Remove deprecated models

[jougs]

Here's a small and hopefully non-controversial one removing deprecated models. I also cleaned up the handling of connection model flags a bit to get shorter and more readable lines.

[jougs]

@stinebuu: many thanks for measuring execution times. I'm actually not sure if this slow-down is to be expected, as the deprecated (and now removed) model iaf_psc_alpha_canon was also a precise variant.

When replacing iaf_psc_alpha_canon with iaf_psc_alpha_ps I just followed the documentation of the former.

@suku248 can you please quickly comment on this?

[suku248]

Regarding @stinebuu 's observation of slower runtimes when using iaf_psc_alpha_ps instead of the deprecated iaf_psc_alpha_canon: The implementations differ in the way they determine the precise location of a threshold crossing. While iaf_psc_alpha_canon used an interpolation method (precision depended on simulation resolution), iaf_psc_alpha_ps uses an iterative method (no dependence on sim res). Hanuschkin et al. (2010) did not observe any significant differences in runtime when comparing the two implementations for the IAF neuron model with exponential PSCs (see Fig. 5). Therefore, I would not have expected to see a substantial slowdown here. Maybe the iterative method doesn't converge as fast as it should be?

[jougs]

@suku248, many thanks for these insights.

I'm really not sure how to proceed here. @heplesser, @abigailm, @diesmann: any thoughts on this? Is there anyone currently working on the precise models who could investigate further?

[heplesser]

I will have another look at the performance problems.

[diesmann]

Thanks HEP. Whether _ps or _canon are faster depends on the computation time step and the requested accuracy. The general observation is that for a given accuracy _ps is faster than _canon because _ps can reach this accuracy already at larger computation time steps. With a fixed computation time step and a low required accuracy _canon might be faster because there are fewer operations to be carried out. The Hanuschkin paper has the details on this relationship.

[stinebuu]

I have been doing some digging. It seams like the problem is the use of propagator_31 and propagator_32 in iaf_psc_alpha_ps' propogate_ function. In canon, the propogate variables are calculated directly, while ps use propagator_31 and propagator_32.

When I use canon's way of doing things in the ps model (see the change here) I get the following times:

type	time
brunel_ps.sli with ps model	101.99 sec
`brunel_ps.sli with canon	93.96 sec
ArtificialSyncrony with ps	5 min 59 sec
ArtificialSyncrony with canon	6 min 39 sec

(brunel_ps with original ps model takes 227.94 sec).

I will try updating propagator_31 and propagator_32 now so they are part of a class, where constants are pre-calculated, similar to what is done with canon.

[jougs]

Merging this still depends on more discussion about the performance implications. Therefore removing the milestone.

[github-actions[bot]]

Pull request automatically marked stale!

[terhorstd]

Hi everyone, has more discussion lead to new insights? – Just a friendly ping.

[heplesser]

I have now re-run benchmarks for the brunel_ps.sli model using the propagator implementation provided in #2385 using iaf_psc_alpha_canon (deprecated, to be removed) and iaf_psc_alpha_ps. Experiments were done on a MacBook Pro with 2 GHz Quad Core Intel Core i5 with Clang 14. Code is from https://github.com/heplesser/nest-simulator/commit/10f643477bf4a2d8d408cb68067d518a7169a130, which provides a new IAFPropagator class, except for the ..._alpha_ps version of brunel_ps.sli, which is taken from this PR. Simulation times are minima of three runs. For comparison, also results for the current master https://github.com/nest/nest-simulator/commit/e49be2ae64b92b6b6d7c451b2ed8027c0975e480 with the old propagator implementation are given. The alpha_canon model uses linear interpolation to find the precise spike time.

Code	Neuron model	Simulation time
heplesser@10f6434	iaf_psc_alpha_canon	41.4 s
heplesser@10f6434	iaf_psc_alpha_ps	55.3 s
master@e49be2a	iaf_psc_alpha_ps	78.9 s

The ps variant is thus about 25% slower than the canon variant, but for two good reasons:

1. ps uses an iterative method to find the spike time, while canon uses linear interpolation
2. ps supports different excitatory and inhibitory synaptic time constants

Notice also that the new IAFPropagator class provided by #2385 significantly improves performance for the ps model compared to current master.

I therefore believe that the qualities of the ps model justify removal of canon once #2385 is merged.

[diesmann]

In

Morrison A., Straube S., Plesser HE., Diesmann M. (2007) Exact Subthreshold Integration with Continuous Spike Times in Discrete-Time Neural Network Simulations. Neural Computation 19:47–79. DOI: 10.1162/neco.2007.19.1.47.

We argue that stating the time required to propagate the implementation of a particular neuron model has no meaning. If the integration error is not specified an implementation can be arbitrarily fast, for example by doing nothing. Therefore one first needs to specify an accuracy goal and then select the implementation which achieves this in the shortest time. In the case of spiking neuron models we have two measures: the precision of the spike times and the number of missed spikes. The _canon model was included in the code base for NEST not for production but for documenting the results of the publication above and as a reference. When comparing _ps implementations among each other and with grid-constrained methods it also needs to be considered that for modern _ps algorithms the computation time step h can be increased because these models jump from incoming spike to incoming spike anyway.

Later results are summarized in:

Hanuschkin A, Kunkel S, Helias M, Morrison A and Diesmann M (2010) A general and efficient method for incorporating precise spike times in globally time-driven simulations. Front. Neuroinform. 4:113

Krishnan J, Porta Mana P, Helias M, Diesmann M and Di Napoli E (2018) Perfect Detection of Spikes in the Linear Sub-threshold Dynamics of Point Neurons. Front. Neuroinform. 11:75

[heplesser]

The figure below shows the median spike time error for 288 spikes recorded over 10 s from a single neuron driven by precise Poisson spike trains mimicking a brunel_ps network with mean rate 28.6 sp/s. Error is computed relative to a reference solution obtained with the iaf_psc_alpha_ps model at resolution $h=2^{-12}$ms. This is similar to the approach of Hanuschkin et al (2010). Errors were obtained for the following models:

• grid: iaf_psc_alpha
• can/lin: iaf_psc_alpha_canon with linear interpolation
• can/cub: iaf_psc_alpha_canon with cubic interpolation
• ps: iaf_psc_alpha_ps

To achieve the same accuracy obtained with ps for $h=0.5$ms, one needs to run can/cub with $h=2*-9$ms. Then, runtimes are (best of three runs, same machine as above)

Neuron model	Simulation time
iaf_psc_alpha_canon (cubic)	73.1 s
iaf_psc_alpha_ps	56.0 s

Accuracy taken into account, iaf_psc_alpha_ps clearly outperforms iaf_psc_alpha_canon and there is no reason to keep iaf_psc_alpha_canon any longer.

[heplesser]

For reference, attached is the notebook used to create the plot above. NEST-PR2294-PrecisionComparison.ipynb.zip