Search found 1585 matches

by hines
Thu Mar 22, 2018 8:25 am
Forum: NEURON + Python
Topic: Truncation of floats upon loading .hoc file from ipython
Replies: 15
Views: 7067

Re: Truncation of floats upon loading .hoc file from ipython

hoc.execute(1/2) prints ".5" in the working case, before returning 1 in the console. In spyder, it returns 1 without printing anything before. I'm guessing you mean hoc.execute('1/2') as otherwise it raises "NEURON: Expecting string argument" RuntimeError: hoc error I use from neuron import h and I...
by hines
Wed Mar 21, 2018 12:25 pm
Forum: NEURON + Python
Topic: Truncation of floats upon loading .hoc file from ipython
Replies: 15
Views: 7067

Re: Truncation of floats upon loading .hoc file from ipython

I have not yet been able to reproduce the problem hines@hines-T7500:~/tmp$ ipython2 Python 2.7.12 (default, Dec 4 2017, 14:50:18) Type "copyright", "credits" or "license" for more information. IPython 5.2.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %qui...
by hines
Sun Mar 11, 2018 7:58 pm
Forum: UNIX/Linux
Topic: Invalid syntax in "hclass3.py to hclass3.pyc"
Replies: 1
Views: 2060

Re: Invalid syntax in "hclass3.py to hclass3.pyc"

A similar issue was posted to https://github.com/nrnhines/nrn/issues/60 I'm getting the following error on Mac OS X High Sierra (Python 2.7.14 provided by pyenv), when compiling Neuron: byte-compiling /Users/werner/local/nrnnogui/lib/python2.7/site-packages/neuron/hclass3.py to hclass3.pyc File "/Us...
by hines
Fri Feb 16, 2018 11:14 am
Forum: UNIX/Linux
Topic: Error in MOD compilation with a Slurm script
Replies: 3
Views: 2088

Re: Error in MOD compilation with a Slurm script

Just as you built nrniv and all the NEURON libraries on the login node. So should you translate mod files and build the libnrnmech.so file on the login node (with nrnivmodl). In your case, it sounds like compute nodes are the same architecture as the login node and most of the development environmen...
by hines
Mon Feb 12, 2018 10:14 am
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2966

Re: Updating extracellular values for all segments!

I tend to make alpha distribution installers irregularly and on request. https://neuron.yale.edu/ftp/neuron/versions/alpha/nrn-7.5.master-1682.x86_64-osx.pkg is what you should get and should work for python 2.7 3.5 and 3.6 . Uninstall the previous version by dragging /Applications/NEURON-7.5 to the...
by hines
Sun Feb 11, 2018 8:44 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 2966

Re: Updating extracellular values for all segments!

That lacuna is fixed in todays github changeset. https://github.com/nrnhines/nrn/commit/d9be9278dbda0b374124c99380fe53d189abf570 The test I used, along with result output is hines@hines-T7500:~/neuron/nrntest/npy$ cat rvarray.py from neuron import h s = h.Section() s.nseg = 5 s.insert("extracellular...
by hines
Sat Feb 03, 2018 9:20 am
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 6433

Re: libnrnpython3 and libnrnpython2 on High Sierra

My guess is that the attempt to launch the gui failed because a bad NRN_PYLIB is already specified in your $HOME/.bash_profile and nrnpyenv.sh did not d o anything because PYTHONHOME already exists in your environment (set in $HOME/.bash_profile as well) # PYTHONHOME exists. Do nothing Thus the expe...
by hines
Fri Feb 02, 2018 3:47 pm
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 6433

Re: libnrnpython3 and libnrnpython2 on High Sierra

In an earlier message, it was stated: $ export NRN_PYLIB="/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation" And I see that you have a first line output of /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python In you case it s...
by hines
Fri Jan 26, 2018 12:37 pm
Forum: Modeling networks
Topic: Obtaining NetCon actual pre-section along fraction x value?
Replies: 5
Views: 2390

Re: Obtaining NetCon actual pre-section along fraction x value?

... relative to the end that has a parent (ie. not relative to the section orientation specified by the the section connection (returned by section.orientation())) That is a bug and fixed in the latest changeset https://github.com/nrnhines/nrn/commit/e786f17df3f5247c87008b46807aa351e8c300b0 A bette...
by hines
Thu Jan 25, 2018 8:45 pm
Forum: Modeling networks
Topic: Obtaining NetCon actual pre-section along fraction x value?
Replies: 5
Views: 2390

Re: Obtaining NetCon actual pre-section along fraction x value?

The change is https://github.com/nrnhines/nrn/commit/af83c99681dd5abe7860baac6fb1401f2355e595 Both preloc and preseg have been changed to return a arc position from 0 to 1 (if the threshold is a voltage variable) which is relative to the end that has a parent (ie. not relative to the section orienta...
by hines
Wed Jan 24, 2018 10:27 am
Forum: Modeling networks
Topic: Obtaining NetCon actual pre-section along fraction x value?
Replies: 5
Views: 2390

Re: Obtaining NetCon actual pre-section along fraction x value?

I will create a new python specific method pyseg = NetCon.preseg() which returns a nrn.Segment object from which you can get NetCon.preseg().x and NetCon.preseg().sec It will return None if the NetCon has no source, the source is on a different process (possible with MPI), or the source is not a vol...
by hines
Thu Jan 18, 2018 5:00 pm
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 6433

Re: libnrnpython3 and libnrnpython2 on High Sierra

Please send me the output from a terminal window of python import os, subprocess pid = os.getpid() cmd = "lsof -p %d"%pid f = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT).stdout for bline in f: fields = bline.decode().split() if len(fields) > 8: print (fields[8]) e...
by hines
Thu Jan 18, 2018 11:08 am
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 6433

Re: libnrnpython3 and libnrnpython2 on High Sierra

Ok. Thinks look right now as though it all should work. But you did not tell me what configure statement you used . Also what do you get with export PYTHONHOME="/anaconda3" export NRN_PYLIB="/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation" nrniv -python from neuron impo...
by hines
Wed Jan 17, 2018 5:34 pm
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 6433

Re: libnrnpython3 and libnrnpython2 on High Sierra

running into an issue with libnrnpython3 and libnrnpython2 This caused me to leap to the conclusion that you had installed a package. I.e very few people use options like --with-nrnpython=dynamic --with-pyexe=python3 --with-nrnpython-only which are useful for making a python independent distributio...
by hines
Mon Jan 15, 2018 9:39 am
Forum: Other questions
Topic: Off-by-a-bit timing problem with NetStim.noise = 0
Replies: 2
Views: 1476

Re: Off-by-a-bit timing problem with NetStim.noise = 0

That was a bug. t was not being updated to correspond to the event time (ParallelContext.t(0) was updated). This is fixed by
https://github.com/nrnhines/nrn/commit/ ... 7ae3132c20
Now should also work with threads (but if cvode is active, do not change values, just record).