[gmx-users] Suggestion for workstation configurations

Johannes Wagner johannes.wagner at h-its.org
Thu May 4 15:01:29 CEST 2017

This seems like quite an overkill for a workstation… That hardware should probably go into a rack in your server room. Money seems not an issue for you, as they are *very* expensive workstation parts. General speaking, here is a paper that benchmarks gromacs with a lot of different CPU/GPU combinations:

“Best bang for your buck: GPU nodes for GROMACS biomolecular simulations” https://arxiv.org/abs/1507.00898 <https://arxiv.org/abs/1507.00898>

Have a read there. In our institute for workstations we use normal consumer hardware, e.g. an GeForce 1070/1080 instead of the quadro models. Considering the use of GPU’s, you should not even think about coupling an old weak Fermi generation GPU like your suggested Quadro M2000 with 192 Cuda cores with a modern 8core Intel cpu. Compare that to your other suggested P5000 with 2560 Cuda cores.

Furthermore we also deploy normal core-i7’s. However now there are the 8core Ryzen 7’s available, which might be better value/performance compared to your suggested 8 core E5-2620v4 or  E5-1660v4. But optimal Ryzen support is available only with gromacs-2017 release (but already works now). Furthermore, gromacs doesn’t need much memory, so 16 or 32GB is more than sufficient. 

Main problem is finding the right combination of CPU with GPU, so that you don’t run in either CPU or GPU limit. And that in turn depends also on your system that you simulate. Using large non-bonded cut-offs puts more load on the GPU.

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