27 Mar
2020
27 Mar
'20
3:06 p.m.
Hi Josh,
I am able to reproduce the problem when I install NEST via conda onder macOS 10.14 and
10.15, while all works well with NEST 2.20.0 if I build it from scratch on my computer.
Obviously, this should not happen. Could you create a bug report on the NEST Github page
(https://github.com/nest/nest-simulator/issues/new?assignees=&labels=&am…
As work-arounds for now, you could use the dockered version of NEST
(https://nest-simulator.readthedocs.io/en/stable/installation/index.html#sta…)
or build NEST yourself. Unfortunately, it seems that our build instructions for NEST on
Mac are currently missing, I will check that asap.
Best,
Hans Ekkehard
On 26 Mar 2020, at 17:07, Joshua Stern
<sternj@college.harvard.edu<mailto:sternj@college.harvard.edu>> wrote:
Thank you for your reply Hans!
I am using Nest-2.20.0 installed with Conda on Mac os 10.14 Mojave. I have just tried
removing the environment and reinstalling using Conda again, but ran into the same issue.
What should I do to troubleshoot this?
Thank you so much and best wishes,
Josh
On Thu, Mar 26, 2020 at 2:52 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Josh,
Thanks for your report! This does not look like a memory issue but may point to some
internal inconsistency in NEST.
A few questions:
- Which version of NEST are you using?
- How did you install NEST (looks like you used conda)?
- Which operating system are you using?
Best,
Hans Ekkehard
On 25 Mar 2020, at 18:29,
sternj@college.harvard.edu<mailto:sternj@college.harvard.edu> wrote:
Hello all,
Hope everyone is staying safe and well in these difficult times.
I am an undergrad who is just getting started with this library, so I want to apologize in
advance for the basic question. I am having issues I believe are memory-related when I
call GetConnections on rather small networks. Here is my script:
import nest
# memory testing
nest.ResetKernel()
n = 5 # number of neurons
epop1 = nest.Create("iaf_psc_alpha",n)
epop2 = nest.Create("iaf_psc_alpha",n)
nest.Connect(epop1,epop2,{'rule': 'all_to_all'})
# we can now query the synapses using GetConnections
conns = nest.GetConnections(epop1,target = epop2)
nest.GetStatus(conns,["target","weight"])
This runs fine for n < 5, but I get the following error with n >=5:
Assertion failed: (source_lid < MAX_LID), function set_source_lid, file
/usr/local/miniconda/conda-bld/nest-simulator_1583214474797/work/nestkernel/target_data.h,
line 264.
Abort trap: 6
I have run some of the example scripts like brunel_alpha_numpy with a few thousand neurons
and they work just fine.
Am I making an improper call to GetConnections here? And if so, what is a better way to
dynamically check connectivity?
Alternatively, might there be something wrong with my Nest environment? And if so, what
should I look at to troubleshoot this?
Thank you so much for your help.
Best wishes,
Josh
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Prof. Dr. Hans Ekkehard Plesser
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Norwegian University of Life Sciences
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_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
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