4 Feb
2020
4 Feb
'20
6:43 a.m.
Dear Daphne,
If you need access to larger computing resources for NEST (or other neuroscience)
simulations, Human Brain Project provides access to some of Europe's largest
supercomputers through the ICEI/FENIX program. It requires a brief application and a
usually quick review, but the process is much more lightweight than standard applications
for supercomputing resources. For more information, see
https://www.humanbrainproject.eu/en/massive-computing/fenix-icei/
Please get in touch if you would like to know more about this option!
Best,
Hans Ekkehard
On 3 Feb 2020, at 10:47, Jochen Martin Eppler
<j.eppler@fz-juelich.de<mailto:j.eppler@fz-juelich.de>> wrote:
Dear Daphne,
TL;DR: NEST does not support GPUs and can easily run simulations of up
to 50k neurons with realistic numbers of synapses on a single computer
with only CPUs.
It is a common misconception that GPUs will make everything faster. In
fact it might make things much slower for a large class of problems.
For the simulation of strongly coupled spiking neuronal networks using
point neuron model, the time to exchange events usually exceeds the time
to update the individual neurons by far. As GPUs are foremost good in
situations where you can run many operations on the same data and don't
read/write from/to memory a lot, they usually don't help here.
If you are interested in running NEST on a cloud service, you might want
to look at the Docker image for NEST: https://github.com/nest/nest-docker/
I suggest to start off by writing and running your simulation on your
local computer using threads and possibly MPI as described in
https://www.nest-simulator.org/parallel-computing/.
https://nest-simulator.readthedocs.io/en/latest/examples/ has heaps of
examples for all kinds of simulations. If this approach gets too slow,
you can move to computer clusters, supercomputers and cloud services.
Cheers,
Jochen!
On 02.02.20 18:45, Daphne Cornelisse wrote:
Hi NEST-team,
I would like to run a simulation of > 1000 neurons, and to make my
computing time faster I am looking into how to use parallel computing
with NEST.
I have seen this <https://www.nest-simulator.org/parallel-computing/>
page but I can't seem to find anything about using the cloud (e.g.
google cloud, colab etc.) and the use of GPU's. I am quite new to this
so it could be I missed something.
- Is it possible to use a GPU for the nest simulations?
- Are the some resources I could learn from?
Thank you!
Best,
Daphne
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--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
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