@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 The MOD file is currently unpublished (and very much a work in progress) and thus not currently available online.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!
but the method I'm using for modeling the stimulus is entirely different. I can send it to you via email. Thanks again!
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
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
https://kg.ebrains.eu/search/instances/Model/a6458de3-a176-4378-9b03-34a26f5da3bd
9 replies
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.
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.
@FrancescoCavarretta I've answer your question in https://github.com/BlueBrain/BluePyOpt/issues/319#issuecomment-675307276
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
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
@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?
I created this: BlueBrain/BluePyOpt#323
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
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!
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!
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.
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
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
I basically meant the name of the point process: https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/mechanisms/ProbAMPANMDA_EMS.mod#L69
I think the notebook in the example I showed could help you with your question of the location
let me know if you have more questions
just pinging @sunzhenyang2018 to make sure you see the reply
Hi, I have a question about CVODE compatibility in mod files. Currently I am trying to run this stochastic synapse model (https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=8115&file=/fluct/Gfluct.mod#tabs-2) with ephys. But when I try to run, it says "NEURON: Gfluct2 cannot be used with CVODE ".
But I could run this mod on NEURON on its own
A search through the NEURON forum tells me that this is because this mod file is not CVODE compatible and instead NEURON runs it using DASPK. Can ephys also do this?
Normally yes, if the only problem is Cvode, then you can disable it in the NrnSimulator class: https://github.com/BlueBrain/BluePyOpt/blob/master/bluepyopt/ephys/simulators.py#L19
Hello, I am very new to BluePyOpt and to coding in general (though I have some experience with Python). I need to get started using BluePyOpt. My question (hopefully not a stupid one) is: Upon downloading the source code, how do I install BluePyOpt? I already have the requisite Neuron with Python support on my Windows laptop.