Jason,
mpirun -np 4 MMPBSA.py.MPI
resulted in
mpirun was unable to launch the specified application as it could not find
an executable:
Executable: MMPBSA.py.MPI
Previously I faced with the problems of compilation of amber using
./configure -mpi
resulted in
testing [C++ / fortran] cross-compile with MPI libs
Error! Could not link C++ mpi code using mpi fortran linker:
"mpif90 -lstdc++ -lmpi_cxx"
[C++ / fortran / MPI] cross-linking is needed for cuda_parallel and EMIL
builds.
Try: "mpif90 -show"
Configure failed due to the errors above!
own.arrakis ~/Documents/simulations/restart_holo $ mpif90 -show
gfortran -I/usr/lib/openmpi/include -pthread -I/usr/lib/openmpi/lib
-L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl
What should be done here?
James
2014-04-30 15:22 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, 2014-04-30 at 09:58 +0400, James Starlight wrote:
> > ... and new error during PB calculations of my test system using:
> > &general
> > endframe=100, keep_files=2, strip_mask=':WAT,CLA,POT,POPE,POPC'
> > &pb
> > istrng=0.150, inp=1, radiopt=0
> >
> > Beginning PB calculations
> > with /home/own/Documents/simulations/amber/amber14/bin/sander
> > calculating complex contribution...
> > calculating receptor contribution...
> > calculating receptor contribution...
> > calculating receptor contribution...
> > calculating receptor contribution...
> > calculating ligand contribution...
> > calculating ligand contribution...
> > calculating ligand contribution...
> > calculating ligand contribution...
>
> You are *still* running parallel simulations incorrectly. The MMPBSA.py
> tutorial (http://ambermd.org/tutorials/advanced/tutorial3/)
>
> What you are doing:
>
> mpirun -np 4 MMPBSA.py -i mmpbsa.in ...
>
> What you SHOULD be doing:
>
> mpirun -np 4 MMPBSA.py.MPI -i mmpbsa.in ...
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu May 01 2014 - 02:30:02 PDT
