27 Mar
2020
27 Mar
'20
3:33 p.m.
I will get the bug report up later today. Thank you again for your
attention here, I really appreciate it.
Best wishes,
Josh
On Fri, Mar 27, 2020 at 10:08 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi!
Just a brief update: The macOS build instructions are at
https://nest-simulator.readthedocs.io/en/stable/installation/install_option…
Best,
Hans Ekkehard
On 27 Mar 2020, at 15:06, Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
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(a)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(a)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(a)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
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
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_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org