On Fri, Aug 18, 2017 at 4:59 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Sat, Aug 19, 2017, JiYuan Liu wrote:
> >
> > I have compiled amber16 with ambertools17 in serial and parallel
> > successfully that used mpich2 v3.1.4, but when I performed
> > MMPBSA.py.MPI, it displayed the error "could not import mpi4py
> > package ! use serial version or instal mpi4py", then I typed
> > the command "from mpi4py import MPI", it also displayed a error
> > "/amber16/lib/python2.7/site-packages/mpi4py/MPI.so:undefined
> > symbol:MPI_File_iread_at_all.
>
> Please see note 2 on p. 25 of the Amber 2017 Reference Manual. What
> operating
> system are you using, and how did you install python? (Did you accept
> the offer to install miniconda?)
> [Developers: our configure_python
> script doesn't attempt to get mpi4py. Is there a reason for this? Should
> we give better instructions in the manual about why this is, and what to
> do?]
>
>
I think not installing mpi4py via configure_python is Jason's intention.
mpi4py conda version is built with openmpi, so it won't work well with
others.
"pip install mpi4py" does not work nicely (due to limitation of pip).
However, if '-mpi' is specified, the configure2 will check if there's
mpi4py, if not, included mpi4py in AmberTools will be built.
Hai
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sat Aug 19 2017 - 00:00:02 PDT
