21 Jun
2024
21 Jun
'24
8:11 p.m.
Hans,
I think I merged your PR with my code (I am not sure I did it correctly). Please, could
you check it?
Xavier
________________________________
From: Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no>
Sent: Friday, June 21, 2024 5:12 PM
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: Enhancement of C++ implementation of DumpLayerConnections()
Hi Xavier,
I have picked up work again on DumpLayerConnections and sent you a PR on Github. With the
changes I sent the code should be in good shape and if we could integrate all by the
middle of next week, it can make it into NEST 3.8.
Please get in touch if you have any questions!
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: Xavier Otazu Porter <xotazu(a)cvc.uab.cat>
Date: Tuesday, 9 April 2024 at 18:50
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: Enhancement of C++ implementation of DumpLayerConnections()
Hi Hans,
When you fixed that bug, tell me and I could take a look at a new possible solution (after
you tell me what this better solution can be ?? ).
I tried not to use the second line, but an error occurred on GetConnections() telling me
to use a NodeCollection as input parameter instead of a list. In fact, I see an example
using GetLocalNodeCollection and the second line in the following python example
code:https://nest-simulator.readthedocs.io/en/v3.3/auto_examples/hpc_benchmark.html?highlight=GetLocalNodeCollection
Anyway, in the next few days I am going to try again my code without that second line.
Thanks!
Xavier
________________________________
From: Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no>
Sent: Tuesday, April 9, 2024 2:40 PM
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: Enhancement of C++ implementation of DumpLayerConnections()
Dear Xavier,
Thank you for your detailed email—do not worry about writing technical here! Overall your
thoughts are sound, but even better solutions should be feasible once I have fixed
https://github.com/nest/nest-simulator/pull/3132.
BTW, you should not need the second line in
local_nodes = nest.GetLocalNodeCollection(target_layer)
local_nodes = nest.NodeCollection(local_nodes)
since GetLocalNodeCollection should return a NodeCollection object.
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: Xavier Otazu <xotazu(a)cvc.uab.cat>
Date: Monday, 8 April 2024 at 16:43
To: users(a)nest-simulator.org <users(a)nest-simulator.org>
Subject: [NEST Users] Enhancement of C++ implementation of DumpLayerConnections()
Hi!
After using some PyNEST functions and modifying the C++ implementation of
DumpLayerConnections(), I was thinking on a possible further improvement of this function
(or creating a new function). But since I do not know the design and architecture of C++
nestkernel code, I prefer to ask.
In my code I normalize the presynaptic connections of every neuron. To do this, I
originally do something like
for i in range(len(target_layer))
conn[i] = nest.GetConnections(source_layer, target_layer, synapse_model)
normalize(conn)
Since I am using MPI and the loop iterates over all the neurons, I modified the previous
code to
local_nodes = nest.GetLocalNodeCollection(target_layer)
local_nodes = nest.NodeCollection(local_nodes)
for i in range(len(local_nodes))
conn[i] = nest.GetConnections(source_layer, local_nodes, synapse_model)
normalize(conn)
This last code is faster that the previous one (I guess that local_nodes variable is local
to every MPI process and, as a consequence, GetConnections() is more efficient because it
only works with local nodes instead of with all of them).
Using the idea of the GetLocalNodeCollection(), I was thinking it could be used into the
C++ implementation of DumpLayerConnections(). Presently, this function obtain all the
connections between source and target layers. Could it be possible to call the equivalent
C++ implementation of GetLocalCollection()? I understand that the problem is that, since
DumpLayerConnections() needs the spatial information of the layers, the node collections
obtained with GetLocalNodeCollection() (I guess similarly its C++ implementation) does not
have this spatial information.
As a second possibility, I was thinking on adding a new method (GetSpatialInformation())
and enhancing DumpLayerConnections() (or add a new function). The GetSpatialInformation()
function could return the spatial information of a collection of nodes (the ones obtained
by GetLocalNodeCollection() ). The DumpLayerConnections() (or a new function) could be
enhanced by changing the target layer parameter to a pair of parameters that contain the
local nodes collection and their spatial information. Something like
DumpLaterConnections(source_layer, local_nodes_collection, spatial_information,
synapse_model). This way DumpLayerConnections() will only used local nodes and would be
much faster.
Sorry for the technical email.
Xavier
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