On 24/12/2010 9:59 PM, Wojtyczka, André wrote:
I'm not sure that PD has any advantage here. From memory it has to
create a 128x1x1 grid, and you can direct that with DD also.
See mdrun -h -hidden for -dd.
Mark
The contents of your .log file will be far more helpful than stdout in
diagnosing what condition led to the problem.
Mark
So the only difference is the number of cores I am using.
I used -dd but then my system consists only of 4 or slightly more domains
which gives me almost no advantage over -pd. The minimum size of a domain
is connected to the largest bond length which in my case is half of the box
size or more.
If it were more than half the box size, then since that restricts the
minimum diameter of the DD cell, surely DD would produce a single
domain. Either way, it sounds like the ratio of system size to bond
length is too small to permit efficient GROMACS-style parallelism. Not
all systems are worth parallelising, even if you have a good algorithm
for the case at hand... and both DD and PD are targeted at the usual
situation in MD where the box size is many times larger than the typical
bond length.
Mark
I will post my .log file but it will probably be next year.
So merry christmas and a jolly time.
André
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