Parallel Neuron with Python support on an Opteron server
Posted: Fri Aug 06, 2010 12:25 pm
Dear All,
I am trying to install Neuron 7.1 with MPI and Python support, but without X11 on an Opteron blade server running Fedora 9, with the ultimate goal of using it with PyNN.
I can compile Neuron with the Python interpreter (using the options --with-nrnpython=/usr/bin/python --with-paranrn --without-x); however, when I attempt to build the Neuron shared library for Python by executing "python setup.py install" in src/nrnpython (and after replacing the IVhines library with ivos as suggested by an earlier post), I get the following error:
No error occurs (I can build and use the shared library in PyNN) if I compile Neuron without MPI, but of course that prevents me from taking advantage of multiple processors and cores.
Could anyone help me with figuring out what to do?
Thanks a lot,
Szabolcs
I am trying to install Neuron 7.1 with MPI and Python support, but without X11 on an Opteron blade server running Fedora 9, with the ultimate goal of using it with PyNN.
I can compile Neuron with the Python interpreter (using the options --with-nrnpython=/usr/bin/python --with-paranrn --without-x); however, when I attempt to build the Neuron shared library for Python by executing "python setup.py install" in src/nrnpython (and after replacing the IVhines library with ivos as suggested by an earlier post), I get the following error:
Code: Select all
running install
running build
running build_py
running build_ext
building 'neuron.hoc' extension
mpic++ -pthread -shared build/temp.linux-x86_64-2.5/inithoc.o -L/home/eperfa/neuron71/nrn/x86_64/lib -L -L/usr/lib64 -lnrnpython -lnrnoc -loc -lnrniv -livoc -lmemacs -lmeschach -lneuron_gnu -lnrnmpi -lscopmath -lsparse13 -lsundials -livos -lreadline -lpython2.5 -o build/lib.linux-x86_64-2.5/neuron/hoc.so -Wl,-R/home/eperfa/neuron71/nrn/x86_64/lib -Wl,-R
/usr/bin/ld: /home/eperfa/mpich2/mpich2-1.2/../lib/libmpich.a(initialized.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/eperfa/mpich2/mpich2-1.2/../lib/libmpich.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'mpic++' failed with exit status 1Could anyone help me with figuring out what to do?
Thanks a lot,
Szabolcs