Hi,
1. Dan: "It seems like somehow your cpptraj was built with MPI but ended up not
being named cpptraj.MPI. What were the exact steps you used to
configure and build amber?"
I have two files named as cpptraj in the amberhome/bin/
[atyagiaa.login-0 bin]$ $AMBERHOME/bin/cpptraj.MPI
CPPTRAJ: Trajectory Analysis. V14.25 MPI
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Running on 1 threads
> exit
TIME: Total execution time: 84634.6979 seconds.
[atyagiaa.login-0 bin]$ $AMBERHOME/bin/cpptraj
CPPTRAJ: Trajectory Analysis. V14.25 MPI
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Running on 1 threads
2. Jason: We are still waiting for your reply to Dan's email. If you didn't get it,
you can find it here: http://archive.ambermd.org/201504/0018.html
Furthermore, this error message makes no sense to me since MMPBSA.py never
tries to use the "ensemble" command. So I really have no idea how this
error could possibly occur.
The errors you are reporting (igb=1 working while igb=5 does not, and the
ensemble error you reported above) are all problems that I have never seen
before. Nor can I come up with an explanation that would explain the
errors you are reporting.
However, if the problems are unique to MMPBSA.py.MPI, it's possible that
there is some weirdness in mpi4py that is causing the problems (I'm just
grasping at straws here). It could be caused by you using the wrong
"mpirun" (i.e., not one from the MPI you used to install Amber), it could
be an mpi4py bug, ... I'm not sure.
Do the parallel MMPBSA.py tests pass?
?
Jason I tried running DO_PARALLEL too and then make test, again same error comes.
3. Dan: Since currently only the 'ensemble' command benefits from MPI in
cpptraj, the only mode allowed by cpptraj.MPI is "ensemble". Somehow
your compilation of cpptraj must have been compiled with MPI. This can
be easily verified by running 'cpptraj'. If you see something like:
CPPTRAJ: Trajectory Analysis. V14.25 MPI
then somehow the serial version of cpptraj was overwritten with
cpptraj.MPI. Please tell us the exact commands you used to configure
and compile your Amber install.
I followed the user manual amber14 to install on cluster.
Thanks
Abhi
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Received on Wed Apr 08 2015 - 21:00:04 PDT
