Hi Robin,
Thanks for pitching in—I'm not an expert in MPI4py myself ;).
local_data = nest.GetConnections(...)
global_data = COMM_WORLD.allgather(local_data)
`global_data` will now be a list of local_data's collected from all the nodes. I suppose `allgather` might be a bit overkill, because all data is gathered on all nodes. There's also `COMM_WORLD.gather` which collects
the data on just 1 node.
This will not quite work and is not as efficient as possible in this case. GetConnections returns a synapse collection which can only be used to access local neurons. One needs to communicate
the actual synapse properties of interest between processes. Furthermore, in this case we only need the total weight of the synapses, so we can first compute that locally and then reduce:
conn = nest.GetConnections(target=neuron, synapse_model='static_synapse')
w_syns = np.array(
conn.weight )
w_total = COMM_WORLD.allreduce(np.abs(w_syns).sum())
if w_total > 0:
w_normed = w_syns /
w_total
...
If you normalize several times during a longer simulation, you should call GetConnections() only the first time you need it, since it can be slow. As long as you do not add or remove connections,
the conn object will remain valid.
I'd be much interested in how these ideas work :).
BTW, we will soon open abstract submission for this year's NEST Conference (https://nest-simulator.org/conference).
You could show your work there and discuss with the NEST community!
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: Robin Gilbert De Schepper <robingilbert.deschepper@unipv.it>
Date: Thursday, 16 March 2023 at 14:30
To: NEST User Mailing List <users@nest-simulator.org>
Subject: [NEST Users] Re: MPI error when using GetConnections
I can lend some insights to the `mpi4py` side of things. You can `pip install mpi4py`, but if your machine contains multiple MPI implementations, make sure to prepend the correct MPI wrappers to the command, e.g.:
CC=mpicc pip install mpi4py
Afterwards you can use:
import nest
from mpi4py.MPI import COMM_WORLD
...
local_data = nest.GetConnections(...)
global_data = COMM_WORLD.allgather(local_data)
`global_data` will now be a list of local_data's collected from all the nodes. I suppose `allgather` might be a bit overkill, because all data is gathered on all nodes. There's also `COMM_WORLD.gather` which collects
the data on just 1 node.
On Thu, 16 Mar 2023 at 14:19, Xavier Otazu Porter <xotazu@cvc.uab.cat> wrote: