Thanks Jason!
Installing Amber in serial does the trick. Apparently MMPBSA.py did install
correctly despite that error.
Best,
Laura
---------- Forwarded message ----------
From: Jason Swails <jason.swails.gmail.com>
Date: Tue, Apr 7, 2015 at 11:36 AM
Subject: Re: [AMBER] MMPBSA.py.MPI Installation Failure
To: AMBER Mailing List <amber.ambermd.org>
On Sat, Apr 4, 2015 at 2:34 PM, Laura Tociu <ltociu.princeton.edu> wrote:
> Hi,
>
> I recently installed Amber14 and AmberTools14. I followed instructions
from
> the IT guys from my group, and did:
>
> tar jxvf AmberTools14.tar.bz2
> tar jxvf Amber14.tar.bz2
> cd amber14
> export AMBERHOME=`pwd`
>
> module purge
>
> module load openmpi
>
> export MKL_HOME=/opt/intel/composer_xe_2013_sp1.0.080/mkl
>
> ./configure -mpi intel
> make install
>
> echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
>
>
> I used MKL because I wanted to decrease the computational time required by
> QM/MM molecular dynamics. I've been able to run QM/MM MD succesfully, but
> as I am now getting ready to start binding energy calculations, I realized
> that MMPBSA did not install correctly. There is no mmpbsa_py_energy in
> $AMBERHOME/bin so I am getting the error that mmpbsa_py_energy could not
be
> found.
>
> I am attaching the mpi4py_install.log file. There seems to be an error in
> there related to mpe.h. I don't really know what other information might
be
> helpful. Let me know what other files might be useful and I will attach
> them.
>
​Google searches suggest to me that MPE is an optional component of OpenMPI
(or maybe the MPI standard itself, I'm not sure). But it doesn't seem to
be installed. Suggested solutions are to either "install MPE" or "build
without it". I'm not sure how to do either of these.
Here are some suggestions:
Build in serial as well​ -- mmpbsa_py_energy is only built in serial.
MMPBSA.py.MPI itself is parallel, but each thread calls a serial program to
evaluate energies.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 08 2015 - 22:30:03 PDT
