Luca Mollica wrote:
Dear users,
I am experiencing some troubles in using GMX 4.0.4 trying to rerun
trajectories and obtaining energies for single residues and/or portion
of proteins. According to the mdrun command help and to my experience
with the previous versions of GROMACS, I have edited my mdp file
including the desired groups for energy calculation, grompped it and
reruned the previous calculation with the "original" trr trajectory.
I have noticed a different behaviour of mdrun plus -rerun flag between
the usage of a single CPU or the original number of CPU used in the
production run: that is, in the original production run I have used 24
CPU (12 for PME, nosum flag used), in the trajectory rerun step I have
tried to use both 24 CPU or single CPU and the result was different and
in the case of parallel run "strange". The parallel rerun energy file
led to an energy file made of a column of the same number, whereas the
single CPU one led to a normal energy trend vs time: interestingly, the
first value of this last calculation coincided with the one repeated in
the previous "strange" file.
Hence, the single CPU recalculation works correctly, despite the fact
that (as expected) it takes longer time for huge trajectories with
respect to parallel run: but what's wrong with parallel rerun ? Is it a
bug of the newer version of the code or am I missing something in the
comprehnsion of how the rerun issue is working at code level ? It seems
to be more likely a code bug ... but I wait for your comments and/or
suggestions.
Ordinarily I'd suggest you'd probably managed to mismatch trajectory or
run input files, but there was another report less than 24 hours ago of
what appears to be a single-processor rerun producing the same numbers.
This suggests that a single-processor rerun is loading a structure that
is the same as the first one loaded by a multi-processor rerun (i.e. the
first one in the trajectory) and then not ever loading a new one
correctly. Can you see if these values are consistent with those
reported for this step for the original simulation? They might differ
slightly because of the timing of neighbour-searching. What step numbers
are being reported in the rerun .log file?
I had a quick look at the code, but couldn't see any problem in do_md().
The first frame gets read with read_first_frame, the data gets copied
from rerun_fr to the appropriate places, and at the end of the loop,
read_next_frame is called. There doesn't appear to be any way you could
get a difference between single- or multi-processor runs in the way you
describe.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
