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"NEURON's CVode method ignores conservation" and &
Posted: Thu Nov 09, 2006 1:01 am
by eacheon
When I do nrnivmodl, what's these info meaning?
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Translating Ih.mod into Ih.c
NEURON's CVode method ignores conservation
and
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Translating VClamp.mod into VClamp.c
Notice: This mechanism cannot be used with CVODE
VECTORIZED
I understand "Notice: This mechanism cannot be used with CVODE", but what does VECTORIZED mean?
Posted: Thu Nov 09, 2006 11:43 am
by hines
Translating Ih.mod into Ih.c
NEURON's CVode method ignores conservation
Kinetic scheme equations are normally not independent with dt = infinity and so CONSERVE is a hint for the fixed step method that substitutes the associated algebraic equation for one of the differential equations. This makes the STEADYSTATE method numerically more accurate. However this substitution cannot be used with the variable step method with the present nmodl translator implementation and so the hint is ignored.
but what does VECTORIZED mean?
Vectorization was a method of organizing variables in memory so that the Cray YMP pipeline could be used in an SIMD style of programming. There are a lot of reasons why nmodl will refuse to vectorize a given model, but the principle one is that it is incompatible with cvode. That is the reason why one hardly ever sees it anymore. It is far more important to work with CVODE than it is to be vectorized. In version 6.0 (still in the experimental development phase) the old style vectorization is obsolete because ALL models now have a different style of memory allocation which tends to be more cache efficient. For large models this speeds up a simulation between a factor of 2 - 4. And I expect further improvement will happen incrementally.