{"action":"created","issue":{"url":"https://api.github.com/repos/nest/nest-simulator/issues/405","repository_url":"https://api.github.com/repos/nest/nest-simulator","labels_url":"https://api.github.com/repos/nest/nest-simulator/issues/405/labels{/name}","comments_url":"https://api.github.com/repos/nest/nest-simulator/issues/405/comments","events_url":"https://api.github.com/repos/nest/nest-simulator/issues/405/events","html_url":"https://github.com/nest/nest-simulator/issues/405","id":161833983,"number":405,"title":"Create iaf_cond_beta","user":{"login":"dnao","id":7260640,"avatar_url":"https://avatars.githubusercontent.com/u/7260640?v=3","gravatar_id":"","url":"https://api.github.com/users/dnao","html_url":"https://github.com/dnao","followers_url":"https://api.github.com/users/dnao/followers","following_url":"https://api.github.com/users/dnao/following{/other_user}","gists_url":"https://api.github.com/users/dnao/gists{/gist_id}","starred_url":"https://api.github.com/users/dnao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dnao/subscriptions","organizations_url":"https://api.github.com/users/dnao/orgs","repos_url":"https://api.github.com/users/dnao/repos","events_url":"https://api.github.com/users/dnao/events{/privacy}","received_events_url":"https://api.github.com/users/dnao/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-06-23T03:40:43Z","updated_at":"2016-07-01T20:00:50Z","closed_at":null,"body":"I am trying to modify the iaf_cond_alpha module to include two synaptic time constants: the rise and decay time of the post-synaptic conductance, as well as external inputs modeled as a constant conductance term. I have committed these changes in my branch: [iaf_cond_beta.cpp](https://github.com/dnao/nest-simulator/blob/condbeta/examples/betacond/iaf_cond_beta.cpp) and [iaf_cond_beta.h](https://github.com/dnao/nest-simulator/blob/condbeta/examples/betacond/iaf_cond_beta.h)\r\n\r\nAs a first step to testing my code I have attempted to modify the MyModule code to suit this model. The full module is in [betacond](https://github.com/dnao/nest-simulator/tree/condbeta/examples/betacond). I have manged to cmake, make, and install successfully to my nest directory, but I have the following errors when I try to run nest.Install('betacond') from Python:\r\n\r\n```python\r\n---------------------------------------------------------------------------\r\nNESTError                                 Traceback (most recent call last)\r\n<ipython-input-4-d8237baed51c> in <module>()\r\n----> 1 nest.Install('betacond')\r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/lib/hl_api_helper.pyc in stack_checker_func(*args, **kwargs)\r\n    228     def stack_checker_func(*args, **kwargs):\r\n    229         if not get_debug():\r\n--> 230             return f(*args, **kwargs)\r\n    231         else:\r\n    232             sr('count')\r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/lib/hl_api_simulation.pyc in Install(module_name)\r\n    151     \"\"\"\r\n    152 \r\n--> 153     return sr(\"(%s) Install\" % module_name)\r\n    154 \r\n    155 \r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/__init__.pyc in catching_sli_run(cmd)\r\n     89         engine.run('clear')\r\n     90         raise _kernel.NESTError(\"{0} in {1}{2}\".format(\r\n---> 91             errorname, commandname, message))\r\n     92 \r\n     93 sli_run = hl_api.sr = catching_sli_run\r\n\r\nNESTError: DynamicModuleManagementError in Install: Module 'betacond' could not be loaded.\r\nThe dynamic loader returned the following error: ''.