How is the output different? From the LAMMPS documentation:
"When LAMMPS is running in parallel, the atom information written to dump files (typically one line per atom) may be written in an indeterminate order. This is because data for a single snapshot is collected from multiple processors. This is always the case for the atom, bond, and custom styles. It is also the case for the xyz style if the dump group is not all. It is not the case for the dcd and xtc styles which always write atoms in sorted order. "
I beleive the newest VMD beta version should be able to read and visualize both parallel and non-parallel dump files.
Joe
Dear Axel,
I'm using the latest versions for both VMD and LAMMPS. Rather than having mistake in visualizing using VMD, I think the reason is related with dump file itself. I install mpich-1.2.7p1 on my desket PC with Core Duo CPU, and I compile lammps's parallel version "lmp_g++" with that mpich library. But when I try to run the example shear simulation via "mpirun -np 2 ./lmp_g++ < in.shear", the dump file is rather different with running with single processor. I doubt there is something wrong with communication to output data file. Do I need to specify the processors to run the simulation before I start simulation?
Best regards,
Damien
2009-07-21
??? Axel Kohlmeyer
??? 2009-07-21 15:34:14
??? zhjjvmd
??? lammps-users
??? Re: [lammps-users] parallel running problem
Dear all,
damien,
I know maybe it's not a LAMMPS's Q, but I still expect some advice
right, it is not.
from you. For the example input "in.shear", the output is normal when
running with single processor. However, the output becomes non-ordered
when running with two processors, as shown in attached figure. Could
you give me some advice about how can I fix this problem? Thanks in
sorry, but i cannot reproduce your problem.
i suspect you are making a mistake when visualizing the trajectory.
how did you do that? since you are obviously using VMD, have you
tried the latest beta version of VMD?
cheers,
axel.