I also tried the following
It's in $AMBERHOME/AmberTools/src, along with the rest of the open source
> codes Amber releases. Just typing "make parallel" in
> $AMBERHOME/AmberTools/src/mmpbsa_py should try to install mpi4py and then
> MMPBSA.py.MPI (if the former was successful) as long as your config.h file
> was made for parallel.
I started good and made a lot of compilations but ended bad:
"_MPIU_external32_buffer_setup", referenced from:
import-atom in libpmpi.dylib
"_MPIU_read_external32_conversion_fn", referenced from:
import-atom in libpmpi.dylib
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [/Users/admin/Data/TOOLS/amber14/bin/mdgx.MPI] Error 1
make: *** [parallel] Error 2
And still
==> MMPBSA.py.MPI
Traceback (most recent call last):
File "/Users/admin/Data/TOOLS/amber14/bin/MMPBSA.py.MPI", line 51, in <module>
raise MMPBSA_Error('Could not import mpi4py package! Use serial version '
MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use serial version or install mpi4py.
Thanks!!
Fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 20 Oct 2015, at 8:59 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Tue, Oct 20, 2015 at 10:08 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
> wrote:
>
>> Great thanks!
>>
>> Only one more thing, I am trying to compile the MPI version on my MAC of
>> MMPBSA.py.MPI, but despite I follow your instructions…. it fails:
>>
>> ==> sudo port install python27 py27-tkinter py27-mpi4py py27-matplotlib
>>
>> ---> Computing dependencies for python27
>> ---> Cleaning python27
>> ---> Computing dependencies for py27-tkinter
>> ---> Cleaning py27-tkinter
>> ---> Computing dependencies for py27-mpi4py
>> ---> Cleaning py27-mpi4py
>> ---> Computing dependencies for py27-matplotlib
>> ---> Cleaning py27-matplotlib
>> ---> Scanning binaries for linking errors
>> ---> No broken files found.
>>
>> ==> MMPBSA.py.MPI
>> Traceback (most recent call last):
>> File "/Users/admin/Data/TOOLS/amber14/bin/MMPBSA.py.MPI", line 51, in
>> <module>
>> raise MMPBSA_Error('Could not import mpi4py package! Use serial
>> version '
>> MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use
>> serial version or install mpi4py.
>>
>
> What do the first couple lines of $AMBERHOME/bin/MMPBSA.py.MPI look like?
>
> You are building mpi4py for Python 2.7 inside /opt/local/bin (built by
> MacPorts). If configure is not picking that Python up as the default
> Python interpreter, then having built that mpi4py won't matter.
>
> Also, building mpi4py this way means you are using the MacPorts MPI install
> (the one that's activated by "port activate mpi <choice>") -- if you are
> using mpirun from a different MPI installation, that won't work, either.
>
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 04:00:03 PDT
