[gmx-users] NVT problem

Dallas Warren dallas.warren at monash.edu
Mon Sep 24 00:51:43 CEST 2018

What do you think the issue is?

What the note states there is that it will not print out the following
summary section at the end of the log file:

     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 28 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
 Neighbor search        1   28      25001     280.413      21148.852   3.8

That section is printed out prior to the "Core ..." line in the text
above.  This has nothing to do with the resulting output from the run,
in the coordinate, energy, trajectory files.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Sun, 23 Sep 2018 at 01:56, AKANXA TIWARI <akanxatiwari24 at gmail.com> wrote:
> hello
> i am trying to simulating a protein after run NVT md run i got a not what i
> will do. is this not show any problem.
> Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
> starting mdrun 'TUBULIN ALPHA CHAIN'
> 50000 steps,    100.0 ps.
> step 49900, remaining wall clock time:    35 s
> Writing final coordinates.
> step 50000, remaining wall clock time:     0 s
> NOTE: Detected invalid cycle counts, probably because threads moved between
> CPU cores that do not have synchronized cycle counters. Will not print the
> cycle accounting.
>                Core t (s)   Wall t (s)        (%)
>        Time:    70001.934    17500.483      400.0
>                          4h51:40
>                  (ns/day)    (hour/ns)
> Performance:        0.494       48.611
> GROMACS reminds you: "Uh-oh .... Right Again" (Laurie Anderson)
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