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cluster:175 [2018/09/21 19:07] hmeij07 [Gromacs] |
cluster:175 [2018/09/22 12:47] hmeij07 [Lammps] |
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**[[cluster: | **[[cluster: | ||
- | ==== GTX vs P100 vs K20 ==== | + | ==== GTX vs P100 & K20 ==== |
- | Comparing these GPUs yields the following data. These are not " | + | Comparing these GPUs yields the following data. These are not " |
Credits: This work was made possible, in part, through HPC time donated by Microway, Inc. We gratefully acknowledge Microway for providing access to their GPU-accelerated compute cluster. | Credits: This work was made possible, in part, through HPC time donated by Microway, Inc. We gratefully acknowledge Microway for providing access to their GPU-accelerated compute cluster. | ||
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==== Amber ==== | ==== Amber ==== | ||
- | Amber16 continues to run best when one MPI process launches the GPU counterpart. | + | Amber16 continues to run best when one MPI process launches the GPU counterpart. |
< | < | ||
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gpu=1 mpi=1 11.94 ns/day | gpu=1 mpi=1 11.94 ns/day | ||
- | any mpi> | + | any mpi> |
[heme@login1 amber]$ ssh node6 ~/p100-info | [heme@login1 amber]$ ssh node6 ~/p100-info | ||
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==== Lammps ==== | ==== Lammps ==== | ||
- | We can also not complain about gpu utilization in this example. | + | We can also not complain about gpu utilization in this example. |
On our GTX server best performance was a ratio of 16:4 cpu:gpu for 932,493 tau/day (11x faster than our K20). However scaling the job to a ratio of cpu:gpu of 4:2 yields 819,207 tau/day which means a quad server can deliver about 1.6 million tau/day. | On our GTX server best performance was a ratio of 16:4 cpu:gpu for 932,493 tau/day (11x faster than our K20). However scaling the job to a ratio of cpu:gpu of 4:2 yields 819,207 tau/day which means a quad server can deliver about 1.6 million tau/day. | ||
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gpu=4 mpi=4 | gpu=4 mpi=4 | ||
Performance: | Performance: | ||
- | any mpi>gpu yielded degraded performance. | + | any mpi>gpu yielded degraded performance... |
index, name, temp.gpu, mem.used [MiB], mem.free [MiB], util.gpu [%], util.mem [%] | index, name, temp.gpu, mem.used [MiB], mem.free [MiB], util.gpu [%], util.mem [%] | ||
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Gromacs has shown vastly improved performance between versions. v5 delivered about 20 ns/day per K20 server and 350 ns/day on GTX server. v2018 delivered 75 ns/day per K20 server and 900 ns/day on GTX server. A roughly 3x improvement. | Gromacs has shown vastly improved performance between versions. v5 delivered about 20 ns/day per K20 server and 350 ns/day on GTX server. v2018 delivered 75 ns/day per K20 server and 900 ns/day on GTX server. A roughly 3x improvement. | ||
- | On the P100 I could not invoke the multidir option of gromacs (have run it on GTX, weird). The utilization of the gpu drops as more and more gpus are deployed. | + | On the P100 I could not invoke the multidir option of gromacs (have run it on GTX, weird). The utilization of the gpu drops as more and more gpus are deployed. |
< | < |