar result.
Any hint on how this could happen and who to fix the problem?
Thanks.
Jyh-Shyong Ho, Ph.D.
Research Scientist
National Center for High Performance Computing
Hsinchu, Taiwan, ROC
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Received on Thu Jul 28 2011 - 17:30:02 PDT
