Hi Bruno,
> The cluster administrator claimed that my ./restart.sh should be a
> BINARY
> file because mpirun only accepts binaries.
This is not strictly true in the real sense of the word BUT you should NOT
be passing a script as an argument to mpirun. From your comment above I
would conclude that you are trying something like:
mpirun -np 2 ./restart.sh
This will definitely NOT work. The mpirun needs to be inside your restart.sh
script in front of the pmemd.MPI or sander.MPI call.
> I guess it's not the case as it recognizes the commands inside. Do you
> have
> any clue about the input files for mpirun? I read the man from mpirun
Sure it recognizes the commands inside but you should probably read up a bit
on what MPI actually is and you will realize what is going on here and why
this does not make sense. If you just do mpirun -np 2 ./restart.sh it will
simply run 2 copies of your restart.sh script and this will just end in a
big steaming pile of FAIL!
Edit your restart.sh and put the mpirun command in front of the sander.MPI
or pmemd.MPI executable and then run the restart script with ./restart.sh.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
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Received on Wed May 25 2011 - 10:00:05 PDT