\r\n```\r\n\r\nOccasionally I get this error:\r\n```python\r\n---------------------------------------------------------------------------\r\nUnicodeDecodeError                        Traceback (most recent call last)\r\n<ipython-input-18-d8237baed51c> in <module>()\r\n----> 1 nest.Install('betacond')\r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/lib/hl_api_helper.pyc in stack_checker_func(*args, **kwargs)\r\n    228     def stack_checker_func(*args, **kwargs):\r\n    229         if not get_debug():\r\n--> 230             return f(*args, **kwargs)\r\n    231         else:\r\n    232             sr('count')\r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/lib/hl_api_simulation.pyc in Install(module_name)\r\n    151     \"\"\"\r\n    152 \r\n--> 153     return sr(\"(%s) Install\" % module_name)\r\n    154 \r\n    155 \r\n\r\n/suphys/dnao/opt/gitnest/lib64/python2.7/site-packages/nest/__init__.pyc in catching_sli_run(cmd)\r\n     85     if not sli_pop():\r\n     86         errorname = sli_pop()\r\n---> 87         message = sli_pop()\r\n     88         commandname = sli_pop()\r\n     89         engine.run('clear')\r\n\r\npynestkernel.pyx in pynestkernel.NESTEngine.pop (/suphys/dnao/opt/nest-build/pynest/pynestkernel.cxx:4523)()\r\n\r\npynestkernel.pyx in pynestkernel.sli_datum_to_object (/suphys/dnao/opt/nest-build/pynest/pynestkernel.cxx:7881)()\r\n\r\nUnicodeDecodeError: 'ascii' codec can't decode byte 0xf3 in position 93: ordinal not in range(128)\r\n```"},"comment":{"url":"https://api.github.com/repos/nest/nest-simulator/issues/comments/230035504","html_url":"https://github.com/nest/nest-simulator/issues/405#issuecomment-230035504","issue_url":"https://api.github.com/repos/nest/nest-simulator/issues/405","id":230035504,"user":{"login":"DimitriPlotnikov","id":8746319,"avatar_url":"https://avatars.githubusercontent.com/u/8746319?v=3","gravatar_id":"","url":"https://api.github.com/users/DimitriPlotnikov","html_url":"https://github.com/DimitriPlotnikov","followers_url":"https://api.github.com/users/DimitriPlotnikov/followers","following_url":"https://api.github.com/users/DimitriPlotnikov/following{/other_user}","gists_url":"https://api.github.com/users/DimitriPlotnikov/gists{/gist_id}","starred_url":"https://api.github.com/users/DimitriPlotnikov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DimitriPlotnikov/subscriptions","organizations_url":"https://api.github.com/users/DimitriPlotnikov/orgs","repos_url":"https://api.github.com/users/DimitriPlotnikov/repos","events_url":"https://api.github.com/users/DimitriPlotnikov/events{/privacy}","received_events_url":"https://api.github.com/users/DimitriPlotnikov/received_events","type":"User","site_admin":false},"created_at":"2016-07-01T20:00:50Z","updated_at":"2016-07-01T20:00:50Z","body":"@dnao @ingablundell \r\n\r\nI did the initial mapping the iaf_psc_delta  ( cf. https://github.com/nest/nestml/blob/master/models/iaf_psc_delta.nestml ) as I found in your fork ( https://github.com/dnao/nest-simulator/blob/condbeta/examples/betacond/iaf_cond_beta.h ). Attached is an example simulation of a single neuron that receives a spike after 200ms:\r\n![iaf_psc_delta](https://cloud.githubusercontent.com/assets/8746319/16532794/88206eba-3fd4-11e6-872b-1155acb67710.png)\r\n\r\nThere is also a description how to use the tooling which is based on docker. Currently, there is a known issue that spikeevents are handled in the conductance based case not correctly ( i.e. in the negative case the weight must be multiplied by -1 )\r\n  ```\r\nvoid iaf_cond_beta_neuron::handle(nest::SpikeEvent &e) {\r\n...\r\nif (weight < 0.0) // inhibitory\r\n  {\r\n    get_spikeInh().add_value(\r\n        e.get_rel_delivery_steps(\r\n            nest::kernel().simulation_manager.get_slice_origin()),\r\n        weight * multiplicity);\r\n  }\r\n}\r\n```\r\nIf you find further problems/issues/improvements just add them the the NESTML issue tracker:\r\nhttps://github.com/nest/nestml/issues\r\n\r\nAnd finally in case you are really use NESTML, it would be kind of you to fill out the following survey:\r\nhttps://www.surveymonkey.co.uk/r/N7LCP3Q "}}
{"actor":{"display_login":"DimitriPlotnikov"}}