Some errors when I run ringtest.py

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
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zyc
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Joined: Sun Feb 19, 2017 9:15 pm

Some errors when I run ringtest.py

Post by zyc » Tue Apr 11, 2017 3:43 am

I installed the neruon from github, the python version is 2.7.12. When I tried to run ringtest.py, there arised some errors.

When import neuron, it prints:

Code: Select all

.libs/libnrnmech.so: undefined symbol: hoc_register_dparam_semantics
When I run "python ringtest.py", it prints: AttributeError 'hoc.HocObject' object has no attribute 'nrnbbcore_write' as follow:

Code: Select all

NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

loading membrane mechanisms from x86_64/.libs/libnrnmech.so
dlopen failed -
x86_64/.libs/libnrnmech.so: undefined symbol: hoc_register_dparam_semantics
[10, 20] [1, 1]
nring=16
cell per ring=8
ncell_per_type=8
ntype=16
created coredat/
0.0400002s created rings
2224 non-zero area compartments
0.00999999s initialized
Traceback (most recent call last):
  File "ringtest.py", line 181, in <module>
    pc.nrnbbcore_write(bbcorewrite_folder)
AttributeError: 'hoc.HocObject' object has no attribute 'nrnbbcore_write'
So I try to use special to run ringtest.py. First I use nrnivmodl to generate x86_64/special and it successed, then I run ringtest.py by "x86_64/special ringtest.py", but it still print an error undefined symbol: hoc_register_dparam_semantics as follow:

Code: Select all

loading membrane mechanisms from /home/zyc/Softwares/GPU-Neuron/sources/ringtest/x86_64/.libs/libnrnmech.so
dlopen failed -
/home/zyc/Softwares/GPU-Neuron/sources/ringtest/x86_64/.libs/libnrnmech.so: undefined symbol: hoc_register_dparam_semantics
Traceback (most recent call last):
  File "ringtest.py", line 1, in <module>
    from args import *
  File "args.py", line 1, in <module>
    import argparse
  File "/usr/lib/python2.7/argparse.py", line 85, in <module>
    import collections as _collections
  File "/usr/lib/python2.7/collections.py", line 20, in <module>
    from _collections import deque, defaultdict
ImportError: /usr/lib/python2.7/_collections.so: undefined symbol: _Py_NotImplementedStruct
Could you please tell me how to solve these errors? Thank you!

ted
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Re: Some errors when I run ringtest.py

Post by ted » Tue Apr 11, 2017 11:05 am

November 2015 is many bug fixes in the past. Suggest you try again with a more recent version of NEURON. Try the most recent alpha installer, or if you can compile from sources, get the most recent development code--see
http://www.neuron.yale.edu/neuron/download/getdevel

zyc
Posts: 18
Joined: Sun Feb 19, 2017 9:15 pm

Re: Some errors when I run ringtest.py

Post by zyc » Tue Apr 11, 2017 11:22 am

The Neuron I use is downloaded from github, and the version is 7.5, not 7.4. I compile it from source. It shows the version information like that because the Neuron on github doesn't have the file "nrnversion.h", I copied nrnversion.h from an already installed neuron.

ted
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Re: Some errors when I run ringtest.py

Post by ted » Tue Apr 11, 2017 11:41 am

Searching github for NEURON turns up 100 pages of results. Which of those is the one you mean?

zyc
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Re: Some errors when I run ringtest.py

Post by zyc » Tue Apr 11, 2017 9:56 pm


ted
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Re: Some errors when I run ringtest.py

Post by ted » Wed Apr 12, 2017 1:54 pm

OK, then, compile from an earlier commit along the main trunk. Or get the most recent alpha installer and use that instead.

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