{"action":"created","issue":{"url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5","labels_url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5/comments","events_url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5/events","html_url":"https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5","id":116198432,"number":5,"title":"Create smaller scale version of network that can run on single processor","user":{"login":"pgleeson","id":1556687,"avatar_url":"https://avatars.githubusercontent.com/u/1556687?v=3","gravatar_id":"","url":"https://api.github.com/users/pgleeson","html_url":"https://github.com/pgleeson","followers_url":"https://api.github.com/users/pgleeson/followers","following_url":"https://api.github.com/users/pgleeson/following{/other_user}","gists_url":"https://api.github.com/users/pgleeson/gists{/gist_id}","starred_url":"https://api.github.com/users/pgleeson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgleeson/subscriptions","organizations_url":"https://api.github.com/users/pgleeson/orgs","repos_url":"https://api.github.com/users/pgleeson/repos","events_url":"https://api.github.com/users/pgleeson/events{/privacy}","received_events_url":"https://api.github.com/users/pgleeson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-10T20:48:26Z","updated_at":"2015-12-20T18:35:42Z","closed_at":null,"body":"Reuse existing scripts to create a smaller scale version of the network (e.g. with a single glomerulus and reduced numbers of granule cells) that can be run (~100ms) on a single processor.\r\n\r\nWill greatly facilitate testing & export of network structure to NML2 (#6)"},"comment":{"url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/comments/166146119","html_url":"https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5#issuecomment-166146119","issue_url":"https://api.github.com/repos/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/5","id":166146119,"user":{"login":"JustasB","id":10732358,"avatar_url":"https://avatars.githubusercontent.com/u/10732358?v=3","gravatar_id":"","url":"https://api.github.com/users/JustasB","html_url":"https://github.com/JustasB","followers_url":"https://api.github.com/users/JustasB/followers","following_url":"https://api.github.com/users/JustasB/following{/other_user}","gists_url":"https://api.github.com/users/JustasB/gists{/gist_id}","starred_url":"https://api.github.com/users/JustasB/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JustasB/subscriptions","organizations_url":"https://api.github.com/users/JustasB/orgs","repos_url":"https://api.github.com/users/JustasB/repos","events_url":"https://api.github.com/users/JustasB/events{/privacy}","received_events_url":"https://api.github.com/users/JustasB/received_events","type":"User","site_admin":false},"created_at":"2015-12-20T18:35:42Z","updated_at":"2015-12-20T18:35:42Z","body":"@pgleeson I'm reading your earlier email to Migliore, and I've found the reason why you were getting errors when you changed the Ngloms, grid_dim parameters. It's because the files that are supplied with the model, mitral.dump and c10.dic, store mitral cell and connection data that was generated for the full 127 glom network. In other words, the two files are tightly coupled with the glom/mitral/cell count params. \r\n\r\nIf one of those params is changed, then the code reads the files incorrectly, and then eventually errors out. (The suggestion to change \"common.nmitral=5\" has the same problem.)\r\n\r\nI've been able to solve the problem mitral.dump problem by making the code that reads the file to ignore any missing mitral cells, and then keeping the reduced number of mitrals we want.\r\n\r\nBut the connection file c10.dic is more challenging. The issue is that it stores the connection data for the full-network again, and the code that reads the file assumes the granule/mitral cells for the full network exist and tries to reference non-existing cells. There is also code that does something to the gids, that I'm still trying to understand what it does, that makes it not as simple as checking if the cell gid exists.\r\n\r\nOverall, it appears that, in order to allow the model reduction based on a parameter will involve reading the full network files and then adjusting the code to handle the missing cells/connections.\r\n\r\nAny tips on alternatives?"}}