{"action":"created","issue":{"url":"https://api.github.com/repos/jsherfey/dnsim/issues/66","labels_url":"https://api.github.com/repos/jsherfey/dnsim/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/jsherfey/dnsim/issues/66/comments","events_url":"https://api.github.com/repos/jsherfey/dnsim/issues/66/events","html_url":"https://github.com/jsherfey/dnsim/issues/66","id":111039449,"number":66,"title":"Current 'dev' simstudy using coder + cluster = broken?","user":{"login":"asoplata","id":661173,"avatar_url":"https://avatars.githubusercontent.com/u/661173?v=3","gravatar_id":"","url":"https://api.github.com/users/asoplata","html_url":"https://github.com/asoplata","followers_url":"https://api.github.com/users/asoplata/followers","following_url":"https://api.github.com/users/asoplata/following{/other_user}","gists_url":"https://api.github.com/users/asoplata/gists{/gist_id}","starred_url":"https://api.github.com/users/asoplata/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/asoplata/subscriptions","organizations_url":"https://api.github.com/users/asoplata/orgs","repos_url":"https://api.github.com/users/asoplata/repos","events_url":"https://api.github.com/users/asoplata/events{/privacy}","received_events_url":"https://api.github.com/users/asoplata/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-10-12T19:30:38Z","updated_at":"2015-10-12T20:30:30Z","closed_at":null,"body":"So, in trying map out the control flow of the program, I was trying to look at this scenario: when you want to use the coder, in a batch job on the cluster. However, it kept completely crashing (as in, MATLAB itself was crashing), and when I was debugging it it was giving me a\r\n\r\n\"cp cannot stat `/$PATHTODNSIM/dnsim/$PATHTODNSIM/dnsim/odefun/default_8/odefun_20151009_<whatever>_mex.mexa64`: no such file\"\r\n\r\nerror. I did some digging, and now I'm really confused, because I'm not sure how the code currently in `simstudy` can properly run in this situation (more in a sec). I also think it's possible that the system/stdout error it was getting was enough (because it was a system error) to tell MATLAB to just halt entirely, but idk much about the interface between MATLAB and the OS.\r\n\r\n@jsherfey @kupiqu **Do either of you run simulations, successfully, using the current `dev` version of the code, with the coder activated, on the cluster?**\r\n\r\n(All of this applies to both the mex-file and the m-file treatment in `simstudy.m`) Currently, on the try block that starts on Line 63 of simstudy https://github.com/jsherfey/dnsim/blob/dev/matlab/functions/simstudy.m#L63 , \"filemex\" contains the full path up to and including odefun_subdir plus the actual mexfile filename. On line 230, the system tries to copy \"fullfile(cwd,filemex)\" to somewhere (cwd is made the pwd on Line 180), but this ends up concatenating the current working directory directly to the string of the entire filepath of the mexfile, creating the false mega-filepath mentioned in the error above. Maybe this was affected by July changes (there were a lot) to \"dnsimulator.m\", but that would mean there would have been big changes to what \"odefun_subdir\" represented, which I think is unlikely (but possible).\r\n\r\nMaybe this scenario can still work, given that your code, and your rootdir, are both in the right place, but I don't know what that combination is - it's certainly not mine and I've tried using dnsim code directly from my personal account, with both a pwd rootdir and a /projectnb rootdir. But going through the filemex code, I just can't see how it would ever work. **Is this the version of using the coder on the cluster that you use? Does it work for anyone? I think Salva doesn't use simstudy, but don't you use it Jason? If not, it's possible that using the coder on the cluster is broken this way...**\r\n\r\n**If not, can either of you test this scenario, using the `dev` version of the code?**"},"comment":{"url":"https://api.github.com/repos/jsherfey/dnsim/issues/comments/147511708","html_url":"https://github.com/jsherfey/dnsim/issues/66#issuecomment-147511708","issue_url":"https://api.github.com/repos/jsherfey/dnsim/issues/66","id":147511708,"user":{"login":"asoplata","id":661173,"avatar_url":"https://avatars.githubusercontent.com/u/661173?v=3","gravatar_id":"","url":"https://api.github.com/users/asoplata","html_url":"https://github.com/asoplata","followers_url":"https://api.github.com/users/asoplata/followers","following_url":"https://api.github.com/users/asoplata/following{/other_user}","gists_url":"https://api.github.com/users/asoplata/gists{/gist_id}","starred_url":"https://api.github.com/users/asoplata/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/asoplata/subscriptions","organizations_url":"https://api.github.com/users/asoplata/orgs","repos_url":"https://api.github.com/users/asoplata/repos","events_url":"https://api.github.com/users/asoplata/events{/privacy}","received_events_url":"https://api.github.com/users/asoplata/received_events","type":"User","site_admin":false},"created_at":"2015-10-12T20:30:29Z","updated_at":"2015-10-12T20:30:29Z","body":"I actually don't know what I would need to change to get a `runsim` simulation, using coder, that dispatches the job to the cluster automatically -- if I just pass all the same arguments to `runsim`, will `runsim` alone properly configure the coder and properly send the job to a cluster batch?"}}