16 Jan
2020
16 Jan
'20
3:43 p.m.
Dear all,
I tried to install a custom module into Nest first using the MyModule
example as described here
https://nest.github.io/nest-simulator/extension_modules
The installation works fine without errors, however when I try to load
the model into pynest with
import nest
import('mymodule')
I get a "Segmentation fault (core dumped)". The last traceback of
debbugging with python pdb is the following:
-> engine.run('{%s} runprotected' % decode(cmd))
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode()
-> def decode(s):
(Pdb) s
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()
-> return s.decode('utf-8')
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod...
Install'
-> return s.decode('utf-8')
(Pdb) s
Segmentation fault (core dumped)
I already added the model path to my LD_LIBRARY_PATH variable so that
the module can be found, but now it cannot be loaded.
It looks like a decoding issue, but I don't know what went wrong during
the installation. Do you have any idea what could be the issue? I am
using python 2.7 and NEST 2.3.1
Thanks!
Benedikt Feldotto
--
Benedikt Feldotto M.Sc.
Research Assistant
Human Brain Project - Neurorobotics
Technical University of Munich
Department of Informatics
Chair of Robotics, Artificial Intelligence and Real-Time Systems
Room HB 2.02.20
Parkring 13
D-85748 Garching b. München
Tel.: +49 89 289 17628
Mail: feldotto(a)in.tum.de
https://www6.in.tum.de/en/people/benedikt-feldotto-msc/
www.neurorobotics.net
/usr/lib/python2.7/encodings/utf_8.py(15)decode()
-> def decode(input, errors='strict'):
(Pdb) s
/usr/lib/python2.7/encodings/utf_8.py(16)decode()
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
/usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb...
Install', 26)
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
17 Jan
17 Jan
2:32 a.m.
Dear Benedikt,
to the best of my knowledge, we have never released a version 2.3.1 of
NEST. Where did you get this? To confirm the version, can you please
send the full output of running "import nest" in Python? This should
print a welcome message, including the version.
A probable reason for your problem is the way you try to load your
custom module into NEST. Your line "import("mymodule") is not the way to
do this - in fact, I don't even know, what that would do. In Python
3.7.5, it just gets me a syntax error.
The proper way of loading modules is to use the Install() function
provided by the Python module of NEST:
import nest
nest.Install("mymodule")
Can you please check if that works?
Cheers,
Jochen!
On 16.01.20 15:43, Benedikt Feldotto wrote:
Dear all,
I tried to install a custom module into Nest first using the MyModule
example as described here
https://nest.github.io/nest-simulator/extension_modules
The installation works fine without errors, however when I try to load
the model into pynest with
import nest
import('mymodule')
I get a "Segmentation fault (core dumped)". The last traceback of
debbugging with python pdb is the following:
-> engine.run('{%s} runprotected' % decode(cmd))
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode()
-> def decode(s):
(Pdb) s
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()
-> return s.decode('utf-8')
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod...
Install'
-> return s.decode('utf-8')
(Pdb) s
Segmentation fault (core dumped)
I already added the model path to my LD_LIBRARY_PATH variable so that
the module can be found, but now it cannot be loaded.
It looks like a decoding issue, but I don't know what went wrong during
the installation. Do you have any idea what could be the issue? I am
using python 2.7 and NEST 2.3.1
Thanks!
Benedikt Feldotto
--
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
/usr/lib/python2.7/encodings/utf_8.py(15)decode()
-> def decode(input, errors='strict'):
(Pdb) s
/usr/lib/python2.7/encodings/utf_8.py(16)decode()
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
/usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb...
Install', 26)
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
9:13 a.m.
Dear Jochen,
thanks for your answer! And sorry for the typos in my mail.. I am using
nest version 2.12.0 (not sure where I got the other version number from)
and yes I already tried to import my custom module with
nest.Install('mymodule'), so that's unfortunately not the source of the
error.
If you still have a hint what might be wrong that would be great.
Best,
Benedikt
On 17.01.20 02:32, Jochen Martin Eppler wrote:
Dear Benedikt,
to the best of my knowledge, we have never released a version 2.3.1 of
NEST. Where did you get this? To confirm the version, can you please
send the full output of running "import nest" in Python? This should
print a welcome message, including the version.
A probable reason for your problem is the way you try to load your
custom module into NEST. Your line "import("mymodule") is not the way to
do this - in fact, I don't even know, what that would do. In Python
3.7.5, it just gets me a syntax error.
The proper way of loading modules is to use the Install() function
provided by the Python module of NEST:
import nest
nest.Install("mymodule")
Can you please check if that works?
Cheers,
Jochen!
