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--
/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--
/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
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--
/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--
/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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
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:
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-- > /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-- > /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@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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:
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-- > /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-- > /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@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-
Benedikt Feldotto -
Jochen Martin Eppler