7 May
2021
7 May
'21
8:09 a.m.
Hi Hans,
Is the Python script available still on today's master branch? I don't
seem to locate it.
Itaru.
On Thu, May 6, 2021 at 6:41 PM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no> wrote:
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>
>
> Hi everyone!
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>
>
> I realized today that profiling PyNEST is easier than I thought. In iPython, you can
just run
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>
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> run -p -s cumulative -D srn.prof ../src/pynest/examples/store_restore_network.py
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>
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> which will run the script, present a summary sorted by cumulative time and write
binary profiling data (pstats format) to file srn.prof.
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>
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> Then run (gprof2dot available from, e.g., PiPy)
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> gprof2dot -f pstats -o srn.dot srn.prof
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>
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> and finally
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> dot -Tpdf srn.dot
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>
> Both tools have lot's of options. In my case (an older version of the script
above, currently under review in #1919, not yet in master), the attached PDF resulted,
showing that getting connection properties indeed takes a lot of time. Note that the graph
only resolves time spent in Python code, time spent in C++ code is hiding behind
"run()".
>
>
>
> Below some more timing results from a network of 1000 neurons with 100,000
connections:
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>
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> In [16]: %time c = nest.GetConnections()
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> CPU times: user 66.5 ms, sys: 8.09 ms, total: 74.6 ms
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> Wall time: 75.7 ms
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>
>
> In [17]: %time c = nest.GetConnections().weight
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> CPU times: user 869 ms, sys: 75.3 ms, total: 944 ms
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> Wall time: 955 ms
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>
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> In [18]: %time c = nest.GetConnections().get("weight",
output="pandas")
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> CPU times: user 1.69 s, sys: 186 ms, total: 1.88 s
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> Wall time: 1.9 s
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>
>
> Clearly, GetConnections() is quite fast, while reading out the weights costs. What
maybe surprised me most is that turning the data as a Pandas DataFrame costs a whole
second extra—I wonder if we do something suboptimal here.
>
>
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> Best,
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> Hans Ekkehard
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>
>
> --
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>
>
> Prof. Dr. Hans Ekkehard Plesser
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> Head, Department of Data Science
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>
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> Faculty of Science and Technology
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> Norwegian University of Life Sciences
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> PO Box 5003, 1432 Aas, Norway
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>
>
> Phone +47 6723 1560
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> Email hans.ekkehard.plesser(a)nmbu.no
>
> Home http://arken.nmbu.no/~plesser
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>
>
>
>
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