Dear all,
I am trying to use music ports for my simulations, which requires continuous transmission of data to NEST. I would like to test them in a toy example before integrating them in my project to make sure I am using them as I should. So, under section "Receiving continuous data" in "Guides\Using NEST with MUSIC" ( https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music...), I found a guide for this functionality of NEST, however, the binary "constsource" is not available. Does anybody have any idea where I can find it?
Thank you very much in advance for your help,
Best wishes,
Mohammad
Dear Mohammad,
the constsource binary is not part of NEST, but of MUSIC. After building and installing MUSIC, you will find it in <MUSIC_INSTALL_PREFIX>/lib/music-<MUSIC_VERSION>.
Cheers, Jochen!
On 02.03.20 16:15, Mohammadreza Mohagheghi Nejad wrote:
Dear all,
I am trying to use music ports for my simulations, which requires continuous transmission of data to NEST. I would like to test them in a toy example before integrating them in my project to make sure I am using them as I should. So, under section "Receiving continuous data" in "Guides\Using NEST with MUSIC" (https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music...), I found a guide for this functionality of NEST, however, the binary "constsource" is not available. Does anybody have any idea where I can find it?
Thank you very much in advance for your help,
Best wishes,
Mohammad
-- Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Dear Jochen,
Thank you very much! Found it there. However, I got the following error, this time, from the python script (given as an example on the website, attached anyways). Maybe this is important for you to know that, with my current compilation of NEST and MUSIC, I could successfully run MUSIC for two NEST simulations communicating spike events between the two.
OS: Ubuntu 18.04.4 LTS, NEST v2.16.0 compiled by cmake downloaded from https://github.com/INM-6/closed-loop-learning-in-autonomous-agents
--------------ERROR-------------- Traceback (most recent call last): File "./conttest.py", line 3, in <module> import nest File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/__init__.py", line 26, in <module> from . import ll_api # noqa File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 72, in <module> from . import pynestkernel as kernel # noqa ImportError: dynamic module does not define init function (initpynestkernel) ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- [warn] Epoll ADD(4) on fd 33 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[59388,1],1] Exit code: 1 -------------------------------------------------------------------------- --------------ERROR--------------
Best wishes,
Mohammad
On Mon, Mar 2, 2020 at 9:10 PM Jochen Martin Eppler j.eppler@fz-juelich.de wrote:
Dear Mohammad,
the constsource binary is not part of NEST, but of MUSIC. After building and installing MUSIC, you will find it in <MUSIC_INSTALL_PREFIX>/lib/music-<MUSIC_VERSION>.
Cheers, Jochen!
On 02.03.20 16:15, Mohammadreza Mohagheghi Nejad wrote:
Dear all,
I am trying to use music ports for my simulations, which requires continuous transmission of data to NEST. I would like to test them in a toy example before integrating them in my project to make sure I am using them as I should. So, under section "Receiving continuous data" in "Guides\Using NEST with MUSIC" (
https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music... ),
I found a guide for this functionality of NEST, however, the binary "constsource" is not available. Does anybody have any idea where I can find it?
Thank you very much in advance for your help,
Best wishes,
Mohammad
-- Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany
https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653
Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi!
Your error looks a lot like a Python 2/3 mixup to me. This usually happens if you compile NEST against Python 2, while you run it using Python 3, or the other way around. Please make sure that your environment is consistent with respect to Python versions.
Please note that we're not supporting Python 2 in all future versions of NEST, as it (finally!) reached it's well-deserved end of life.
Cheers, Jochen!
On 03.03.20 10:32, Mohammadreza Mohagheghi Nejad wrote:
Dear Jochen,
Thank you very much! Found it there. However, I got the following error, this time, from the python script (given as an example on the website, attached anyways). Maybe this is important for you to know that, with my current compilation of NEST and MUSIC, I could successfully run MUSIC for two NEST simulations communicating spike events between the two.
