Search found 84 matches

by salvadord
Fri Nov 17, 2017 6:08 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 15984

Re: C++ memory? error, using NetPyNE

thanks. Now I'm getting a bunch of these messages: "Id not found in <neuroml> element. All ids: ['CavL', 'CavN', ... ]" and then error: "ValueError: argument not a density mechanism name." I tried nrnivmodl on the mod files in root folder and then symlinking x86_64 folder in /NeuroML2/network but th...
by salvadord
Thu Nov 16, 2017 9:31 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 15984

Re: C++ memory? error, using NetPyNE

Getting this error: IOError: ``HippocampalNet_scale500_oc.net.nml.h5`` does not exist

maybe need to add that file to the repo?

thanks
by salvadord
Tue Nov 14, 2017 6:26 pm
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 15984

Re: C++ memory? error, using NetPyNE

Hmm the spike times don't really use up that much space so can probably them from all cells. Cell traces however do require more memory, so the 40 traces might be causing the problem. Can you point me again to the repo with code you are running and I'll try myself to see if can find any issues? than...
by salvadord
Wed Oct 25, 2017 11:17 am
Forum: NetPyNE
Topic: C++ memory? error, using NetPyNE
Replies: 10
Views: 15984

Re: C++ memory? error, using NetPyNE

Hi András, Thanks for your question. We had a similar post recently: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=45&t=3727&sid=30e51a901a2f8d0a62f85ee9ab8424ad The conclusion from that post was that if the amount of data to be gathered and the number of cores used is above a threshold, the mpi...
by salvadord
Sun Oct 22, 2017 10:13 pm
Forum: NetPyNE
Topic: Setup for multiple runs of the same model
Replies: 3
Views: 9953

Re: Setup for multiple runs of the same model

I added a short tutorial on running batch simulations: http://www.neurosimlab.org/netpyne/tuto ... tutorial-8

Hope it helps... and please let me know if you have any more questions.
by salvadord
Fri Oct 20, 2017 12:56 pm
Forum: NetPyNE
Topic: Setup for multiple runs of the same model
Replies: 3
Views: 9953

Re: Setup for multiple runs of the same model

Hi Sergio, thanks for using the tool and asking this useful question! If you just want to explore parameters manually, you can modify them in simConfig and netParams and then just change 'simLabel' (in simConfig) so the output is saved to different output files. However, NetPyNE has a built-in Batch...
by salvadord
Wed Oct 18, 2017 7:06 pm
Forum: NetPyNE
Topic: Issue running model with 20 cores or more
Replies: 7
Views: 11311

Re: Issue running model with 20 cores or more

FYI, I tested your full model using 24 cores and also got an mpi error during gathering for 276sec and 50sec sims; but it ran ok for 10sec sims. So seems to be related to a memory issue when gathering too much output data (long sims) from many cores. If you definitely need those long simulation time...
by salvadord
Mon Oct 16, 2017 3:56 pm
Forum: NetPyNE
Topic: Issue running model with 20 cores or more
Replies: 7
Views: 11311

Re: Issue running model with 20 cores or more

I'm looking at this issue now, sorry for the delay. Tried running your code but its missing LA_Template.py -- can you please send the missing file (or a full updated version of your model) ? I also noticed that you are trying to run the simulation for 276 seconds, which is a relatively long time -- ...
by salvadord
Thu Oct 05, 2017 6:20 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 19
Views: 12994

Re: VERSION RELEASES

# Version 0.7.4 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.4 - Added polarity param to analysis.plotEPSPAmp() - Added sim.gitChangeset() function and store netpyne_changeset in every output file - Added function ijsonLoad() to load faster and save tags conns to json - Fixed bug in con...
by salvadord
Fri Sep 01, 2017 1:12 pm
Forum: NetPyNE
Topic: Examples how to use the plotShape function
Replies: 7
Views: 12911

Re: Examples how to use the plotShape function

Ah ok! Problem is you are calling the plotShape() function before even creating the network. It should go after sim.createSimulateAnalyze() Note netpyne is a declarative language so nothing gets executed/created until you call sim.createSimulateAnalyze(). Alternatively, you can include plotShape in ...
by salvadord
Fri Sep 01, 2017 11:02 am
Forum: NetPyNE
Topic: Examples how to use the plotShape function
Replies: 7
Views: 12911

Re: Examples how to use the plotShape function

So I assume you followed all the steps in prev post? Can you please run python and include here the output of import netpyne; print netpyne.__file__ ? Then go to whatever folder shows up and include here the output of git branch and git log -1 ? We need to make sure the development version of netpyn...
by salvadord
Thu Aug 31, 2017 2:38 pm
Forum: NetPyNE
Topic: Examples how to use the plotShape function
Replies: 7
Views: 12911

Re: Examples how to use the plotShape function

1) Remove any current version via pip uninstall netpyne 2) cd parent_folder_where_you_want_netpyne_repo 3) git clone https://github.com/Neurosim-lab/netpyne.git 4) cd netpyne 5) git checkout developmnet 6) pip install -e . pip will add a symlink in the default python packages folder to the cloned ne...
by salvadord
Wed Aug 30, 2017 9:18 pm
Forum: NetPyNE
Topic: Examples how to use the plotShape function
Replies: 7
Views: 12911

Re: Examples how to use the plotShape function

Hi Vittorio, I've updated the plotShape documentation and added some examples: http://www.neurosimlab.org/netpyne/reference.html#analysis-related-functions At the moment its not possible to create a movie via netpyne (will add to github list of requests), but you can of course generate multiple snap...
by salvadord
Wed Aug 30, 2017 8:18 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 19
Views: 12994

Re: VERSION RELEASES

Version 0.7.3 https://github.com/Neurosim-lab/netpyne/releases/tag/v0.7.3 - Option to create section lists based on y displacement from soma (addCellParamsSecList) - Converted popParams, cellParams etc to object of their own class and added method to set param - Added 'disynapticBias' option to incr...
by salvadord
Tue Aug 15, 2017 11:18 pm
Forum: NetPyNE
Topic: Issue running model with 20 cores or more
Replies: 7
Views: 11311

Re: Issue running model with 20 cores or more

Yes, please share your code; also any info on the machine/software you are running this on would be useful -- e.g. OS, number of cores, NEURON version, netpyne version, etc. We have tested netpyne simulations on up to 512 cores on supercomputers, but I will check running your code on 20+ cores and l...