12 Jul
2019
12 Jul
'19
12:41 p.m.
Hello everyone!
I need to take track of the weight of a set of synapses through time. I know that there
already is a device to do that implemented in nest. According to its documentation, the
'weight recorder' should be created and, then, specified in a synapse model
through the command:
wr = nest.Create('weight_recorder')
nest.CopyModel('stdp_synapse', 'model_name', {'weight_recorder':
wr})
nest.Connect(..., syn_spec = 'model_name')
The problem is that my synapses have weights distributed by a uniform distribution defined
as:
'weight': {"distribution": "uniform", "low": w_min,
"high": w_max}
but whenever I try to set this in CopyModel I get the following error:
terminate called without an active exception
[q035:13577] *** Process received signal ***
[q035:13577] Signal: Aborted (6)
[q035:13577] Signal code: (-6)
[q035:13577] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b4ae83d4370]
[q035:13577] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b4ae8d1f1d7]
[q035:13577] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b4ae8d208c8]
[q035:13577] [ 3]
/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b4b3cb049d5]
[q035:13577] [ 4] /lib64/libstdc++.so.6(+0x5e946)[0x2b4b3cb02946]
[q035:13577] [ 5] /lib64/libstdc++.so.6(+0x5e973)[0x2b4b3cb02973]
[q035:13577] [ 6]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(+0x85edc)[0x2b4b3b2eeedc]
[q035:13577] [ 7] /lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b4b3cdbb08f]
[q035:13577] [ 8]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager21set_synapse_defaults_EmRK12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x65)[0x2b4b3b2eaae5]
[q035:13577] [ 9]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager10copy_modelE4NameS1_12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x2bd)[0x2b4b3b2ecfdd]
[q035:13577] [10]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule23CopyModel_l_l_DFunction7executeEP14SLIInterpreter+0x112)[0x2b4b3b2f93f2]
[q035:13577] [11]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x123)[0x2b4b3bf70473]
[q035:13577] [12]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x312)[0x2b4b3bf6d382]
[q035:13577] [13]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKSs+0x128)[0x2b4b3bf6d8a8]
[q035:13577] [14]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/pynestkernel.so(+0x23cf5)[0x2b4b3a160cf5]
[q035:13577] [15] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6d62)[0x2b4ae80dea62]
[q035:13577] [16] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd)[0x2b4ae80de4bd]
[q035:13577] [17] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [18] /lib64/libpython2.7.so.1.0(+0x7088d)[0x2b4ae806a88d]
[q035:13577] [19] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b4ae80458e3]
[q035:13577] [20] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd)[0x2b4ae80d94fd]
[q035:13577] [21] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [22] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c)[0x2b4ae80de33c]
[q035:13577] [23] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [24] /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b4ae80e0f42]
[q035:13577] [25] /lib64/libpython2.7.so.1.0(+0x10037f)[0x2b4ae80fa37f]
[q035:13577] [26]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x150)[0x2b4ae80fc430]
[q035:13577] [27]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5e)[0x2b4ae80fc61e]
[q035:13577] [28] /lib64/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x3e)[0x2b4ae80fccae]
[q035:13577] [29] /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x2b4ae810d91f]
[q035:13577] *** End of error message ***
Annullato (core dumped)
Can somebody help me?
Thank you!
Chiara
12 Jul
12 Jul
1:14 p.m.
Hi Chiara,
you can try the following approach:
wr = nest.Create('weight_recorder')
nest.CopyModel('stdp_synapse', 'model_name')
nest.SetDefaults('model_name',{'weight_recorder': wr[0]})
nest.Connect(..., syn_spec = 'model_name')
OR
nest.Connect(...,'one_to_one',{'model': 'model_name',
'weight': {"distribution":
"uniform", "low": w_min, "high": w_max}
})
I hope this helps.
Ciao,
Alberto
Alberto Antonietti, Ph.D.
