Comments (2)
@lungd Bear in mind that what jNeuroML is doing there is spawning an external process (Neuron), running it and waiting until it completes. All of the simulation of the worm takes place in Neuron and this should be the bulk of the time of the whole process.
In some small networks it may be quicker to run the simulation in jNeuroML itself, it's inherently slower (and normally required a smaller dt, e.g. 0.01 ms) but you don't have the overhead of writing Neuron py/hoc/mod files, compiling the mod file and launching an external process.
One way or another you should experiment with adjusting the dt value, as this is the biggest factor in determining the run time of simulations. If you are running many simulations, you might get away with 0.1 ms in Neuron, but always check the behaviour against runs at 0.01 in nrn (or 0.001 in jnml natively) to make sure the overall behavour is captured.
from org.neuroml.export.
NeuronWriter creates a file with a content containing snippets with following structure:
f = open(...)
num_points = len(py_v_time)
for i in range(num_points):
f.write(...)
f.close()
A possible improvement would be to create a string first and call write only once, e.g:
num_points = len(py_v_time)
file_string = ''.join(... for i in range(len(py_v_time)))
with open(...) as f:
f.write(file_string)
from org.neuroml.export.
Related Issues (20)
- [neuron-writer] how can one set the tolerance value? HOT 14
- List of LEMS/NML2 examples that can't be exported to neuron HOT 1
- Weighted synapses in Ex21 are not exported correctly to neuron HOT 2
- Workarounds for fractionAlong != (0 or 1)? HOT 3
- Incorrect generated mod for kinetic scheme initialisation HOT 1
- q10 for Kinetic Scheme based channels HOT 1
- exported mod always uses cnexp solver HOT 4
- NeuronWriter does not create unidirectional gap junctions? HOT 1
- What does the value of 318.91927 represent in abstract cell CM? HOT 4
- [*nix] Mod file compilation only checks for statically linked libnrnmech file (libnrnmech.la), but should also check for shared objects (libnrnmech.so) HOT 1
- Graphwriter needs to replace "-" with "_" in the component ID HOT 2
- NeuronWriter needs to replace tokens that are reserved in Python HOT 2
- Use LEMS model language symbol with SED-ML
- [BUG]: `getPulseGenMethod` for Brian 2 doesn't properly account for the simulation time line
- Support for MinGW and newer versions of NEURON? HOT 1
- Neuron mechanism fails with MacOS .dylib files[Bug] HOT 4
- generated `time.dat` does not seem to put each time value on new line
- Improve path related errors to help users figure out what is wrong with their paths HOT 2
- [Bug] JSONSerializer always puts all sections into an `all` NEURON section list, even if the NeuroML cell morphology has a `all` segment group that does not include all segments/segment groups in it
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from org.neuroml.export.