OS: Ubuntu 18.04.4 LTS, NEST v2.16.0 compiled by cmake downloaded from https://github.com/INM-6/closed-loop-learning-in-autonomous-agents
--------------ERROR-------------- Traceback (most recent call last): File "./conttest.py", line 3, in <module> import nest File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/__init__.py", line 26, in <module> from . import ll_api # noqa File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 72, in <module> from . import pynestkernel as kernel # noqa ImportError: dynamic module does not define init function (initpynestkernel)
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
[warn] Epoll ADD(4) on fd 33 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[59388,1],1] Exit code: 1
--------------ERROR--------------
Best wishes,
Mohammad
On Mon, Mar 2, 2020 at 9:10 PM Jochen Martin Eppler <j.eppler@fz-juelich.de mailto:j.eppler@fz-juelich.de> wrote:
Dear Mohammad, the constsource binary is not part of NEST, but of MUSIC. After building and installing MUSIC, you will find it in <MUSIC_INSTALL_PREFIX>/lib/music-<MUSIC_VERSION>. Cheers, Jochen! On 02.03.20 16:15, Mohammadreza Mohagheghi Nejad wrote: > Dear all, > > I am trying to use music ports for my simulations, which requires > continuous transmission of data to NEST. I would like to test them in a > toy example before integrating them in my project to make sure I am > using them as I should. So, under section "Receiving continuous data" in > "Guides\Using NEST with MUSIC" > (https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music.html), > I found a guide for this functionality of NEST, however, the binary > "constsource" is not available. Does anybody have any idea where I can > find it? > > Thank you very much in advance for your help, > > Best wishes, > > Mohammad > > -- > Mohammadreza Mohagheghi Nejad > > Postdoctoral researcher in computational neuroscience, > Institute of Neural Computation, > Ruhr University Bochum, Germany > https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/ > > _______________________________________________ > 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> > -- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ 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>-- Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
HI,
So, I tried to run the script on a NEST live media downloaded from NEST website ( https://nest-simulator.org/downloads/gplreleases/lubuntu-18.04_nest-2.16.0.o...). I did this because I imagined that Python2/3 mix up shouldn't be a problem in the live media. However, I got a similar error.
Best, Mohammad
On Tue, Mar 3, 2020 at 11:11 AM Jochen Martin Eppler j.eppler@fz-juelich.de wrote:
Hi!
Your error looks a lot like a Python 2/3 mixup to me. This usually happens if you compile NEST against Python 2, while you run it using Python 3, or the other way around. Please make sure that your environment is consistent with respect to Python versions.
Please note that we're not supporting Python 2 in all future versions of NEST, as it (finally!) reached it's well-deserved end of life.
Cheers, Jochen!
On 03.03.20 10:32, Mohammadreza Mohagheghi Nejad wrote:
Dear Jochen,
Thank you very much! Found it there. However, I got the following error, this time, from the python script (given as an example on the website, attached anyways). Maybe this is important for you to know that, with my current compilation of NEST and MUSIC, I could successfully run MUSIC for two NEST simulations communicating spike events between the two.
