[NEST Users] Re: GetConnections in distributed simulation

Dear Hans Ekkehard, We are not using mpi4py. We simply set the number of virtual processes at the begining of simulation:nest.total_num_virtual_procs = 32 for example We want to collect weights of stdp synapses before and after the simulation. Getting connections however, we observed different source and target before and after we run the simulation. I suppose this is because GetConnections returns only a portion of connections but how to obtain all portions is not clear for us. Best,Petia On Tuesday, June 6, 2023 at 09:24:30 AM GMT+3, Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no> wrote:   Dear Petia,   On each MPI rank, GetConnections() will only collect connections for which the post-synaptic neuron is on that MPI rank. You then need to find a way to collect this information across ranks. If you only need that information for offline processing, it might be easiest to write the connection information to file from each rank and then collect across ranks (you probably don't want to store the result from GetConnections(), but rather get the status of the synapses and store that). As a starting point, you could take the   https://nest-simulator.readthedocs.io/en/v3.4/auto_examples/store_restore_n…   example. There, connections (and neurons) are stored with      network= {}     network["n_vp"]= nest.total_num_virtual_procs     network["e_nrns"]=self.neurons.get(["V_m"], output="pandas")     network["i_nrns"]=self.neurons.get(["V_m"], output="pandas")       network["e_syns"]= nest.GetConnections(synapse_model="e_syn").get(         ("source","target","weight"), output="pandas")     network["i_syns"]= nest.GetConnections(synapse_model="i_syn").get(         ("source","target","weight"), output="pandas")      withopen(dump_filename,"wb")as f:         pickle.dump(network, f, pickle.HIGHEST_PROTOCOL)   You might not need the data on neurons, and you would have to write one file per MPI rank. Depending on your synapse type, you may want to store more parameters than source, target and weight.   If you need the information at runtime, you could try to use mpi4py to aggregate the connection information across ranks.   Best, Hans Ekkehard   --    Prof. Dr. Hans Ekkehard Plesser Head, 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(a)nmbu.no Home http://arken.nmbu.no/~plesser       From: Petia Koprinkova <pkoprinkova(a)yahoo.com> Date: Monday, 5 June 2023 at 13:11 To: NEST User Mailing List <users(a)nest-simulator.org> Subject: [NEST Users] GetConnections in distributed simulation Dear NEST Support team, We are trying to get the weights of stdp synapses during a distributed simulation. According to NEST documentation and our experience function GetConnections returns only local connections but not all connections in our model. Could you please advise us how to get all connections in such a case? Best regards, Petia Koprinkova-Hristova _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org