[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 &lt;hans.ekkehard.plesser(a)nmbu.no&gt; Sent: Tuesday, April 9, 2024 2:40 PM To: NEST User Mailing List &lt;users(a)nest-simulator.org&gt; 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 &lt;xotazu(a)cvc.uab.cat&gt; Date: Monday, 8 April 2024 at 16:43 To: users(a)nest-simulator.org &lt;users(a)nest-simulator.org&gt; 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 Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>