Hello,
At the moment I am doing some benchmarks with Amber 12 on our new K20 GPU cards. It is a pity that I do not have access to the latest Amber (v14) -- I am waiting for the site license and that is out of my hands. Amber 12 does not work with CUDA 6*, however it does work with CUDA 5* and actually v5.0 is recommended by the developers. So, in other words, this Amber cannot take advantage of all the latest technology -- GPUDIRECT and all that. I'm just trying to get a feel for how I'm doing. In other words do the benchmark figures that I have quoted in this mail make sense?
To do these benchmarks I decided to download a copy of the MVAPICH2 source, and build it from scratch. We have OFED 2.1 and access to CUDA 5.0, and as a start I decided to go for a fairly simple MVAPICH configure:
./configure --with-cuda=/local/software/cuda/5.0.35 --prefix=/local/software/mvapich2/2.0.1/intel-cuda5.0
Once MVAPICH2 was built I then installed Amber 12, using the Intel compilers and MKL libraries, with CUDA/MPI support. The results were OK, however not really impressive. Actually I had earlier build the same Amber executable with OpenMPI (with CUDA support). We have 2 GPU K20 cards per node. Here are the results of one of the Amber benchmarks (PME/Cellulose_production_NPT):
Time(s) ns/day
CUDA *1 393 4.47
MVAPICH
CUDA *2 323 5.47
CUDA *4 286 6.27
OpenMPI
CUDA *2 324 5.46
CUDA *4 254 7.15
It is interesting to see that OpenMPI seems to perform pretty well these days. When I last tried this comparison at least a couple of years ago I found that OpenMPI performed terribly. It seems that the OpenMPI team have put a lot of work in to getting it "working with" GPU cards. Am I, however, correct in thinking that MVAPICH could still do better, and if so how would you recommend that I configure it for OFED/GPU support, please?
On the other hand I am really keen to some Amber 14 benchmarks and try out CUDA 6* with MVAPICH2-GDR. It is a real pity that I am still waiting for a colleague in the chemistry department to sort out our site license. Does anyone, by any chance, have any results for Amber 14 plus all the latest GPU/CUDA technology, please?
Best regards -- David.
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Received on Tue Dec 16 2014 - 04:30:02 PST
