Dear Users,
I am installing Amber 12 parallel version on a cluster. Serial version is
successfully installed but there is problem in MMPBSA.py.MPI installations.
Following are the output of mpi4py_install.log.
*running build
running build_py
creating build
creating build/lib.linux-x86_64-2.4
creating build/lib.linux-x86_64-2.4/mpi4py
copying src/__init__.py -> build/lib.linux-x86_64-2.4/mpi4py
copying src/rc.py -> build/lib.linux-x86_64-2.4/mpi4py
creating build/lib.linux-x86_64-2.4/mpi4py/include
creating build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI_api.h ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.MPI.h ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.h ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pxd ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi_c.pxd ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/MPI.pxd ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/__init__.pyx ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi.pxi ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
copying src/include/mpi4py/mpi4py.i ->
build/lib.linux-x86_64-2.4/mpi4py/include/mpi4py
running build_ext
MPI C compiler: /opt/software/mpich2/default//bin/mpicc
MPI C++ compiler: /opt/software/mpich2/default//bin/mpicxx
MPI linker: /opt/software/mpich2/default//bin/mpicc
checking for MPI compile and link ...
/opt/software/mpich2/default//bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
-I/usr/include/python2.4 -c _configtest.c -o _configtest.o
/opt/software/mpich2/default//bin/mpicc _configtest.o -o _configtest
success!*
*removing: _configtest.c _configtest.o _configtest
writing build/lib.linux-x86_64-2.4/mpi4py/mpi.cfg
building 'mpi4py.MPI' extension
creating build/temp.linux-x86_64-2.4
creating build/temp.linux-x86_64-2.4/src
/opt/software/mpich2/default//bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
-I/usr/include/python2.4 -c src/MPI.c -o
build/temp.linux-x86_64-2.4/src/MPI.o
/opt/software/mpich2/default//bin/mpicc -shared
build/temp.linux-x86_64-2.4/src/MPI.o -o
build/lib.linux-x86_64-2.4/mpi4py/MPI.so
/usr/bin/ld:
/opt/software/mpich2/default/lib/libmpich.a(comm_create_keyval.o):
relocation R_X86_64_32 against `a local symbol' can not be used when making
a shared object; recompile with -fPIC
/opt/software/mpich2/default/lib/libmpich.a: could not read symbols: Bad
value
collect2: ld returned 1 exit status
error: command '/opt/software/mpich2/default//bin/mpicc' failed with exit
status 1*
Unfortunately, I haven't root access. I will appreciate your helps for
successful installation of MMPBSA.py.
--
With best regards
*******************************************************************************************************************
Kshatresh Dutta Dubey, PhD
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
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Received on Mon May 13 2013 - 11:30:04 PDT
