Memory issues arising in small neural networks

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sternj＠college.harvard.edu

25 Mar 2020 25 Mar '20

6:29 p.m.

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

Show replies by date

Hans Ekkehard Plesser

26 Mar 26 Mar

7:52 a.m.

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.edumailto:sternj@college.harvard.edu wrote:

Hello all,

Hope everyone is staying safe and well in these difficult times.

# 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.

Thank you so much for your help.

Best wishes, Josh _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto: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@nmbu.no Home http://arken.nmbu.no/~plesser

Joshua Stern

5:07 p.m.

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> 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 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 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to 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@nmbu.no Home http://arken.nmbu.no/~plesser

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

Hans Ekkehard Plesser

27 Mar 27 Mar

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=&...

As work-arounds for now, you could use the dockered version of NEST (https://nest-simulator.readthedocs.io/en/stable/installation/index.html#stan...) 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.edumailto:sternj@college.harvard.edu> wrote:

Thank you for your reply Hans!

Thank you so much and best wishes, Josh

On Thu, Mar 26, 2020 at 2:52 AM Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.nomailto: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.edumailto:sternj@college.harvard.edu wrote:

Hello all,

Hope everyone is staying safe and well in these difficult times.

# 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.

Thank you so much for your help.

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@nmbu.nohttp://nmbu.no/ Home http://arken.nmbu.no/~plesser

_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto: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@nmbu.no Home http://arken.nmbu.no/~plesser

Hans Ekkehard Plesser

3:08 p.m.

Hi!

Just a brief update: The macOS build instructions are at https://nest-simulator.readthedocs.io/en/stable/installation/install_options...

Best, Hans Ekkehard

On 27 Mar 2020, at 15:06, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no> wrote:

Hi Josh,

Best, Hans Ekkehard

On 26 Mar 2020, at 17:07, Joshua Stern <sternj@college.harvard.edumailto:sternj@college.harvard.edu> wrote:

Thank you for your reply Hans!

Thank you so much and best wishes, Josh

On Thu, Mar 26, 2020 at 2:52 AM Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.nomailto: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.edumailto:sternj@college.harvard.edu wrote:

Hello all,

Hope everyone is staying safe and well in these difficult times.

# 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.

Thank you so much for your help.

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@nmbu.nohttp://nmbu.no/ Home http://arken.nmbu.no/~plesser

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@nmbu.no Home http://arken.nmbu.no/~plesser

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@nmbu.no Home http://arken.nmbu.no/~plesser

Joshua Stern

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@nmbu.no> wrote:

...

Hi!

Just a brief update: The macOS build instructions are at https://nest-simulator.readthedocs.io/en/stable/installation/install_options...

Best, Hans Ekkehard

On 27 Mar 2020, at 15:06, Hans Ekkehard Plesser < hans.ekkehard.plesser@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=&... )?

As work-arounds for now, you could use the dockered version of NEST ( https://nest-simulator.readthedocs.io/en/stable/installation/index.html#stan...) 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 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> 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 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 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to 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@nmbu.no Home http://arken.nmbu.no/~plesser

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

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to 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@nmbu.no Home http://arken.nmbu.no/~plesser

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to 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@nmbu.no Home http://arken.nmbu.no/~plesser

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

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Hans Ekkehard Plesser
Joshua Stern
sternj＠college.harvard.edu