I’ve successfully installed mmpbsa.py.MPI on the Mac Pro following the instructions given in:
http://jswails.wikidot.com/installing-amber12-and-ambertools-13.
I followed the same installation procedure on a PowerBook Pro (OS X v.10.10.3). Prior to the installation, I deleted the /opt directory and re-installed it.
I selected the proper compilers (see below)
Selecting 'mp-gcc48' for 'gcc' succeeded. 'mp-gcc48' is now active.
Selecting 'mpich-gcc48-fortran' for 'mpi' succeeded. 'mpich-gcc48-fortran' is now active.
Completing the parallel installation of amber through out no error messages. However, mmpbsa.py.MPI was NOT installed.
mpi4py_install.log indicates that file _configtest.o was built for the wrong architecture (i386) and not for x86_64.
Anything that can be done to save the day? Thanks in advance for any suggestions
George
The complete .log file is below.
unning build
running build_py
creating build
creating build/lib.macosx-10.10-intel-2.7
creating build/lib.macosx-10.10-intel-2.7/mpi4py
copying src/__init__.py -> build/lib.macosx-10.10-intel-2.7/mpi4py
copying src/rc.py -> build/lib.macosx-10.10-intel-2.7/mpi4py
creating build/lib.macosx-10.10-intel-2.7/mpi4py/include
creating build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.h -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI.h -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI_api.h -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pxd -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/MPI.pxd -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi_c.pxd -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pyx -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi.pxi -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.i -> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
running build_ext
MPI C compiler: /opt/local/bin/mpicc
MPI C++ compiler: /opt/local/bin/mpicxx
MPI linker: /opt/local/bin/mpicc
checking for MPI compile and link ...
/opt/local/bin/mpicc -arch x86_64 -arch i386 -pipe -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _configtest.c -o _configtest.o
_configtest.c: In function 'main':
_configtest.c:6:7: warning: variable 'ierr' set but not used [-Wunused-but-set-variable]
int ierr;
^
/opt/local/bin/mpicc _configtest.o -o _configtest
ld: warning: ignoring file _configtest.o, file was built for i386 which is not the architecture being linked (x86_64): _configtest.o
Undefined symbols for architecture x86_64:
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot compile/link MPI programs. Check your configuration!!!
> On 9 May 2015, at 14:02, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Fri, May 8, 2015 at 3:24 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I’m using AmberTools13 on OSX v.10.9.5 2x6 core Intel Xeon processor.
>>
>> MPI versions of pmemd, etc work fine but somehow mmpbsa.py.MPI was NOT
>> installed.
>>
>
> If I had to guess, it's because the mpi4py installation failed. The error
> *should* have been printed to
> $AMBERHOME/AmberTools/src/mpi4py_install.log. In my experience the most
> common cause is that the MPI library was not compiled with -fPIC, which
> means that your MPI needs to be rebuilt (setting CFLAGS to include -fPIC)
> before MMPBSA.py.MPI will work.
>
>
>> The serial installation of mmpbsa.py works fine.
>>
>>
>> I’d like to install the MPI version without reinstalling AmberTools de
>> novo. $AMBERHOME/src does not contain a mmpbsa_py directory. So I’m stuck.
>>
>
> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Fri May 15 2015 - 13:30:02 PDT
