[gmx-developers] Running Gromacs Binaries on both KNLs and SKXs

Schulz, Roland roland.schulz at intel.com
Thu Dec 7 23:43:31 CET 2017


Why do you want to use the same binary instead of compiling 2 times for the two different processors? Are you trying to run a single simulation using both CPU types?
You won’t get optimal performance if you use the same binary.

If you want to do it nonetheless, you should use GMX_SIMD=AVX_512. For ICC you will need to use CFLAGS=CXXFLAGS=-xCOMMON-AVX512 .
You will also want to set GMX_NBNXN_EWALD_ANALYTICAL as an environment variable before running your simulation at least for KNL.

Any follow-up should go to the gmx-users list. This isn’t about any development work.


From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Kevin Chen
Sent: Thursday, December 7, 2017 2:11 PM
To: gmx-developers at gromacs.org
Subject: [gmx-developers] Running Gromacs Binaries on both KNLs and SKXs


I’m trying to use the same Gromacs(V2016.3) binary on a HPC machine has both KNLs and SKXs. And all KNLs and SKXs nodes are sharing the same compilers, mpi stacks and file systems. The issues I’m running into is that Gromacs only allow one SIMD setting during the building process. So my question is what value should I pick for -DGMX_SIMD to get most of both CPU types, AVX_512, AVX_512_KNL or AVX2_256?

Thanks in advance!


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