8 Apr
2024
8 Apr
'24
4:43 p.m.
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
9 Apr
9 Apr
2:40 p.m.
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
6:50 p.m.
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
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3 participants
participants (3)
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Hans Ekkehard Plesser -
Xavier Otazu -
Xavier Otazu Porter