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Werner Van Geit
@wvangeit
import morphio
morph = morphio.mut.Morphology("filename.asc")
morph.write("filename.swc" )
Johanna Frost Nylen
@jofrony
Hi I have another question about the DEAP algorithm. The optimiser uses double float and then it's the whole number which would be randomised and not only between the boundaries I set for each parameter, i.e. a simple example would be bounds like [1,1e-7] would randomise numbers at position 1e-8 etc. (I hope my question is clear). Thank you!
Werner Van Geit
@wvangeit
maybe the issue is that the interval you give has a max bound that is larger than the lower bound. Did you mean [1e-7, 1] ?
Johanna Frost Nylen
@jofrony
Hi, sorry I think my question was a bit unclear. I mean, for example if I have a parameter in my optimisation where I would only like to have integer solutions, but as the algorithm uses double floats (I assume), it would randomise 15 decimal precision. However, I would like to be able to control the level of precision (i.e. the number of decimals).
Werner Van Geit
@wvangeit
Ok, thanks, that make things clearer
Mmm, I don't think that's possible with the current algorithm
a lot of the implementation is done in the DEAP (external) framework
I think most of the operators we use don't work in a discrete space
the only 'hack' I can think of is that in your evaluation function you discretize the parameters yourself. But not sure if that's really what you really want.
Aman Aberra
@Aman-A

Hi, I'm getting a strange error when running the examples (stochkvcell.py and opt_l5pc.py).
After reaching the 'run' call, the program hangs for a while, then prints this error:
(bpopt_env) Amans-MacBook-Pro:stochkv amanaberra$ python stochkvcell.py
Exception in thread Thread-3:
Traceback (most recent call last):
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/threading.py", line 926, in _bootstrap_inner
self.run()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/threading.py", line 870, in run
self._target(self._args, *self._kwargs)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/pebble/pool/process.py", line 178, in message_manager_loop
pool_manager.process_next_message(SLEEP_UNIT)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/pebble/pool/process.py", line 210, in process_next_message
message = self.worker_manager.receive(timeout)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/pebble/pool/process.py", line 342, in receive
return self.pool_channel.recv()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/pebble/pool/channel.py", line 63, in recv
return self.reader.recv()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/multiprocessing/connection.py", line 250, in recv
buf = self._recv_bytes()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/multiprocessing/connection.py", line 407, in _recv_bytes
buf = self._recv(4)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/multiprocessing/connection.py", line 383, in _recv
raise EOFError
EOFError

Traceback (most recent call last):
File "stochkvcell.py", line 173, in <module>
main()
File "stochkvcell.py", line 135, in main
run_stochkv_model(deterministic=deterministic)
File "stochkvcell.py", line 103, in run_stochkv_model
sim=nrn)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/bluepyopt/ephys/evaluators.py", line 160, in run_protocol
timeout=timeout)
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/site-packages/bluepyopt/ephys/protocols.py", line 235, in run
responses = tasks.result()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/concurrent/futures/_base.py", line 435, in result
return self.get_result()
File "/opt/anaconda3/envs/bpopt_env/lib/python3.7/concurrent/futures/_base.py", line 384, in
get_result
raise self._exception
pebble.common.ProcessExpired: Abnormal termination

strawcup
@strawcup

Hi, I get the following error after I run nrn = ephys.simulators.NrNSimulator() in simplecell.ipynb:

/Users/jyang/opt/anaconda3/lib/python3.7/site-packages/bluepyopt/ephys/simulators.py:75: UserWarning: Unable to find Neuron hoc shared library in /Applications/NEURON-7.7/nrn/lib/python/neuron, not disabling banner
'not disabling banner' % nrnpy_path)

Could you please look into it? Thanks in advance.

Werner Van Geit
@wvangeit
@strawcup , does this stop the execution? It's a warning and normally shouldn't affect the execution itself.
Tanguy Damart
@DrTaDa
@Aman-A Hello, have you checked if your NEURON installation works outside of BluePyOpt ?
1 reply
strawcup
@strawcup

@wvangeit , thanks for the response. You're right-- it doesn't stop the execution itself, but I get the following error message when I run the next line 'responses = twostep_protocol.run(cell_model=simple_cell, param_values=default_params, sim=nrn)':

ProcessExpired Traceback (most recent call last)

<ipython-input-16-b41867be1955> in <module>
1 default_params = {'gnabar_hh': 0.1, 'gkbar_hh': 0.03}
----> 2 responses = twostep_protocol.run(cell_model=simple_cell, param_values=default_params, sim=nrn)

~/opt/anaconda3/lib/python3.7/site-packages/bluepyopt/ephys/protocols.py in run(self, cell_model, param_values, sim, isolate, timeout)
81 sim=sim,
82 isolate=isolate,
---> 83 timeout=timeout)
84 except TypeError as e:
85 if "unexpected keyword" in str(e):

