[gmx-users] Vacuum simulation in Gromacs 5

[Jan Jirsák]

Hi,

I did the test and found out that -nt 8 is even slower than -nt 1 !!
However, I think that simulation hasn't even properly started with 8
threads and got stuck somewhere in the beginning.

Details:
I used a short run (1000 steps) for testing. mdrun -nt 1 finished
after ca 11 hours, whereas not a single checkpoint or run log record
have been saved for mdrun -nt 8 (and simulation is still running). Not
even starting energies were displayed - last record in a log file is a
SETTLE citation.

In top I noticed both processes used up to 100% CPU, but considerably
differed in the use of memory. Relevant lines:
PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
117710 jan       20   0 5313776 4.642g   9940 R  98.9  3.7  52:47.19
mdrun
117686 jan       20   0  547344  24456   8712 R  92.7  0.0  54:48.92 mdrun

The first listed process (117710) is the single thread simulation (-nt 1).

Thank you for any insight,
Jan

2015-06-12 14:35 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> Hi,
>
> Top need not be indicative. Run the same with -nt 1 and observe whether the
> performance changes. And don't run anything else on these cores.
>
> Mark