Nearlab - NeuroEngineering And medical Robotics Laboratory
Department of Electronics, Information and Bioengineering
Politecnico di Milano
Department of Brain and Behavioral Sciences - Unit of Neurophysiology
University of Pavia, Italy
http://www.nearlab.polimi.it/
http://www-5.unipv.it/dangelo/
On 12/07/2019 12:41,
deluca.1665541@studenti.uniroma1.it<mailto:deluca.1665541@studenti.uniroma1.it>
wrote:
Hello everyone!
I need to take track of the weight of a set of synapses through time. I know that there
already is a device to do that implemented in nest. According to its documentation, the
'weight recorder' should be created and, then, specified in a synapse model
through the command:
wr = nest.Create('weight_recorder')
nest.CopyModel('stdp_synapse', 'model_name', {'weight_recorder':
wr})
nest.Connect(..., syn_spec = 'model_name')
The problem is that my synapses have weights distributed by a uniform distribution defined
as:
'weight': {"distribution": "uniform", "low": w_min,
"high": w_max}
but whenever I try to set this in CopyModel I get the following error:
terminate called without an active exception
[q035:13577] *** Process received signal ***
[q035:13577] Signal: Aborted (6)
[q035:13577] Signal code: (-6)
[q035:13577] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b4ae83d4370]
[q035:13577] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b4ae8d1f1d7]
[q035:13577] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b4ae8d208c8]
[q035:13577] [ 3]
/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b4b3cb049d5]
[q035:13577] [ 4] /lib64/libstdc++.so.6(+0x5e946)[0x2b4b3cb02946]
[q035:13577] [ 5] /lib64/libstdc++.so.6(+0x5e973)[0x2b4b3cb02973]
[q035:13577] [ 6]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(+0x85edc)[0x2b4b3b2eeedc]
[q035:13577] [ 7] /lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b4b3cdbb08f]
[q035:13577] [ 8]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager21set_synapse_defaults_EmRK12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x65)[0x2b4b3b2eaae5]
[q035:13577] [ 9]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager10copy_modelE4NameS1_12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x2bd)[0x2b4b3b2ecfdd]
[q035:13577] [10]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule23CopyModel_l_l_DFunction7executeEP14SLIInterpreter+0x112)[0x2b4b3b2f93f2]
[q035:13577] [11]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x123)[0x2b4b3bf70473]
[q035:13577] [12]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x312)[0x2b4b3bf6d382]
[q035:13577] [13]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKSs+0x128)[0x2b4b3bf6d8a8]
[q035:13577] [14]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/pynestkernel.so(+0x23cf5)[0x2b4b3a160cf5]
[q035:13577] [15] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6d62)[0x2b4ae80dea62]
[q035:13577] [16] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd)[0x2b4ae80de4bd]
[q035:13577] [17] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [18] /lib64/libpython2.7.so.1.0(+0x7088d)[0x2b4ae806a88d]
[q035:13577] [19] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b4ae80458e3]
[q035:13577] [20] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd)[0x2b4ae80d94fd]
[q035:13577] [21] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [22] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c)[0x2b4ae80de33c]
[q035:13577] [23] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [24] /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b4ae80e0f42]
[q035:13577] [25] /lib64/libpython2.7.so.1.0(+0x10037f)[0x2b4ae80fa37f]
[q035:13577] [26]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x150)[0x2b4ae80fc430]
[q035:13577] [27]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5e)[0x2b4ae80fc61e]
[q035:13577] [28] /lib64/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x3e)[0x2b4ae80fccae]
[q035:13577] [29] /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x2b4ae810d91f]
[q035:13577] *** End of error message ***
Annullato (core dumped)
Can somebody help me?
Thank you!
Chiara
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15 Jul
15 Jul
10:27 p.m.
Dear Chiara,
glad to hear that your problem got solved by Alberto's suggestion.
