Does IPython offer any profiling? Does regular Python profiling work? I would recommend to start a profiling session before the last statement, and to end it immediately after. A tool like snakeviz can them visualize it for you.

On Fri, Mar 8, 2024, 18:26 Xavier Otazu Porter xotazu@cvc.uab.cat wrote:

I am not a python expert, but same behaviour here ...

NEST 3.6 (git master HEAD from february 12), Python 3.8.12, Rocky Linux 8.5

Xavier

*From:* Hans Ekkehard Plesser hans.ekkehard.plesser@nmbu.no *Sent:* Friday, March 8, 2024 3:24 PM *To:* users@nest-simulator.org users@nest-simulator.org *Subject:* [NEST Users] Strange interaction between NEST and IPython

Dear Python experts among the NEST Users!

I just notice a strange interaction between NEST and Ipython. In a freshly started Ipython, I execute the following three statements

import nest

n = nest.Create('parrot_neuron', positions=nest.spatial.free([(x, 0) *for* x *in* range(10000)]))

n

The last one takes extraordinarily long, over 10 seconds, I think. But if I instead do

print(n)

it executes instantaneously.

Also, if I do the same thing in python directly, just entering

n

shows the NodeCollection immediately.

Can anyone reproduce this and does anyone have an idea what might be going on?

I am on macOS 14.3.1 with Python 3.12.2, Ipython 8.22.2, and have checked with NEST 3.6 and a branch of recent master.

Best,

Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser

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

Computer Vision Center http://www.cvc.uab.cat CONFIDENTIALITY WARNING http://www.cvc.uab.es/?page_id=7475

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Hi Harold,

Nice to hear from you and thanks a lot for the detailed explanations and the solution for this mystery 😊!

Would you want to prepare a PR for this, so you get credit assigned for the solution? Ideally today, since we plan to roll NEST 3.7-RC1 very, very soon now.

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser

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.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

From: Harold Gutch nest-hg@gutch.de Date: Monday, 11 March 2024 at 22:52 To: NEST User Mailing List users@nest-simulator.org Subject: [NEST Users] Re: Strange interaction between NEST and IPython [Du mottar ikke ofte e-post fra nest-hg@gutch.de. Finn ut hvorfor dette er viktig p? https://aka.ms/LearnAboutSenderIdentification ]

Hello Hans,

On Fri, Mar 08, 2024 at 02:24:17PM +0000, Hans Ekkehard Plesser wrote:

Dear Python experts among the NEST Users!

I just notice a strange interaction between NEST and Ipython. In a freshly started Ipython, I execute the following three statements

import nest n = nest.Create('parrot_neuron', positions=nest.spatial.free([(x, 0) for x in range(10000)])) n

The last one takes extraordinarily long, over 10 seconds, I think. But if I instead do

print(n)

it executes instantaneously.

What happens is that IPython's pretty printing calls (a bit down the line) the IPythonDisplayFormatter() class. The first thing that does is test if for the given object there is an _ipython_display_() method - if that exists, it calls that, otherwise it falls back to a more generic method. In your case the latter happens, it falls back to the more generic method and that is what then produces the output.

When looking up if there is an _iython_display_() method, the first thing IPython does is check for a method called _ipython_canary_method_should_not_exist_() - and it is precisely this lookup that takes so long. You can verify this by

getattr(n, "_ipython_canary_method_should_not_exist_")

which will also take rather long. As the output here also contains some SLI things, one might need to dig deeper to actually speed this up.

Instead, adding a check specifically for exactly the above mentioned lookup of _ipython_canary_method_should_not_exist_() also does the job (for me), see the attachment. With that workaround, your example returns instantaneously - as one would expect it to.

regards, Harold

Hi Harold,

Done, see https://github.com/nest/nest-simulator/pull/3145

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser

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.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

From: Harold Gutch nest-hg@gutch.de Date: Tuesday, 12 March 2024 at 09:56 To: NEST User Mailing List users@nest-simulator.org Subject: [NEST Users] Re: Strange interaction between NEST and IPython [Du mottar ikke ofte e-post fra nest-hg@gutch.de. Finn ut hvorfor dette er viktig på https://aka.ms/LearnAboutSenderIdentification ]

Hi Hans Ekkehard,

On Tue, Mar 12, 2024 at 08:40:50AM +0000, Hans Ekkehard Plesser wrote:

Hi Harold,

Nice to hear from you and thanks a lot for the detailed explanations and the solution for this mystery 😊!

Would you want to prepare a PR for this, so you get credit assigned for the solution? Ideally today, since we plan to roll NEST 3.7-RC1 very, very soon now.

I don't have a Github account :). Could you do that? Don't think too much about how to credit me etc., just do it however is the easiest for you. From my side, you may see my diff as as close to Public Domain as possible - so if that's the easiest for you, just put it in there "as your contribution" or so. I'm happy if it helps :).

regards, Harold _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org