{"action":"created","issue":{"url":"https://api.github.com/repos/cmu-phil/tetrad/issues/122","labels_url":"https://api.github.com/repos/cmu-phil/tetrad/issues/122/labels{/name}","comments_url":"https://api.github.com/repos/cmu-phil/tetrad/issues/122/comments","events_url":"https://api.github.com/repos/cmu-phil/tetrad/issues/122/events","html_url":"https://github.com/cmu-phil/tetrad/issues/122","id":123984563,"number":122,"title":"TETRAD cmd search doesn't work for dataset with more than 100 nodes","user":{"login":"biotech25","id":15758093,"avatar_url":"https://avatars.githubusercontent.com/u/15758093?v=3","gravatar_id":"","url":"https://api.github.com/users/biotech25","html_url":"https://github.com/biotech25","followers_url":"https://api.github.com/users/biotech25/followers","following_url":"https://api.github.com/users/biotech25/following{/other_user}","gists_url":"https://api.github.com/users/biotech25/gists{/gist_id}","starred_url":"https://api.github.com/users/biotech25/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biotech25/subscriptions","organizations_url":"https://api.github.com/users/biotech25/orgs","repos_url":"https://api.github.com/users/biotech25/repos","events_url":"https://api.github.com/users/biotech25/events{/privacy}","received_events_url":"https://api.github.com/users/biotech25/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-12-27T16:04:25Z","updated_at":"2015-12-28T04:25:44Z","closed_at":null,"body":"Hi Dr. Ramsey, \r\n\r\nI have a question about running command line TETRAD PC Search algorithm. I am running it on a dataset that has several hundreds nodes, but it doesn't work. I found that command line TETRAD doesn't work if the dataset has more than 100 nodes (predictors and target), which means that it works for a dataset with only up to 100 nodes.   The number of cases doesn't matter; it works well for a dataset with > 1000 cases, once the number of nodes is less than 100. However, it seems that it doesn't work if the number of nodes exceeds 100. Innumerable error messages were made and it flew over the windows command.  I got a screenshot of error messages and attached here. Command line TETRAD has a limitation to be run on a dataset with less than 100 nodes or something?\r\n\r\nSanghoon \r\n\r\n![errormessage_morethan100nodes](https://cloud.githubusercontent.com/assets/15758093/12010940/2434a472-ac89-11e5-8b6b-108deaf864f3.png)\r\n"},"comment":{"url":"https://api.github.com/repos/cmu-phil/tetrad/issues/comments/167480525","html_url":"https://github.com/cmu-phil/tetrad/issues/122#issuecomment-167480525","issue_url":"https://api.github.com/repos/cmu-phil/tetrad/issues/122","id":167480525,"user":{"login":"biotech25","id":15758093,"avatar_url":"https://avatars.githubusercontent.com/u/15758093?v=3","gravatar_id":"","url":"https://api.github.com/users/biotech25","html_url":"https://github.com/biotech25","followers_url":"https://api.github.com/users/biotech25/followers","following_url":"https://api.github.com/users/biotech25/following{/other_user}","gists_url":"https://api.github.com/users/biotech25/gists{/gist_id}","starred_url":"https://api.github.com/users/biotech25/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biotech25/subscriptions","organizations_url":"https://api.github.com/users/biotech25/orgs","repos_url":"https://api.github.com/users/biotech25/repos","events_url":"https://api.github.com/users/biotech25/events{/privacy}","received_events_url":"https://api.github.com/users/biotech25/received_events","type":"User","site_admin":false},"created_at":"2015-12-28T04:25:44Z","updated_at":"2015-12-28T04:25:44Z","body":"Thank you for your advice.  I followed your advice and tested many things. First, I tested the heap size extension (-cp -Xmx4g) on the dataset with 79 nodes, and confirmed it was working.  Then, I applied the heap size extension on the dataset with 502 nodes.  \r\n\r\njava -cp -Xmx4096m -jar lib-tetrad-5.3.0-20151113.150857-1-tetradcmd.jar -data tgen_imputed_apoe_ChiSqaure_501SNPs_p0.001.txt -datatype discrete -algorithm pc -depth -1 -significance 0.01\r\n\r\nWhen I set the heap size extension and ran command line TETRAD on the dataset with 502 nodes, I still got the same error massages flowing over fast, but I just waited until it ends.  Even though I got error messages, surprisingly I got TETRAD output. The output correctly detected direct causes as I expected. \r\n\r\nTherefore, this time I didn't set the heap size extention, ran TETRAD search, and just waited until it ends. Yes, I got the output files, but the output content (direct causes and the number of edge pairs) was different from the first output.  It is strange.\r\n\r\nI set the heap size extension and ran TETRAD search several times. Strangely, I got different output contents whenever I ran TETRAD with the same condition. I tested this in the Linux workstation, but I got the same problem.  I don't think the heap map extension is working at list in my computer as I still get the same error messages and different output contents in each TETRAD run.  \r\n\r\nI am going to test more tomorrow and let you know if I find something. "}}