[gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
ljggmx at yahoo.com.sg
Tue Jun 4 16:02:53 CEST 2013
Has anyone has Gromacs benchmark on Bluegene/Q?
I recently installed gromacs-461 on BG/Q using the following command:
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
After that, I did a benchmark simulation using a box of pure water containing 140k atoms.
The command I used for the above test is:
srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log >& job_md1
And I got the following performance:
Num. cores hour/ns
The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q.
I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling?
Any comments/suggestions are appreciated, thank you very much!
Have a nice day!
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