Dear Petia,
Are you invoking your simulation script using MPI (e.g. mpiexec python script.py) or are you just using a single process (e.g. python script.py)? In the latter case, increasing the number of virtual processes (using nest.total_num_virtual_procs) simply increases the number of threads used by that single process which is internally used for OpenMP shared-memory parallelization which therefore runs NEST in a non-distributed way.
When using a single process, GetConnections (if called without any parameters) returns all connections in the whole simulation. Calling GetConnections before and after the first call to Simulate (or Prepare) is indeed expected to return the connections in a different order. To massively increase the performance of the simulation, all connections are sorted by their corresponding source node prior to the first update cycle in the simulation.
If you want to collect weights for connections in the same order before and after the simulation, please run "nest.Prepare()" once before your first call to Simulate. While this call is redundant (as it will be called inside Simulate as well), it will ensure that all connections are already sorted. After your call to Prepare, you can call GetConnections to retrieve information about all connections in the correct order.
Please note that it is not yet possible to get precise STDP weights yet due to some internal optimizations, while the weight for most synapses will be correct and precise, it is not guaranteed to be the case for each individual synapse. If you need to get exact weights for individual synapses, please let me know, as I am currently actively working on that. If you are just interested in stochastic analysis of weights, you can safely assume that weights are sufficiently accurate across a whole population.
Best,
Jan
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_network.html
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")
with open(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@nmbu.no
Home http://arken.nmbu.no/~plesser
From: Petia Koprinkova <pkoprinkova@yahoo.com>
Date: Monday, 5 June 2023 at 13:11
To: NEST User Mailing List <users@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