~/opt/anaconda3/lib/python3.7/site-packages/bluepyopt/ephys/protocols.py in run(self, cell_model, param_values, sim, isolate, timeout)
233 timeout=timeout)
234 try:
--> 235 responses = tasks.result()
236 except TimeoutError:
237 logger.debug('SweepProtocol: task took longer than '

~/opt/anaconda3/lib/python3.7/concurrent/futures/_base.py in result(self, timeout)
433 raise CancelledError()
434 elif self._state == FINISHED:
--> 435 return self.__get_result()
436 else:
437 raise TimeoutError()

~/opt/anaconda3/lib/python3.7/concurrent/futures/_base.py in get_result(self)
382 def
get_result(self):
383 if self._exception:
--> 384 raise self._exception
385 else:
386 return self._result

ProcessExpired: Abnormal termination

1 reply
mphillipsneuro
@mphillipsneuro
Hi @wvangeit,
I'm currently attempting to use bluepyopt to optimize parameters for a model of NMDA receptor kinetics (i.e. rate constants for transitions between states, number of receptors, etc.). My stimulus (agonist and antagonist applications on a single vclamped cell) is built into my .mod file and works great for simulations and parameter optimization just using NEURON, but I'm having trouble figuring out how to use it with bluepyopt. You mention above that it is possible to create a custom "subclass of Stimulus and use your mod mechanism in the implementation of that new class". Could you elaborate on how this can be done, or point me in the direction of an example?
Thanks!
Werner Van Geit
@wvangeit
@strawcup do you mind creating an issue in the bluepyopt tracker, then we can investigate it further over there
@mphillipsneuro is your MOD file open source, could we have a look at it? For an example how e.g. a protocol is overwritten, you could have a look here: https://github.com/BlueBrain/BluePyOpt/blob/master/examples/thalamocortical-cell/CellEvalSetup/protocols.py
mphillipsneuro
@mphillipsneuro
@wvangeit Thanks for the response and example. I believe I've successfully written a voltage clamp stimulus subclass, but the agonist/drug applications are proving to be tricky. The MOD file is currently unpublished (and very much a work in progress) and thus not currently available online. The closest is found here https://senselab.med.yale.edu/ModelDB/ShowModel?model=145836&file=/MoradiEtAl2012/SynNMDA16_2.mod#tabs-2
but the method I'm using for modeling the stimulus is entirely different. I can send it to you via email. Thanks again!
IlaCar
@IlaCar

Hi @wvangeit and hi everyone, I have this strange error :

File "/home/miseno/.local/lib/python3.6/site-packages/bluepyopt/ephys/morphologies.py", line 128, in instantiate
imorphology.input(str(self.morphology_path))
RuntimeError: hoc error

when I run a code that works perfectly on another machine. Can you please point me to the right direction to solve the problem?
Thank you.

