Problem with using neuron module from Python 2.7 in PyCharm
Posted: Mon Apr 28, 2014 12:02 pm
Hello,
First of all, I am amazed that such a small team is somehow able to heroically troubleshoot the problems of an army of users that have different machines with different software versions. Thank you for your help.
My ultimate goal is to be able to run network models on a cluster, with python code as a base for some high level abstraction, output handling, data analysis, and model optimization, and running NEURON models (hoc code) via the Python neuron module.
My OS is OSX 10.9.2.
My NEURON version is 7.3.
My Python version is 2.7.6.
I followed the installation instructions here:
http://www.neuron.yale.edu/neuron/downl ... ilestd_osx
There were a lot of errors produced during installation, but I appear to now have a functioning NEURON 7.3 that runs fine from the command line. The brief test of open mpi installation succeeded as well.
I would like to be able to use the Community Edition of PyCharm as an IDE for writing and debugging Python code. The strange thing is, I can get Python to execute hoc code in 2/3 places. I am able to execute the following from 1) the command line, 2) the Python 2.7.6 Shell from IDLE, but get an error when executing from 3) the Python Console within PyCharm:
import neuron
h = neuron.hoc.HocObject()
h("create soma")
som = h.soma
the error I receive is:
NEURON: nseg not a USERPROPERTY that can be pointed to
near line 0
create soma
^
Process finished with exit code 139
As far as I can tell, all three of these consoles are referring to the same version of Python and importing the same modules with the same directories extending the sys.path. The reason I would prefer to use PyCharm is the intelligent way that it recognizes method calls and variable references while typing into the console. Any ideas what is going wrong here?
First of all, I am amazed that such a small team is somehow able to heroically troubleshoot the problems of an army of users that have different machines with different software versions. Thank you for your help.
My ultimate goal is to be able to run network models on a cluster, with python code as a base for some high level abstraction, output handling, data analysis, and model optimization, and running NEURON models (hoc code) via the Python neuron module.
My OS is OSX 10.9.2.
My NEURON version is 7.3.
My Python version is 2.7.6.
I followed the installation instructions here:
http://www.neuron.yale.edu/neuron/downl ... ilestd_osx
There were a lot of errors produced during installation, but I appear to now have a functioning NEURON 7.3 that runs fine from the command line. The brief test of open mpi installation succeeded as well.
I would like to be able to use the Community Edition of PyCharm as an IDE for writing and debugging Python code. The strange thing is, I can get Python to execute hoc code in 2/3 places. I am able to execute the following from 1) the command line, 2) the Python 2.7.6 Shell from IDLE, but get an error when executing from 3) the Python Console within PyCharm:
import neuron
h = neuron.hoc.HocObject()
h("create soma")
som = h.soma
the error I receive is:
NEURON: nseg not a USERPROPERTY that can be pointed to
near line 0
create soma
^
Process finished with exit code 139
As far as I can tell, all three of these consoles are referring to the same version of Python and importing the same modules with the same directories extending the sys.path. The reason I would prefer to use PyCharm is the intelligent way that it recognizes method calls and variable references while typing into the console. Any ideas what is going wrong here?