6 Jun
2023
6 Jun
'23
12:50 p.m.
Hi Petia,
Given that the comparison of sets suggested by Hans Ekkehard are equal, you can, for
instance, use the following to sort the connections for easier inspection before and after
simulation:
# Retrieve SynapseCollection
syn_collection = nest.GetConnections()
# Create DataFrame from parameter dictionary of the connections
df_conns = pandas.DataFrame.from_dict(syn_collection.get())
# Sort connections by, in decreasing order of priority, the
# target thread id, source node id and target node id
df_conns.sort_values(
by=["target_thread", "source", "target"],
ignore_index=True, inplace=True
)
print(df_conns)
Best,
Nicolai
________________________________
From: Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no>
Sent: 06 June 2023 12:27
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: GetConnections in distributed simulation
Hello Petia,
If you call GetConnections() once before and once after Simulate() and get source and
target lists, and for source-target pairs, then the before and after source-target pairs
should be identical except for ordering, so comparing them as sets they should compare
equal. If not, something would be seriously wrong.
As for the precise weight of synapses at a given time point, NEST only updates synaptic
weights when a spike passes through, so for now you will get the weight of the synapse at
the time the most recent spike passed the synapse.
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<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Petia Koprinkova <pkoprinkova(a)yahoo.com>
Date: Tuesday, 6 June 2023 at 12:18
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: GetConnections in distributed simulation
Dear Jan,
Thank you very much for exhaustive answer.
We are using single mpi process (python3 sctipt.py) with given number of virtual
processes. However, GetConnections returns different source neurons as well, e.g.:
Before Simulate: source = [21, 21, 22, 23, 24,....]
After Simulate: source=[23, 24, 24, 27,....]
We've noticed that sources are ordered while targets are not but still there is some
missmatch before and after simulation.
I have to point out that our network is designed as 3D structure with stdp synapses
generated based on the distance between each pair of neurons and with given probability as
follows:
conn_dict = {
'rule': 'pairwise_bernoulli',
'p': nest.spatial_distributions.exponential(nest.spatial.distance, beta =
50),
'mask': {'spherical': {'radius': 60}},
'allow_autapses': True,
'allow_multapses': False
}
We aim to obtain exact weights of the stdp synapses after presenting some input to the
network and then to fix the weights so we appreciate your help very much.
Best wishes,
Petia
On Tuesday, June 6, 2023 at 12:14:30 PM GMT+3, Vogelsang, Jan
<j.vogelsang(a)fz-juelich.de> wrote:
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
________________________________
From: Petia Koprinkova <pkoprinkova(a)yahoo.com>
Sent: Tuesday, June 6, 2023 10:38:38 AM
To: NEST User Mailing List
Subject: [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")
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<mailto:hans.ekkehard.plesser@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
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