Ilaria

Werner Van Geit
@wvangeit
@DrTaDa could you have a look what might be causing the above error? Thanks.
Tanguy Damart
@DrTaDa
Hello @IlaCar, do you have the same version of NEURON, Python and BluePyOpt and the two machines ? Also, what is the format and the origin of the morphology file you are using ? If you morphology is open, could you send it to us ?
IlaCar
@IlaCar
Hello @DrTaDa, yes, I have the same version of NEURON, Python and BluePyOpt. I use the swc format. Here you find the morphologies:
https://kg.ebrains.eu/search/instances/Model/a6458de3-a176-4378-9b03-34a26f5da3bd
9 replies
sunzhenyang2018
@sunzhenyang2018
Respected devs of BluePyOpt, I wonder whether your code works on windows. My concerns lie in the use of mod files, because compiling mod files is different between windows and linux/mac. (e.g. in linux libnrnmech.so is stored somwhere in the x86 folder, and in windows nrnmech.dll is created in the folder where the mod files are; windows has nrniv.exe while linux has something else. etc.) Since my model is quite dependent on these mod files, it would be really nice if BluePyOpt is compatible to using mod files on windows, or can be configured to do so easily.
Werner Van Geit
@wvangeit
dear @sunzhenyang2018, unfortunately we don't have access to Windows machines, nor do we have access to testing infrastructure for Windows, so we're not really supporting it at the moment. Would it be possible for you to use a VM or the Windows Linux subsystem? Is there any particular error you're getting? Another would be that you subclass the Simulator class to handle the loading of the dll file.
sunzhenyang2018
@sunzhenyang2018
Dear @wvangeit, it worked perfectly for me on windows without using any VM or linux-like environment! That was quite surprising but a welcomed one.
Werner Van Geit
@wvangeit
@sunzhenyang2018 , ok, good to hear that it worked for you
FrancescoCavarretta
@FrancescoCavarretta
if I try to run BluePyOpt in parallel using ipyparallel,
do I need to pass a map_function to DEAPOptimisation?
What kind of map function I may use?
Werner Van Geit
@wvangeit
@FrancescoCavarretta I've answer your question in https://github.com/BlueBrain/BluePyOpt/issues/319#issuecomment-675307276
FrancescoCavarretta
@FrancescoCavarretta
@wvangeit just seen today. thank you so much.
sunzhenyang2018
@sunzhenyang2018
Hi, I also have a question about parallelization, but mine is about setting it up on Neuroscience Gateway (NSG). I have a optimization that has 200 generations and 100 offspring, with python's built in map function. How many processes are present in each generation, and how many cores should I assign to this optimization job?
3 replies
Aman Aberra
@Aman-A
Hi, I've had a couple optimization runs fail due to out of memory error while saving the checkpoint file on our cluster, which causes the checkpoint file to be empty and all progress to be lost. I can just restart with more memory from the beginning in this case, but for longer runs, this would be pretty unpleasant. Have you thought about implementing a version of checkpointing where each generation is a different file, or they're batched together in some way, so that the new checkpoint file isn't overwriting the old file. This way any error or interruption wouldn't lose the data from past generations
Werner Van Geit
@wvangeit
@Aman-A I'm not sure we ever encountered this issue, but it's a valid point. I'm rather reluctant to save all the checkpoints to save disk space. But one thing we could do is save the checkpoint first to a temporary filename and then overwrite the main checkpoint file with a copy operation (which should be failry atomic). We can also keep the temporary file as an extra backup. What do you think?
Aman Aberra
@Aman-A
@wvangeit Ya, I was gonna say the previous generation files could be deleted at some point, but this sounds like a better solution to the main problem. So with each generation, you would over-write the temporary file then copy the temporary file over the cp_filename?
Werner Van Geit
@wvangeit
Yep, that's the idea
I created this: BlueBrain/BluePyOpt#323
Aman Aberra
@Aman-A
Hi, I was wondering if there's a way to work with custom sectionlists using the Morphology class. So if I write an swc file and use 5+ for e.g. myelin, how could I specify this when instantiating a Morphology and CellModel? Or would I need to use the HocModel class?
Werner Van Geit
@wvangeit
I'm not 100% sure, but I don't think Neuron will create sectionlists other than the default ones
If you know which sections have the specific type, you could however read the morphology using the normal class, and assign the relevant sections to sectionlists you create
Aman Aberra
@Aman-A
Ok I think a better approach may be to load the somatodendritic morphology in the swc, then generate custom axons with neuron code using the replace_axon_hoc option. Is there any reason not to make seclist_names and secarray_names customizable in the CellModel class?
Werner Van Geit
@wvangeit
There is no specific api to changes seclist_names/secarray_names. But after constructing the object, they are just attributes of the object. So normally you can customize them that way.
9 replies
William Scott Thompson
@wstho
Hi! Wondering if anyone has come across this error before: " File "/cfs/klemming/nobackup/w/wst23/local/tegner/lib/python3.6/site-packages/bluepyopt/ephys/parameterscalers.py", line 81, in scale
return self.multiplier * value + self.offset
TypeError: can't multiply sequence by non-int of type 'float' ". Have had bluepyopt running fine on this machine in the past, not sure what would have caused this. Cheers!
Werner Van Geit
@wvangeit
It looks like one of the values in 'self.multiplier * value' is a sequence (probably a string). Possibly somewhere you feed a string instead of a float into the arguments of the methods.
Russell Jarvis
@russelljjarvis
Hi Werner I finally made a Pull Request on Github concerning the integration of BluePyOpt with NeuronUnit. I am having trouble getting the tox continuous integration tests to pass, I think thats because my version of setup.py has requirements that are git repositories. If possible I am hoping to get feedback about the Pull Request. Best, Russell.
Russell Jarvis
@russelljjarvis
Also I wonder if there is any apetite for a streamlit interactive frontend for BluePyOpt? I have done something like this for my examples, but I didn't include it in the Pull Request. The approach can be integrated with standard blue py opt examples.
sunzhenyang2018
@sunzhenyang2018
Hi, I am confused about how to how to set up point process. The few things that confused my are like suffix and location. As far as I know, mod files for point process doesn't explicitly declare a suffix. The other thing is location, specifically NrnPointProcessLocation. The constructor expect the second argument to be a string, but then in instantiate, the line self.pprocess_mech.pprocesses is run which doesn't work if pprocess_mech is a str. If it is not a str, then do I need create the point process before the location, and pass the point process to it? If so, what location value should I pass to the point process's constructor?
It would be really helpful if you could provide me with an example of setting up a default point process from NEURON
Werner Van Geit
@wvangeit
hi
here there is an example of setting up a point process: https://github.com/BlueBrain/BluePyOpt/tree/master/examples/expsyn
you're right, the naming is confusing. Suffix is similar to a channel, but indeed, in a point process it's not explicitely called Suffix