NEURON 6.0.1

News about new releases of NEURON, bug fixes, development threads, courses/conferences/workshops, meetings of the NEURON Users' Group etc.
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NEURON 6.0.1

Post by ted » Thu Jun 14, 2007 6:41 pm

Release 6.0.1 (1780) 2007-06-12 is now available from
This new standard distribution provides numerous improvements of performance for
model setup and simulation in general. Particularly noteworthy features include:
  • New command line switches for nrngui or nrniv.
    -h prints a summary of command line options
    -c "statement" causes execution of the hoc command "statement" on startup
  • Simulations of large models now execute up to twice as fast as previously
    because of improved cache efficiency. This continues to be an area of active
  • On parallel hardware:
    1. make -j will execute a distributed compilation of NEURON.
    2. Individual cells can be distributed over multiple hosts for "multisplit"
    simulations. This is useful for load balance when the number of cells is
    small compared to the number of processes.
    3. MPI barrier, allreduce, and allgather are now available from hoc.
    4. SaveState has been upgraded to work with parallel simulations of networks.
  • A spike event queueing method called bin queue is now available which allows
    faster execution of network simulations that use fixed time steps.
  • Python can be used as an alternative interpreter for NEURON, with convenient
    and full access to all hoc built-in and user defined functions, procedures,
    objects, strings, and values. Intensive development continues, so serious
    Python developers will want to keep up to date with the latest alpha versions.

Anything evaluatable, assignable, or callable in hoc can also be done in Python.
Objects and values can be scalars or any dimensioned arrays.
All methods and fields of objects are accessible.
POINT_PROCESSes are objects and so all aspects are accessible.
Sections, both top level and within objects, are accessible via the object notation
implemented in the nrnpy_nrn.cpp file, and all segments, mechanisms, and range
variables are accessible via the object notation.

Basic Python usage

Code: Select all

import hoc
h = hoc.HocObject?() # accessibility to everything in hoc
h('obfunc newvec() { return new Vector($1) }') # execute any statement
v = h.newvec(5) # call any user defined function, v is now a hoc Vector[]
v.indgen() # can call any method
v.x[3] = 25 # assign to any field
h.finitialize(-65) # call any built-in function
print h.PI # or evaluate any built-in variable
h('objref m')
h('m = new Matrix(2,3)')
h.m.x[1][2] = 12 # how to deal with hoc object names 
Many hoc functions require call by reference for strdef and objref and return
changed arguments. In Python this is supported by first wrapping an object,
string, or numeric value in a hoc.ref Python object, and using that as the
argument when call by reference is needed. For example:

Code: Select all

h('proc chstr() { $s1 = "goodbye" }') # call by ref hoc procedure
y = h.ref('hello') # python string wrapper 
print y[0] #prints 'hello'
print y[0] #prints 'goodbye'
The source code contains some of the development efforts in interfacing numpy by
Andrew Davison and Eilif Mueller.
The cache efficiency improvements were done in collaboration with Hubert Eichner.
Last edited by ted on Fri Jun 15, 2007 9:13 pm, edited 1 time in total.

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Post by pcoskren » Fri Jun 15, 2007 8:09 am

Congratulations, gentlemen!

Wonderful news; I'm looking forward to downloading it and starting to put it through its paces. The cache issues and Python sound particularly exciting.

<> :-)


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Location: Yale University School of Medicine

Bug fixes already!

Post by ted » Fri Jun 15, 2007 9:16 pm

This release has already been superceded by version 6.0.2, which fixes printing problems
under OS X and MSWin, and MSWin problems with closing the rxvt window.

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