Hello,
First I want to say that I am excited abou= t the upcoming GPU support in
AMBER 11. Thanks for the information Ross Wal= ker.
I have since moved on to ptraj,MPI while I wa= it for AMBER 11. Both OpenMPI
1.4.1, Ambertools 1.3, and parallel ptraj com= piled without error on my
Ubuntu system. I used the GNU compilers, gcc 4.4.= However, when running
<mpirun -np 4 ptraj.MPI> command, top shows al= l of the processes are in
the "D" state. The processes seem to randomly go = in the "R" state for no
more than a second, and I've never seen all process= es running at the same
time. Furthermore, running <mpirun -np 4 ptraj.MP= I> on a trajectory takes
longer than -np 2, which takes longer than seri= al ptraj. OpenMPI seems to
be creating the overhead to mulithread, but no u= suable multithreading is
occuring. Running just regular <mpirun ptraj.MP= I> produces no "D" state in
the single process.
This is probably more of a OpenMPI issue perhaps, but I thought I'd post m y experience on the AMBER board to see if anyone has had this experience. I 've been trying to figure out how to go about debugging OpenMPI, and it see ms like a bear.
On a side note about ptraj.MPI (bu= t perhaps pertinent)--the traditional
ptraj command [ptraj prmtop < infi= le] does not work for me with mpirun -np
4 ptraj.MPI. It exits with the err= or "MULTIPTRAJ must be run with <TOP>
and <INPUT>". My fix to t= his problem is leaving out the < sign, and
ptraj.MPI worked.
<= br>
Trevor
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Received on Mon Feb 22 2010 - 16:30:02 PST
