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cluster:175 [2018/09/22 12:51] hmeij07 [Gromacs] |
cluster:175 [2018/09/25 12:35] hmeij07 |
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**[[cluster: | **[[cluster: | ||
- | ==== GTX vs P100 & K20 ==== | + | ==== P100 vs GTX & K20 ==== |
- | Comparing these GPUs yields the following | + | ^ ^ P100 ^ GTX ^ K20 ^ ^ |
+ | | cores | 3,584 | 3,584 | 2,496 | count | | ||
+ | | mem | 12/16 | 11 | 5 | gb | | ||
+ | | ghz | 2.6 | 1.6 | 0.7 | speed | | ||
+ | | flops | 4.7/ | ||
+ | |||
+ | Comparing these GPUs yields the following | ||
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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</ | </ | ||
+ | |||
+ | Look at these gpu temperatures, | ||
==== Lammps ==== | ==== Lammps ==== | ||
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</ | </ | ||
+ | |||
+ | === WZ === | ||
+ | |||
+ | a) 1GPU with X CPUs | ||
+ | |||
+ | #cpus | ||
+ | 4 89.6 | ||
+ | 2 61.6 | ||
+ | 1 34.3 | ||
+ | |||
+ | b) 4 GPUs with 4 CPUs | ||
+ | 92 ns/day | ||
+ | |||
+ | ---------- | ||
+ | compare these results to | ||
+ | |||
+ | 1 K20 GPU + 4 CPUs 37 ns/day | ||
+ | 1 K20 GPU + 6 CPUs 47 ns/day | ||
+ | 1 GTX GPU + 4 CPUs 73 ns/day | ||
+ | 1 GTX GPU + 6 CPUs 90 ns/day | ||
+ | |||
+ | ---- | ||
+ | Test dir location | ||
+ | / | ||
+ | |||
+ | |||
+ | -------------- | ||
+ | I am running a material called PMMA (https:// | ||
+ | |||
+ | The reason for the different benchmark than yours is that the PMMA simulations require the calculation of molecular bonds, which is not implemented in GPU. | ||
==== Gromacs ==== | ==== Gromacs ==== | ||
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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 test node, 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 test node, 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. |
< | < | ||
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localhost, | localhost, | ||
localhost, | localhost, | ||
- | gmx_mpi mdrun -gpu_id 0123 -ntmpi 0 \ | + | gmx_mpi mdrun -gpu_id 0123 -ntmpi |
-s topol.tpr -ntomp 4 -npme 1 -nsteps 20000 -pin on -nb gpu | -s topol.tpr -ntomp 4 -npme 1 -nsteps 20000 -pin on -nb gpu | ||
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| | ||
- | gpu=4 mpi=25 ntomp=4 -npme 1 | + | gpu=4 mpi=25 |
Performance: | Performance: | ||
gpu=3 (same) | gpu=3 (same) | ||
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</ | </ | ||
+ | |||
+ | ==== What to Buy ==== | ||
+ | |||
+ | * Amber folks: does not matter | ||
+ | * Lammps folks: P100 nodes please | ||
+ | * Gromacs folks: GTX nodes please | ||
+ | |||
+ | Remember that GTX gpus placed in Data Center voids their warranty. | ||
+ | |||
\\ | \\ |