Include also mods into the possible path for mod files

mattions commented 12 years ago

One of the model available on ModelDB, 140471, is storing the mods into the mod files.

The compilation fails and all the software crash.

This is the log:

INFO neuronvisio.modeldb.ModelDB 117   Downloading model for 'Jaffe et al., 2011'
INFO neuronvisio.modeldb.ModelDB 149   Creating Models/140471.zip
INFO neuronvisio.modeldb.ModelDB 158   Done.
INFO neuronvisio.modeldb.ModelDB 119   Download complete.
INFO neuronvisio.modeldb.ModelDB 164   Extracting 'Models/140471.zip' into Models/140471
INFO neuronvisio.modeldb.ModelDB 170   Trancating file at location 1402360.
INFO neuronvisio.modeldb.ModelDB 192   Done.
INFO neuronvisio.controls 457   Path changed to /home/mattions/Work/model/MSN/Neuronvisio/src/Models/140471
Creating x86_64 directory for .o files.

/home/mattions/Work/model/MSN/Neuronvisio/src/Models/140471
*.mod
*.mod
make: *** No rule to make target `mod_func.c.lo', needed by `libnrnmech.la'. Stop.
NEURON mechanisms not found in ./.
NEURON: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"
    1 
INFO neuronvisio.controls 471   Loading model in Models/140471
    1 
    1 
    1 
NEURON: syntax error
 in figure5.hoc near line 170
     insert Ca              // Ca Channesl
             ^
        xopen("figure5.hoc")
      execute1("{xopen("figure5.hoc")}")
    load_file("figure5.hoc")
  xopen("mosinit.hoc")
and others
    0 
NEURON: syntax error
 in figure5.hoc near line 175
    insert aabBK                // BK Channels
               ^
        xopen("mosinit.hoc")
      execute1("{xopen("mosinit.hoc")}")
    load_file("k")
Assertion failed: file cabcode.c, line 1736
NEURON: sec->nnode > 0
 in figure5.hoc near line 175
 ^
        doNotify()
INFO neuronvisio.controls 475   Path changed back to /home/mattions/Work/model/MSN/Neuronvisio/src
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 552, in __bootstrap_inner
    self.run()
  File "/usr/local/lib/python2.7/dist-packages/neuron/gui.py", line 36, in run
    self.fun()
  File "/usr/local/lib/python2.7/dist-packages/neuron/gui.py", line 17, in process_events
    h.doNotify()
RuntimeError: hoc error

Segmentation fault

We should include also mods, in the possible path to compilation, and we should manage the compilation a bit more gracefully, maybe using an Exception.

mattions commented 12 years ago

@uricohen do you want to give this a go?

uricohen commented 12 years ago

Yes, ok!

On Tue, Dec 20, 2011 at 12:49 PM, Michele Mattioni < reply@reply.github.com

wrote:

@uricohen do you want to give this a go?

Reply to this email directly or view it on GitHub: https://github.com/mattions/neuronvisio/issues/35#issuecomment-3217254

        Uri Cohen

mattions / neuronvisio

Include also mods into the possible path for mod files #35