That said, a segfault should definitely not happen here. Can you please
send us the original simulation script that you used to trigger the crash?
If that's confidential, I'd be most interested in how many threads you
used and possibly some more details for the code snipped below in order
to give us a complete but minimal reproducer.
Many thanks,
Jochen!
On 12.07.19 12:41, deluca.1665541(a)studenti.uniroma1.it wrote:
Hello everyone!
I need to take track of the weight of a set of synapses through time. I know that there
already is a device to do that implemented in nest. According to its documentation, the
'weight recorder' should be created and, then, specified in a synapse model
through the command:
wr = nest.Create('weight_recorder')
nest.CopyModel('stdp_synapse', 'model_name', {'weight_recorder':
wr})
nest.Connect(..., syn_spec = 'model_name')
The problem is that my synapses have weights distributed by a uniform distribution
defined as:
'weight': {"distribution": "uniform", "low": w_min,
"high": w_max}
but whenever I try to set this in CopyModel I get the following error:
terminate called without an active exception
[q035:13577] *** Process received signal ***
[q035:13577] Signal: Aborted (6)
[q035:13577] Signal code: (-6)
[q035:13577] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b4ae83d4370]
[q035:13577] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b4ae8d1f1d7]
[q035:13577] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b4ae8d208c8]
[q035:13577] [ 3]
/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b4b3cb049d5]
[q035:13577] [ 4] /lib64/libstdc++.so.6(+0x5e946)[0x2b4b3cb02946]
[q035:13577] [ 5] /lib64/libstdc++.so.6(+0x5e973)[0x2b4b3cb02973]
[q035:13577] [ 6]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(+0x85edc)[0x2b4b3b2eeedc]
[q035:13577] [ 7] /lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b4b3cdbb08f]
[q035:13577] [ 8]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager21set_synapse_defaults_EmRK12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x65)[0x2b4b3b2eaae5]
[q035:13577] [ 9]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager10copy_modelE4NameS1_12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x2bd)[0x2b4b3b2ecfdd]
[q035:13577] [10]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule23CopyModel_l_l_DFunction7executeEP14SLIInterpreter+0x112)[0x2b4b3b2f93f2]
[q035:13577] [11]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x123)[0x2b4b3bf70473]
[q035:13577] [12]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x312)[0x2b4b3bf6d382]
[q035:13577] [13]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKSs+0x128)[0x2b4b3bf6d8a8]
[q035:13577] [14]
/opt/NEST-nesters/lib64/python2.7/site-packages/nest/pynestkernel.so(+0x23cf5)[0x2b4b3a160cf5]
[q035:13577] [15] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6d62)[0x2b4ae80dea62]
[q035:13577] [16] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd)[0x2b4ae80de4bd]
[q035:13577] [17] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [18] /lib64/libpython2.7.so.1.0(+0x7088d)[0x2b4ae806a88d]
[q035:13577] [19] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b4ae80458e3]
[q035:13577] [20] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd)[0x2b4ae80d94fd]
[q035:13577] [21] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [22] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c)[0x2b4ae80de33c]
[q035:13577] [23] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d]
[q035:13577] [24] /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b4ae80e0f42]
[q035:13577] [25] /lib64/libpython2.7.so.1.0(+0x10037f)[0x2b4ae80fa37f]
[q035:13577] [26]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x150)[0x2b4ae80fc430]
[q035:13577] [27]
/lib64/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5e)[0x2b4ae80fc61e]
[q035:13577] [28] /lib64/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x3e)[0x2b4ae80fccae]
[q035:13577] [29] /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x2b4ae810d91f]
[q035:13577] *** End of error message ***
Annullato (core dumped)
Can somebody help me?
Thank you!
Chiara
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)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
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1986
days inactive
1989
days old
3 comments
3 participants
participants (3)
-
Alberto Antonietti -
deluca.1665541＠studenti.uniroma1.it -
Jochen Martin Eppler