usable mindelay is 0
Posted: Tue May 20, 2014 1:03 am
Hi folks,
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:
Parallel error
A couple of things I've tried so far:
- 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.
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.