{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/seqan/issues/919","labels_url":"https://api.github.com/repos/seqan/seqan/issues/919/labels{/name}","comments_url":"https://api.github.com/repos/seqan/seqan/issues/919/comments","events_url":"https://api.github.com/repos/seqan/seqan/issues/919/events","html_url":"https://github.com/seqan/seqan/issues/919","id":64670828,"number":919,"title":"cant join StringSet<DnaString> to another StringSet<DnaString> using AppendValue()","user":{"login":"fari-99","id":8443932,"avatar_url":"https://avatars.githubusercontent.com/u/8443932?v=3","gravatar_id":"","url":"https://api.github.com/users/fari-99","html_url":"https://github.com/fari-99","followers_url":"https://api.github.com/users/fari-99/followers","following_url":"https://api.github.com/users/fari-99/following{/other_user}","gists_url":"https://api.github.com/users/fari-99/gists{/gist_id}","starred_url":"https://api.github.com/users/fari-99/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fari-99/subscriptions","organizations_url":"https://api.github.com/users/fari-99/orgs","repos_url":"https://api.github.com/users/fari-99/repos","events_url":"https://api.github.com/users/fari-99/events{/privacy}","received_events_url":"https://api.github.com/users/fari-99/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"h-2","id":2996863,"avatar_url":"https://avatars.githubusercontent.com/u/2996863?v=3","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2015-03-27T01:27:11Z","updated_at":"2015-03-31T03:26:56Z","closed_at":null,"body":"is it appendValue thread safe? \r\n\r\ni'm using OpenMP parallel for sequencing. but i kinda stuck in appendValue for stored my sequence. it's always say \"segmentation fault\". So i tried to parting my variable for storing into 4 part (ex: spectrumLocal[thread] with thread = 4). but i can't join them using appendValue() (ex: appendValue(spectrumGlobal, spectrumLocal[id]). \r\n\r\ncan someone give solution or alternative code? \r\n\r\nthanks.\r\nbest regards.\r\n\r\nfadhlan.\r\n\r\nnote: \r\ni already using appendValue(spectrumGlobal, value), but its critical, so the performance slow down, if not critical then the program will crash because segmentation fault. \r\n\r\ni already use ConcurrentQueue for using it, it's very good, but i cant store the value, btw the value is string not a number (ex: \"ACGT\"). "},"comment":{"url":"https://api.github.com/repos/seqan/seqan/issues/comments/87921209","html_url":"https://github.com/seqan/seqan/issues/919#issuecomment-87921209","issue_url":"https://api.github.com/repos/seqan/seqan/issues/919","id":87921209,"user":{"login":"fari-99","id":8443932,"avatar_url":"https://avatars.githubusercontent.com/u/8443932?v=3","gravatar_id":"","url":"https://api.github.com/users/fari-99","html_url":"https://github.com/fari-99","followers_url":"https://api.github.com/users/fari-99/followers","following_url":"https://api.github.com/users/fari-99/following{/other_user}","gists_url":"https://api.github.com/users/fari-99/gists{/gist_id}","starred_url":"https://api.github.com/users/fari-99/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fari-99/subscriptions","organizations_url":"https://api.github.com/users/fari-99/orgs","repos_url":"https://api.github.com/users/fari-99/repos","events_url":"https://api.github.com/users/fari-99/events{/privacy}","received_events_url":"https://api.github.com/users/fari-99/received_events","type":"User","site_admin":false},"created_at":"2015-03-31T03:26:56Z","updated_at":"2015-03-31T03:26:56Z","body":"i'm sorry maybe i'm making you confusing with my explanation earlier.\n\nso my program looks like this (not exactly like this but i made it simpler\nthough).\n\nint main()\n{\n    StringSet<DnaString> pool;\n    StringSet<DnaString> sekuens;\n\n    //no parallel\n    for(int i = 0; i < 12; i++)\n    {\n        appendValue(pool, \"ACGT\");\n        appendValue(sekuens, \"ACGT\");\n    }\n\n    //parallel critical\n    #pragma omp parallel\n    {\n        #pragma omp for\n        for(int i = 0; i < 12; i++)\n        {\n            #pragma omp critical\n            {\n                appendValue(pool, \"ACGT\");\n                appendValue(sekuens, \"ACGT\");\n            }\n        }\n    }\n\n    //parallel without critical\n    StringSet<DnaString> poolLocal[4];\n    StringSet<DnaString> sekuensLocal[4];\n    int id;\n    #pragma omp parallel num_threads(4) private(id)\n    {\n        id = omp_get_thread_num();\n        int subTotal, start, finish;\n        subTotal = 3;\n        start = id * subTotal;\n        finish = (id + 1) * subTotal;\n\n        for(int i = start; i < finish; i++)\n        {\n            appendValue(poolLocal[id], \"ACGT\");\n            appendValue(sekuensLocal[id], \"ACGT\");\n        }\n    }\n\n    for(int j = 0; j < 4; j++)\n    {\n        /* join the data\n        appendValue or append? //the problem is here.\n        appendValue(pool3, poolLocal[i]);\n        append(pool3,poolLocal[i]);\n        //*/\n    }\n\n    return 0;\n}\n\n\ni can using critical parallel, but because the overhead waiting thread to\nrelease, the sequential much better. so i tried using with non critical,\nbut i can't join them in the last. i want the result not like a sequence\n(if using append).\n\nthanks\n\nbest regards.\n\n\n\n\n\n2015-03-30 17:54 GMT+07:00 Hannes Hauswedell <notifications@github.com>:\n\n> Hm, that's strange. Can you give me a more complete error log?\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/seqan/seqan/issues/919#issuecomment-87634412>.\n>\n"}}