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ld: library not found for -lX11

It appears that XQuartz is not installed. You can do that from xquartz.org

The problem with VecStim is that the mod file implementation did not envision this style of usage. I would recommend adding a restart procedure which, after you replace the Vector in the middle of a simulation, would set the counter to the first element of the Vector and do a net_send to activate th...

Yes. It is not enough any longer that the package be signed, it must also be notarized (now a $100 annual fee). Notarization means that Apple scanned the app for known malicious software. From https://support.apple.com/en-us/HT202491 How to open an app that hasn’t been notarized or is from an uniden...

MODLUNIT and NEURONHOME should be export MODLUNIT=/home/ziemek/usr/local/nrn/share/nrn/lib/nrnunits.lib export NEURONHOME=/home/ziemek/usr/local/nrn/share/nrn (I'm not sure but if you have NEURONHOME set, you may not need MODLUNIT) If you want to launch python and import neuron then export PYTHONPAT...

I had forgotten about that. It was the default for SCoP. The fix on our part will be to replace the existing adrunge implementation with a thread safe version. Nevertheless, adrunge generally makes little sense in a NEURON context since the extra accuracy does not translate into a more accurate simu...

You did not mention whether the 7.7 version hangs on your Macbook pro and on comet. Or if NEURON 7.5 has no problem on Manjaro linux. There have been a lot of mpi changes since 7.5. If it does not take too long to run an example, you can send me a zip file with sufficient code to exhibit the problem...

So I assume that I can just add libs by hand to the PYTHONPATH, but could you tell me where I can find export PYTHONPATH=/where/you/installed/nrn/lib #often /usr/local/nrn/lib The default build installs the NEURON module in <prefix>/lib/python in order to be python independent of the python version...

On my machine (macOS Catalina Version10.15 Beta (19A573a)) (my most recent build in /Applications/NEURON-7.7 is NEURON -- VERSION 7.7.1-38-g1f3d46d9+ master (1f3d46d9+) 2019-09-13 ) I'm seeing for a typical libnrnmech.so created by nrnivmodl $ otool -L x86_64/.libs/libnrnmech.so ... /usr/lib/libncur...

An old way of getting the PARAMETER names of a mechanism is from neuron import h ms = h.MechanismStandard("hh", 1) parm_name = h.ref("") for i in range(ms.count()): ms.name(parm_name, i) print(parm_name[0]) https://www.neuron.yale.edu/neuron/static/py_doc/programming/mechstan.html#MechanismStandard....

Segmentation Fault errors under MPI with gap junctions when I had h.cvode.cache_efficient(1) I'd like to attempt to fix this bug. Can you send me a (hopefully small) version of your model that exhibits this error. (Michael.hines@yale.edu) An unrelated point is that it is now possible to avoid the "...

It appears nothing has been done in this area since late 2007. There was a hook added in python for rxd in 2013 but is not being used. The translation of the soma stack to a centroid of 3-d points with diam continues to be: Approximate each contour of the stack as a circle. Center is the average of ...

computational cost is at each time step of recording into numerous Vectors (for each segment You definitely want only one vector per thread for storage for a recording location. A POINTER for each segment in a thread would all point to the same scalar accumulator and the mod file would add a weight...

use POINTER variables for (1) aggregation I don't think you can use the source_var/target_var pattern for this purpose because there is no way for one target to receive an increment from many sources. (the opposite is natural: a source can copy its value to many targets.) This assumes I correctly i...

Please try providing N as /cygdrive/c/nrn
The problem with c:/nrn is that the ':' in a pathlist is a separator.
The problem with /c/nrn is that msys2 apparently no longer supports that style.

I'm happy your nmodl mechanism resolves the issue. So this response is a bit stale. The channel builder with ligand would also suffice, Just
invent a ligand name with 0 charge and have another mechanism that modifies the ligand concentration according to your desire function.