Search found 11 matches

by schmuker
Wed Feb 24, 2010 8:16 am
Forum: UNIX/Linux
Topic: --with-gnu-ld is required for compilation on openSuSE 11.2
Replies: 0
Views: 2065

--with-gnu-ld is required for compilation on openSuSE 11.2

After struggling for some time with this and finally having found the solution, I'd like to share with you that on openSuSE 11.2 I had to use the --with-gnu-ld option for configure. Otherwise, nrnivmodl will not compile any mod files, and terminate with an error message indicating that /usr/lib64/li...
by schmuker
Wed Sep 02, 2009 4:02 am
Forum: NEURON + Python
Topic: ImportError when compiled with MPI support
Replies: 6
Views: 4085

Re: ImportError when compiled with MPI support

I found the error. src/nrnpython/setup.py and config.status both used the right compilers. But there was an old nrnpython/build directory from a non-MPI build still hanging around which make clean did not make clean :) So I guess setup.py used the old libraries and installed them, instead of compili...
by schmuker
Tue Sep 01, 2009 3:59 pm
Forum: NEURON + Python
Topic: ImportError when compiled with MPI support
Replies: 6
Views: 4085

Re: ImportError when compiled with MPI support

ldd mypython/lib64/python2.5/site-packages/neuron/hoc.so gives no MPI libs here. I tried on a SUSE system (which has a somewhat awkward way to set up openmpi) and on debian 4.0. I'm on 64 bit, if that's important. On SUSE I need to set MPICC and MPICXX environment vars when configuring paranrn, bec...
by schmuker
Tue Sep 01, 2009 5:28 am
Forum: NEURON + Python
Topic: ImportError when compiled with MPI support
Replies: 6
Views: 4085

ImportError when compiled with MPI support

Hi, when using nrnpython with MPI support (--with-paranrn), I get an ImportError when doing from neuron import h Traceback (most recent call last): [...] ImportError: neuron.hoc module not found. Are you perhaps importing neuron in the nrnpython source directory? Please move out of this directory an...
by schmuker
Wed Aug 27, 2008 8:55 am
Forum: UNIX/Linux
Topic: IV Build Fails at OS/math.cpp on Fedora 9
Replies: 8
Views: 4552

Re: IV Build Fails at OS/math.cpp on Fedora 9

FYI: Same problem on openSUSE 11.0, same solution :)

Cheers,

Michael
by schmuker
Sun Sep 09, 2007 4:58 pm
Forum: UNIX/Linux
Topic: MPI problem
Replies: 9
Views: 8429

Just checked it on a i686 with openmpi version 1.2.3: Revision 1848 passed all tests in src/parallel without complaining! Great, thanks a lot!

Cheers,

Michael
by schmuker
Thu Sep 06, 2007 9:15 am
Forum: UNIX/Linux
Topic: MPI problem
Replies: 9
Views: 8429

OK, no problem. I'll use mpich2 for the time being. Let me know if I can help testing!

Cheers,

Michael
by schmuker
Thu Sep 06, 2007 6:13 am
Forum: UNIX/Linux
Topic: MPI problem
Replies: 9
Views: 8429

Thanks for the prompt reply! However, I still get the error message, although sometimes it runs without complaining. When I tried it the first few times, it always worked, now it crashes almost always... mpiexec -np 2 nrniv -mpi ~/sims/srcs/neuron6/nrn/src/parallel/test1.hoc numprocs=2 NEURON -- VER...
by schmuker
Wed Sep 05, 2007 2:33 am
Forum: UNIX/Linux
Topic: MPI problem
Replies: 9
Views: 8429

The configure line I used is

Code: Select all

./configure --with-iv=~/sims/neuron/iv --with-paranrn --with-mpi --with-nrnpython --prefix=~/sims/neuron/nrn
I didn't use mpich2, but openmpi (version 1.1). Which MPI library is recommended for neuron?
by schmuker
Tue Sep 04, 2007 9:38 am
Forum: UNIX/Linux
Topic: MPI problem
Replies: 9
Views: 8429

MPI problem

Hi all, I'm trying to get neuron working with mpi on an dual 4-core Intel (ubuntu 7.04). I'm using today's trunk from svn. It compiles nicely, and src/parallel/test0.hoc runs without errors. But test1.hoc crashes: :~/sims$ mpirun -np 2 nrniv -mpi src/parallel/test1.hoc numprocs=2 NEURON -- VERSION 6...
by schmuker
Wed Aug 22, 2007 8:29 am
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 25237

The line to change in the config.status file given above did nod work for me. In detail, I had to change the line s,@NRNPYTHON_DEFINES@,|#_!!_#|-DWITH_NUMPY,g to this: s,@NRNPYTHON_DEFINES@,|#_!!_#|-UWITH_NUMPY,g With this change, neuron compiled smoothly and nrniv -python works. Cheers, Michael