{"action":"created","issue":{"url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/8","labels_url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/8/comments","events_url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/8/events","html_url":"https://github.com/GaloisInc/ppaml-cp6/issues/8","id":114728967,"number":8,"title":"Index out of bounds running `run.sh`","user":{"login":"mhuesch","id":1151946,"avatar_url":"https://avatars.githubusercontent.com/u/1151946?v=3","gravatar_id":"","url":"https://api.github.com/users/mhuesch","html_url":"https://github.com/mhuesch","followers_url":"https://api.github.com/users/mhuesch/followers","following_url":"https://api.github.com/users/mhuesch/following{/other_user}","gists_url":"https://api.github.com/users/mhuesch/gists{/gist_id}","starred_url":"https://api.github.com/users/mhuesch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhuesch/subscriptions","organizations_url":"https://api.github.com/users/mhuesch/orgs","repos_url":"https://api.github.com/users/mhuesch/repos","events_url":"https://api.github.com/users/mhuesch/events{/privacy}","received_events_url":"https://api.github.com/users/mhuesch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":12,"created_at":"2015-11-03T02:26:44Z","updated_at":"2015-11-05T01:33:37Z","closed_at":null,"body":"Hi,\r\n\r\nI have been poking around trying to get `run.sh` working and encountered the following error:\r\n\r\n```\r\nAttempted to access model.pairs(:,1); index out of bounds because size(model.pairs)=[0,0].\r\n\r\nError in find_node2pair_arrays_ver2 (line 12)\r\nfor(c=1:length(model.pairs(:,1)))\r\n\r\nError in database_model (line 58)\r\n[model.N1, model.N2] = find_node2pair_arrays_ver2(model);%!!! Not sure what this is used for\r\n\r\nError in extract_marbl_model_data_files (line 56)\r\nmodel = database_model(1,length(data_locs),nvals, cliq_mat);%This is the format for the JGMT crf model, but this toolbox only handles pairwise cliques\r\n\r\nError in wrapper_crf_database_labeling_v2 (line 206)\r\n                extract_marbl_model_data_files(cliq_flags, ex_train_locs, TopN, img_info_list, ...\r\n\r\nError in run (line 63)\r\nevalin('caller', [script ';']);\r\n \r\n12  for(c=1:length(model.pairs(:,1)))\r\n```\r\n\r\nI followed the README instructions (I think), downloading the archive `CP5-ImageLabeling > evaluation > sandboxes > round-1-public-sandbox.tgz` from MIDAS. I downloaded marbl and swapped out the learn_CRF.cpp file. I modified `marbl_path` in crf_config_file.m to point to the marbl_master directory which contains the build artifacts. Is there something I'm missing?\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/comments/153925466","html_url":"https://github.com/GaloisInc/ppaml-cp6/issues/8#issuecomment-153925466","issue_url":"https://api.github.com/repos/GaloisInc/ppaml-cp6/issues/8","id":153925466,"user":{"login":"mhuesch","id":1151946,"avatar_url":"https://avatars.githubusercontent.com/u/1151946?v=3","gravatar_id":"","url":"https://api.github.com/users/mhuesch","html_url":"https://github.com/mhuesch","followers_url":"https://api.github.com/users/mhuesch/followers","following_url":"https://api.github.com/users/mhuesch/following{/other_user}","gists_url":"https://api.github.com/users/mhuesch/gists{/gist_id}","starred_url":"https://api.github.com/users/mhuesch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhuesch/subscriptions","organizations_url":"https://api.github.com/users/mhuesch/orgs","repos_url":"https://api.github.com/users/mhuesch/repos","events_url":"https://api.github.com/users/mhuesch/events{/privacy}","received_events_url":"https://api.github.com/users/mhuesch/received_events","type":"User","site_admin":false},"created_at":"2015-11-05T01:33:37Z","updated_at":"2015-11-05T01:33:37Z","body":"Cool, I have tried that and it works.\r\n\r\nMy long run in the \"round-1-public\" sandbox just errored out with this:\r\n```\r\n../marbl-master/learn_CRF: /home/peval/packages/MATLAB/R2014a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by ../marbl-master/learn_CRF)\r\n../marbl-master/infer_CRF: /home/peval/packages/MATLAB/R2014a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by ../marbl-master/infer_CRF)\r\nIndex exceeds matrix dimensions.\r\n\r\nError in wrapper_crf_database_labeling_v2 (line 262)\r\n            cell_node_marginals= cellfun(@str2num,marginal_file(1:test_model.nnodes),'uniformoutput',false);\r\n\r\nError in run (line 63)\r\nevalin('caller', [script ';']);\r\n \r\n262             cell_node_marginals= cellfun(@str2num,marginal_file(1:test_model.nnodes),'uniformoutput',false);\r\n```\r\n\r\nI've saved the debug output and can send it to Eran. I assume you guys are able to run to completion on your end by following the README instructions?"}}