I'm trying to get the model by Brette et al. 2007 "Simulation of networks of spiking neurons: a review of tools and strategies" (accession 83319) working in Neuron-7.3 on OS X Mavericks 10.9.2.
I have done the following:
1) Fresh install of Neuron from the DMG, set up path in .bash_profile
2) Install openmpi via homebrew ($ brew install openmpi)
3) Run the test scripts in ~/neuron/nrn/src/parallel ($ mpirun -n 4 nrniv -mpi test0.hoc, etc)
The test scripts test0.hoc to test7.hoc, and also testsw1.hoc, all run without error.
However, when I do a fresh download of the Brette model (http://senselab.med.yale.edu/modeldb/Sh ... odel=83319) and run it with the following, I get errors in both parallel and serial mode.
Serial error:
Code: Select all
$ cd ~/src/delta/destexhe_benchmarks/NEURON
$ nrnivmodl coba cuba cubadv
... (output, no errors) ...
$ cd cobahh
$ nrngui init.hoc
NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2b0c984183df
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits
Created 4000 cells; 4000 on host 0
Created 320000 connections to targets on host 0
SetupTime: 0.75999999
/Applications/NEURON-7.3/nrn/x86_64/bin/nrniv: Segmentation violation
in init.hoc near line 27
prun() // in common/perfrun.hoc
^
ParallelContext[0].psolve(1000)
ParallelNetManager[0].psolve(1000)
prun()
Parallel error
Code: Select all
$ mpirun -n 4 nrniv -mpi init.hoc
numprocs=4
NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2b0c984183df
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits
Created 4000 cells; 1000 on host 0
Created 80000 connections to targets on host 0
SetupTime: 0.21000004
0 nrniv: usable mindelay is 0 (or less than dt for fixed step method)
0 in init.hoc near line 27
0 prun() // in common/perfrun.hoc
^
0 finitialize(-60)
0 init()
0 stdinit()
0 prun()
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
- The intrinsic mode (i.e. running intrinsic.hoc instead of init.hoc) works fine
- I tried also manually downloading and compiling openmpi from source (from directions here http://www.neuron.yale.edu/neuron/downl ... ilestd_osx) and setting the paths (LD_LIBRARY_PATH). The same errors still occur
I am running out of things to try, short of trying on a different machine. Any ideas?
Also, Ted, many thanks for your help with my prior questions. Based on your reply to my "Best Practices" thread (viewtopic.php?f=15&t=3076), I've decided that the best way to produce clean code is to start with this example network and add my mechanisms from there.