[gmx-users] No performance increase with single vs multiple nodes

[Matthew W Hanley]

> There's several dozen lines of performance analysis at the end of the log

> file, which you need to inspect and compare if you want to start to
> understand what is going on :-)

Thank you for the feedback.  Fair warning, I'm more of a system administrator than a regular gromacs user.  What is it that I should be focused on, and more importantly how do I find the bottleneck?  Gromacs does recommend using AVX2_256, but I was unable to get Gromacs to build using that.  Here is more of the log file:


On 32 MPI ranks


 Computing:          Num   Num      Call    Wall time         Giga-Cycles

                     Ranks Threads  Count      (s)         total sum    %

-----------------------------------------------------------------------------

 Domain decomp.        32    1       1666      18.920       1509.802   3.8

 DD comm. load         32    1       1666       0.017          1.394   0.0

 DD comm. bounds       32    1       1666       0.206         16.406   0.0

 Vsite constr.         32    1      50001       4.624        369.013   0.9

 Neighbor search       32    1       1667      19.646       1567.793   4.0

 Comm. coord.          32    1      48334       8.291        661.640   1.7

 Force                 32    1      50001     339.477      27090.350  68.6

 Wait + Comm. F        32    1      50001      12.691       1012.783   2.6

 NB X/F buffer ops.    32    1     146669      13.563       1082.352   2.7

 Vsite spread          32    1      50001       8.716        695.518   1.8

 Write traj.           32    1          2       0.080          6.366   0.0

 Update                32    1      50001      37.268       2973.983   7.5

 Constraints           32    1      50001      25.674       2048.789   5.2

 Comm. energies        32    1       5001       0.965         77.013   0.2

 Rest                                           4.385        349.931   0.9

-----------------------------------------------------------------------------

 Total                                        494.524      39463.132 100.0

-----------------------------------------------------------------------------?



If that's not helpful, I would need more specifics on what part of the log file would be.  Failing that, if anyone could recommend some good documentation for optimizing performance I would greatly appreciate it, thank you!

-Matt


Matthew Hanley
IT Analyst
College of Engineering and Computer Science
Syracuse University
mwhanley at syr.edu