[gmx-users] Only 2 ns/day
alexanderwien2k at gmail.com
Mon Jun 18 17:39:12 CEST 2018
I use 2 nodes (each has 32 cores) for a system of 41933 atoms (containing
water-short polymer on a solid surface). The performance is too poor, only
2.43 ns/day, although the imbalance is normal and around 4.9 %.
The submission command I used is:
gmx_mpi mdrun -ntomp 1 -deffnm eql1 -s eql1.tpr -rdd 1.5 -dds 0.9999 -npme
4 -ntomp_pme 1 -g eql1.log -v
I had to use -rdd 1.5 otherwise the DD error would show up. I also tested
manually different -npme and among all those only -npme 4 and -npme 24
works with these 64 cores.
I checked the -npme manually because I am not familiar with the gmx
Below I have shared the log file of the simulation and I would be so
appreciated if one could help me improve the performance.
Thank you very much.
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