And this is my $AMBERHOME/AmberTools/src/mpi4py_install.log
Can you please try to help me where is the flaw? (I cannot follow…).
Thanks!!
Fabian
running build
running build_py
creating build
creating build/lib.macosx-10.10-x86_64-2.7
creating build/lib.macosx-10.10-x86_64-2.7/mpi4py
copying src/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/mpi4py
copying src/rc.py -> build/lib.macosx-10.10-x86_64-2.7/mpi4py
creating build/lib.macosx-10.10-x86_64-2.7/mpi4py/include
creating build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.h -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI.h -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI_api.h -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pxd -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/MPI.pxd -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi_c.pxd -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pyx -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi.pxi -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.i -> build/lib.macosx-10.10-x86_64-2.7/mpi4py/include/mpi4py
running build_ext
MPI C compiler: /Users/fabian/TOOLS/amber14/bin/mpicc
MPI C++ compiler: /Users/fabian/TOOLS/amber14/bin/mpicxx
MPI linker: /Users/fabian/TOOLS/amber14/bin/mpicc
checking for MPI compile and link ...
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/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;
^
/Users/fabian/TOOLS/amber14/bin/mpicc _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
writing build/lib.macosx-10.10-x86_64-2.7/mpi4py/mpi.cfg
building 'mpi4py.MPI' extension
creating build/temp.macosx-10.10-x86_64-2.7
creating build/temp.macosx-10.10-x86_64-2.7/src
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/MPI.c -o build/temp.macosx-10.10-x86_64-2.7/src/MPI.o
In file included from src/mpi4py.MPI.c:200:0,
from src/MPI.c:3:
src/atimport.h: In function 'PyMPI_StartUp':
src/atimport.h:105:7: warning: variable 'ierr' set but not used [-Wunused-but-set-variable]
int ierr = MPI_SUCCESS;
^
src/atimport.h: In function 'PyMPI_CleanUp':
src/atimport.h:131:7: warning: variable 'ierr' set but not used [-Wunused-but-set-variable]
int ierr = MPI_SUCCESS;
^
In file included from src/MPI.c:3:0:
src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_mpi_active':
src/mpi4py.MPI.c:4071:7: warning: variable '__pyx_v_ierr' set but not used [-Wunused-but-set-variable]
int __pyx_v_ierr;
^
src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_startup':
src/mpi4py.MPI.c:4175:7: warning: variable '__pyx_v_ierr' set but not used [-Wunused-but-set-variable]
int __pyx_v_ierr;
^
src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_cleanup':
src/mpi4py.MPI.c:4222:7: warning: variable '__pyx_v_ierr' set but not used [-Wunused-but-set-variable]
int __pyx_v_ierr;
^
src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_atexit':
src/mpi4py.MPI.c:4269:7: warning: variable '__pyx_v_ierr' set but not used [-Wunused-but-set-variable]
int __pyx_v_ierr;
^
In file included from src/MPI.c:3:0:
src/mpi4py.MPI.c: In function '__pyx_pf_6mpi4py_3MPI_4Comm_Alltoallw':
src/mpi4py.MPI.c:51413:13: warning: variable '__pyx_v_recvbuf' set but not used [-Wunused-but-set-variable]
PyObject *__pyx_v_recvbuf = 0;
^
src/mpi4py.MPI.c:51412:13: warning: variable '__pyx_v_sendbuf' set but not used [-Wunused-but-set-variable]
PyObject *__pyx_v_sendbuf = 0;
^
src/mpi4py.MPI.c: In function '__pyx_pf_6mpi4py_3MPI_Close_port':
src/mpi4py.MPI.c:63998:12: warning: variable '__pyx_v_cinfo' set but not used [-Wunused-but-set-variable]
MPI_Info __pyx_v_cinfo;
^
src/mpi4py.MPI.c: In function 'initMPI':
src/mpi4py.MPI.c:84316:3: warning: 'ompi_mpi_ub' is deprecated (declared at /Users/fabian/TOOLS/amber14/include/mpi.h:910): MPI_UB is deprecated in MPI-2.0 [-Wdeprecated-declarations]
__pyx_t_3 = ((PyObject *)__pyx_f_6mpi4py_3MPI_new_Datatype(MPI_UB)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[16]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
src/mpi4py.MPI.c:84331:3: warning: 'ompi_mpi_lb' is deprecated (declared at /Users/fabian/TOOLS/amber14/include/mpi.h:909): MPI_LB is deprecated in MPI-2.0 [-Wdeprecated-declarations]
__pyx_t_3 = ((PyObject *)__pyx_f_6mpi4py_3MPI_new_Datatype(MPI_LB)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[16]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
/Users/fabian/TOOLS/amber14/bin/mpicc -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib -L/usr/local/opt/tcl-tk/lib build/temp.macosx-10.10-x86_64-2.7/src/MPI.o -o build/lib.macosx-10.10-x86_64-2.7/mpi4py/MPI.so
checking for MPE availability ...
checking for header 'mpe.h' ...
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _configtest.c -o _configtest.o
_configtest.c:3:17: fatal error: mpe.h: No such file or directory
#include <mpe.h>
^
compilation terminated.
failure.
removing: _configtest.c _configtest.o
failure.
building 'mpi4py.MPE' extension
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/MPE.c -o build/temp.macosx-10.10-x86_64-2.7/src/MPE.o
/Users/fabian/TOOLS/amber14/bin/mpicc -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib -L/usr/local/opt/tcl-tk/lib build/temp.macosx-10.10-x86_64-2.7/src/MPE.o -o build/lib.macosx-10.10-x86_64-2.7/mpi4py/MPE.so
checking for dlopen availability ...
checking for header 'dlfcn.h' ...
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
succes!
checking for library 'dl' ...
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _configtest.c -o _configtest.o
/Users/fabian/TOOLS/amber14/bin/mpicc _configtest.o -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_DLFCN_H=1 -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/dynload.c -o build/temp.macosx-10.10-x86_64-2.7/src/dynload.o
/Users/fabian/TOOLS/amber14/bin/mpicc -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib -L/usr/local/opt/tcl-tk/lib build/temp.macosx-10.10-x86_64-2.7/src/dynload.o -ldl -o build/lib.macosx-10.10-x86_64-2.7/mpi4py/dl.so
running build_exe
MPI C compiler: /Users/fabian/TOOLS/amber14/bin/mpicc
MPI C++ compiler: /Users/fabian/TOOLS/amber14/bin/mpicxx
MPI linker: /Users/fabian/TOOLS/amber14/bin/mpicc
building 'python2.7-mpi' executable
/Users/fabian/TOOLS/amber14/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/python.c -o build/temp.macosx-10.10-x86_64-2.7/src/python.o
creating build/exe.macosx-10.10-x86_64-2.7
/Users/fabian/TOOLS/amber14/bin/mpicc -u _PyMac_Error /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/Python build/temp.macosx-10.10-x86_64-2.7/src/python.o -L/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib -L/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -o build/exe.macosx-10.10-x86_64-2.7/python2.7-mpi -L/usr/local/lib -L/usr/local/opt/sqlite/lib -L/usr/local/opt/tcl-tk/lib -ldl -framework CoreFoundation
____________________
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Thu Oct 22 2015 - 04:00:05 PDT
