GetConnections is too slow- can i obtain connection ids as I connect the neurons? (nest v2.20)
3 Jul
2023
3 Jul
'23
10:55 a.m.
Hello,
I have a serious bottleneck in terms of runtime in my simulations.
I have a modular cortical network and i need to 'manually' change weights in some
specific connections before i start the simulation.
The modularity means that this happens inside a for loop for all populations pairs.
so, before simulation starts i have a function that goes over all population pairs and
does this:
AMPA_conns = nest.GetConnections(source=pre_pop,target=post_pop,
synapse_model='AMPA_synapse_longrange') # RETRIEVE ALL AMPA CONNECTIONS BETWEEN
SOURCE AND TARGET POPULATION
nest.SetStatus(AMPA_conns, {'weight': pattern_weight}) # CHANGE CONNECTION
WEIGHT
NMDA_conns = nest.GetConnections(source=pre_pop,target=post_pop,
synapse_model='NMDA_synapse_longrange') # RETRIEVE ALL NMDA CONNECTIONS BETWEEN
SOURCE AND TARGET POPULATION
nest.SetStatus(NMDA_conns, {'weight': pattern_weight * nmda2ampa_ratio}) # CHANGE
CONNECTION WEIGHT
commenting out these 4 lines reduces my runtime by 8 hours.
for reference, the model consists of ~27000neurons, is created in 20 minutes (nodes
generated and connections drawn) and the actual simulation runs for about 15 minutes.
so my question is: is there a way to obtain the connection ids as i draw the connections
(right after the nest.Connect() function) so that i can store them in a data structure and
avoid this expensive operation of searching? or perhaps it is the setstatus that makes it
expensive?
*I havent yet migrated to nest v3, this concerns version 2.20.
thank you for your time!
angeliki
23 Aug
23 Aug
5:24 a.m.
hey again!
let me know if you are aware of this issue and whether to the best of this knowledge it is
resolved in nest 3.0.
thank you for your time
angeliki
24 Aug
24 Aug
3:20 a.m.
Hello Angeliki,
GetConnections() takes time, but eight hours compared to 20 + 15 minutes for a network of
27.000 neurons seems very slow. I would definitely suggest that you try with the newest
NEST version, 3.5. NEST 2.20 is quite old by now and we have made a large number of
improvements in the meantime.
NEST 3.5 allows parameterization of neurons and connections while they are created
directly at the C++ level, which saves a lot of time (20 minutes to build a 27.000 neuron
network seems slow). Depending on what kind of "manual" manipulation of synaptic
weights you need to do, it might even be possible to include this in connection creation,
so you can avoid GetConnections() altogether.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Angeliki Papadimitriou <angpap(a)kth.se>
Date: Wednesday, 23 August 2023 at 11:24
To: users(a)nest-simulator.org <users(a)nest-simulator.org>
Subject: [NEST Users] Re: GetConnections is too slow- can i obtain connection ids as I
connect the neurons? (nest v2.20)
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hey again!
let me know if you are aware of this issue and whether to the best of this knowledge it is
resolved in nest 3.0.
thank you for your time
angeliki
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
6:05 a.m.
Thank you for the reply.
I will attempt to migrate to 3.5 and see if it works faster.
i know for a fact that i can benefit from the collocated synapse class to draw both ampa
and nmda connections between the same neurons.
but can you elaborate a bit on the last thing you mentioned:
"Depending on what kind of "manual" manipulation of synaptic
weights you need to do, it might even be possible to include this in connection creation,
so you can avoid GetConnections() altogether."
the scenario: i initially draw non specific recurrent connections within the global neuron
population using a connection probability. The network is organized in hypercolumns that
contain minicolumns. Knowing the minicolumn index of the pre and post populations i want
to upregulate the weight. Can that be done without a call to getconnections?
Thank you for your time
Angeliki
6:43 a.m.
Hello Angeliki,
IN NEST 3.5, one can provide relatively complex expressions for connection rules,
including weights, see
https://nest-simulator.readthedocs.io/en/stable/neurons/parametrization.htm…
This mostly applies to networks with spatial structure, though.
If you would be willing to share more details about your network and simulation scripts, I
could provide more detailed suggestions. You can send that information directly to my mail
address if you do not want to make it public on the mailing list.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Angeliki Papadimitriou <angpap(a)kth.se>
Date: Thursday, 24 August 2023 at 12:05
To: users(a)nest-simulator.org <users(a)nest-simulator.org>
Subject: [NEST Users] Re: GetConnections is too slow- can i obtain connection ids as I
connect the neurons? (nest v2.20)
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Thank you for the reply.
I will attempt to migrate to 3.5 and see if it works faster.
i know for a fact that i can benefit from the collocated synapse class to draw both ampa
and nmda connections between the same neurons.
but can you elaborate a bit on the last thing you mentioned:
"Depending on what kind of "manual" manipulation of synaptic
weights you need to do, it might even be possible to include this in connection creation,
so you can avoid GetConnections() altogether."
the scenario: i initially draw non specific recurrent connections within the global neuron
population using a connection probability. The network is organized in hypercolumns that
contain minicolumns. Knowing the minicolumn index of the pre and post populations i want
to upregulate the weight. Can that be done without a call to getconnections?
Thank you for your time
Angeliki
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
7:10 a.m.
Oh I see what you mean now.
There was a similar functionality in the v2.20 using the 'distribution'
parametrization. This is not applicable in my case however as the network organization
relies on abstract indexing and not spatial coordinates.
Thank you all the same.
Best
Angeliki
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Angeliki Papadimitriou -
Hans Ekkehard Plesser