Thanks Peter and Mark!
I'll try running on single cores ...
however, comparing the timings I believe the bottleneck might be the time spent
in I/O(reading/writing to disk) and here running several jobs on a single node
with multiple coresmight make things even worse.
also funny: In the log
Hi,
As Peter notes, there are cases where the GPU won't be used for the rerun
(specifically, when you request more than one energy group, for which it
would likely be prohibitively slow, even if we'd write and run such a
kernel on the GPU; but that is not the case here). The reason things take a
Hi,
On the new machine your CUDA runtime and driver versions are lower than
on the old machine. Maybe that could explain it? (is the GPU even used
with -rerun?) You would need to recompile gromacs.
Peter
On 27-03-17 15:51, Michael Brunsteiner wrote:
> Hi,I have to run a lot (many thousands)
Hi,I have to run a lot (many thousands) of very short MD reruns with gmx.Using
gmx-2016.3 it works without problems, however, what i see is thatthe overall
performance (in terms of REAL execution time as measured with the unix time
command)which I get on a relatively new computer is poorer