OS: Ubuntu 18.04.4 LTS, NEST v2.16.0 compiled by cmake downloaded from https://github.com/INM-6/closed-loop-learning-in-autonomous-agents
--------------ERROR-------------- Traceback (most recent call last): File "./conttest.py", line 3, in <module> import nest File
"/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/__init__.py",
line 26, in <module> from . import ll_api # noqa File
"/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py",
line 72, in <module> from . import pynestkernel as kernel # noqa ImportError: dynamic module does not define init function
(initpynestkernel)
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
[warn] Epoll ADD(4) on fd 33 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[59388,1],1] Exit code: 1
--------------ERROR--------------
Best wishes,
Mohammad
On Mon, Mar 2, 2020 at 9:10 PM Jochen Martin Eppler <j.eppler@fz-juelich.de mailto:j.eppler@fz-juelich.de> wrote:
Dear Mohammad, the constsource binary is not part of NEST, but of MUSIC. Afterbuilding
and installing MUSIC, you will find it in <MUSIC_INSTALL_PREFIX>/lib/music-<MUSIC_VERSION>. Cheers, Jochen! On 02.03.20 16:15, Mohammadreza Mohagheghi Nejad wrote: > Dear all, > > I am trying to use music ports for my simulations, which requires > continuous transmission of data to NEST. I would like to test them in a > toy example before integrating them in my project to make sure Iam
> using them as I should. So, under section "Receiving continuous data" in > "Guides\Using NEST with MUSIC" > (https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music... ),
> I found a guide for this functionality of NEST, however, thebinary
> "constsource" is not available. Does anybody have any idea where I can > find it? > > Thank you very much in advance for your help, > > Best wishes, > > Mohammad > > -- > Mohammadreza Mohagheghi Nejad > > Postdoctoral researcher in computational neuroscience, > Institute of Neural Computation, > Ruhr University Bochum, Germany >https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
> > _______________________________________________ > 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> > -- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
_______________________________________________ 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>-- Mohammadreza Mohagheghi Nejad
Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany
https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653
Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi,
Thanks, that was the problem. I was running with python2 accidentally because I forgot to change the path to Python interpreter from the default path (#!/usr/bin/python) to the Python 3 path I was using (#!/usr/bin/env python).
Best,
Mohammad
On 3. Mar 2020, at 11:11, Jochen Martin Eppler j.eppler@fz-juelich.de wrote:
Hi!
Your error looks a lot like a Python 2/3 mixup to me. This usually happens if you compile NEST against Python 2, while you run it using Python 3, or the other way around. Please make sure that your environment is consistent with respect to Python versions.
Please note that we're not supporting Python 2 in all future versions of NEST, as it (finally!) reached it's well-deserved end of life.
Cheers, Jochen!
On 03.03.20 10:32, Mohammadreza Mohagheghi Nejad wrote:
Dear Jochen, Thank you very much! Found it there. However, I got the following error, this time, from the python script (given as an example on the website, attached anyways). Maybe this is important for you to know that, with my current compilation of NEST and MUSIC, I could successfully run MUSIC for two NEST simulations communicating spike events between the two. OS: Ubuntu 18.04.4 LTS, NEST v2.16.0 compiled by cmake downloaded from https://github.com/INM-6/closed-loop-learning-in-autonomous-agents --------------ERROR-------------- Traceback (most recent call last): File "./conttest.py", line 3, in <module> import nest File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/__init__.py", line 26, in <module> from . import ll_api # noqa File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 72, in <module> from . import pynestkernel as kernel # noqa ImportError: dynamic module does not define init function (initpynestkernel)
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
[warn] Epoll ADD(4) on fd 33 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[59388,1],1] Exit code: 1
--------------ERROR-------------- Best wishes, Mohammad On Mon, Mar 2, 2020 at 9:10 PM Jochen Martin Eppler <j.eppler@fz-juelich.de mailto:j.eppler@fz-juelich.de> wrote: Dear Mohammad, the constsource binary is not part of NEST, but of MUSIC. After building and installing MUSIC, you will find it in <MUSIC_INSTALL_PREFIX>/lib/music-<MUSIC_VERSION>. Cheers, Jochen! On 02.03.20 16:15, Mohammadreza Mohagheghi Nejad wrote: > Dear all, > > I am trying to use music ports for my simulations, which requires > continuous transmission of data to NEST. I would like to test them in a > toy example before integrating them in my project to make sure I am > using them as I should. So, under section "Receiving continuous data" in > "Guides\Using NEST with MUSIC" > (https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_music...), > I found a guide for this functionality of NEST, however, the binary > "constsource" is not available. Does anybody have any idea where I can > find it? > > Thank you very much in advance for your help, > > Best wishes, > > Mohammad > > -- > Mohammadreza Mohagheghi Nejad > > Postdoctoral researcher in computational neuroscience, > Institute of Neural Computation, > Ruhr University Bochum, Germany > https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/ > > _______________________________________________ > 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 > -- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653
Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
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
Mohammadreza Mohagheghi Nejad Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/ _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653
Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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Jochen Martin Eppler -
Mohammadreza Mohagheghi Nejad