On 16.01.20 15:43, Benedikt Feldotto wrote:
--
Benedikt Feldotto M.Sc.
Research Assistant
Human Brain Project - Neurorobotics
Technical University of Munich
Department of Informatics
Chair of Robotics, Artificial Intelligence and Real-Time Systems
Room HB 2.02.20
Parkring 13
D-85748 Garching b. München
Tel.: +49 89 289 17628
Mail: feldotto(a)in.tum.de
https://www6.in.tum.de/en/people/benedikt-feldotto-msc/
www.neurorobotics.net
Dear all,
I tried to install a custom module into Nest first using the MyModule
example as described here
https://nest.github.io/nest-simulator/extension_modules
The installation works fine without errors, however when I try to load
the model into pynest with
import nest
import('mymodule')
I get a "Segmentation fault (core dumped)". The last traceback of
debbugging with python pdb is the following:
-> engine.run('{%s} runprotected' % decode(cmd))
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode()
-> def decode(s):
(Pdb) s
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()
-> return s.decode('utf-8')
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod...
Install'
-> return s.decode('utf-8')
(Pdb) s
Segmentation fault (core dumped)
I already added the model path to my LD_LIBRARY_PATH variable so that
the module can be found, but now it cannot be loaded.
It looks like a decoding issue, but I don't know what went wrong during
the installation. Do you have any idea what could be the issue? I am
using python 2.7 and NEST 2.3.1
Thanks!
Benedikt Feldotto
--
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(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org /usr/lib/python2.7/encodings/utf_8.py(15)decode()
-> def decode(input, errors='strict'):
(Pdb) s
/usr/lib/python2.7/encodings/utf_8.py(16)decode()
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
/usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb...
Install', 26)
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
10:42 a.m.
Dear Benedikt,
thanks for the clarifications.
NEST 2.12.0 was released almost 4 years ago and the problem you are
experiencing might well be fixed in one of the newer releases. Git
master saw 3591 commits since the version you are using came out, and we
unfortunately don't have the capacity for chasing ghosts.
Can you please upgrade to the newest release or Git master and check if
you have the same issue there?
Cheers,
Jochen!
On 17.01.20 09:13, Benedikt Feldotto wrote:
Dear Jochen,
thanks for your answer! And sorry for the typos in my mail.. I am using
nest version 2.12.0 (not sure where I got the other version number from)
and yes I already tried to import my custom module with
nest.Install('mymodule'), so that's unfortunately not the source of the
error.
If you still have a hint what might be wrong that would be great.
Best,
Benedikt
On 17.01.20 02:32, Jochen Martin Eppler wrote:
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
Dear Benedikt,
to the best of my knowledge, we have never released a version 2.3.1 of
NEST. Where did you get this? To confirm the version, can you please
send the full output of running "import nest" in Python? This should
print a welcome message, including the version.
A probable reason for your problem is the way you try to load your
custom module into NEST. Your line "import("mymodule") is not the way to
do this - in fact, I don't even know, what that would do. In Python
3.7.5, it just gets me a syntax error.
The proper way of loading modules is to use the Install() function
provided by the Python module of NEST:
import nest
nest.Install("mymodule")
Can you please check if that works?
Cheers,
Jochen!
On 16.01.20 15:43, Benedikt Feldotto wrote:
Dear all,
I tried to install a custom module into Nest first using the MyModule
example as described here
https://nest.github.io/nest-simulator/extension_modules
The installation works fine without errors, however when I try to load
the model into pynest with
import nest
import('mymodule')
I get a "Segmentation fault (core dumped)". The last traceback of
debbugging with python pdb is the following:
-> engine.run('{%s} runprotected' % decode(cmd))
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode()
-> def decode(s):
(Pdb) s
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()
-> return s.decode('utf-8')
(Pdb) s
--Call--
/home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod...
Install'
-> return s.decode('utf-8')
(Pdb) s
Segmentation fault (core dumped)
I already added the model path to my LD_LIBRARY_PATH variable so that
the module can be found, but now it cannot be loaded.
It looks like a decoding issue, but I don't know what went wrong during
the installation. Do you have any idea what could be the issue? I am
using python 2.7 and NEST 2.3.1
Thanks!
Benedikt Feldotto
--
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(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org /usr/lib/python2.7/encodings/utf_8.py(15)decode()
-> def decode(input, errors='strict'):
(Pdb) s
/usr/lib/python2.7/encodings/utf_8.py(16)decode()
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
/usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb...
Install', 26)
-> return codecs.utf_8_decode(input, errors, True)
(Pdb) s
--Return--
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days inactive
1801
days old
3 comments
2 participants
participants (2)
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Benedikt Feldotto -
Jochen Martin Eppler