{"action":"created","issue":{"url":"https://api.github.com/repos/dmtcp/dmtcp/issues/710","repository_url":"https://api.github.com/repos/dmtcp/dmtcp","labels_url":"https://api.github.com/repos/dmtcp/dmtcp/issues/710/labels{/name}","comments_url":"https://api.github.com/repos/dmtcp/dmtcp/issues/710/comments","events_url":"https://api.github.com/repos/dmtcp/dmtcp/issues/710/events","html_url":"https://github.com/dmtcp/dmtcp/issues/710","id":363750983,"node_id":"MDU6SXNzdWUzNjM3NTA5ODM=","number":710,"title":"spades program hangs when run with dmtcp_launch","user":{"login":"aclum","id":8196591,"node_id":"MDQ6VXNlcjgxOTY1OTE=","avatar_url":"https://avatars3.githubusercontent.com/u/8196591?v=4","gravatar_id":"","url":"https://api.github.com/users/aclum","html_url":"https://github.com/aclum","followers_url":"https://api.github.com/users/aclum/followers","following_url":"https://api.github.com/users/aclum/following{/other_user}","gists_url":"https://api.github.com/users/aclum/gists{/gist_id}","starred_url":"https://api.github.com/users/aclum/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aclum/subscriptions","organizations_url":"https://api.github.com/users/aclum/orgs","repos_url":"https://api.github.com/users/aclum/repos","events_url":"https://api.github.com/users/aclum/events{/privacy}","received_events_url":"https://api.github.com/users/aclum/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-09-25T20:23:07Z","updated_at":"2018-11-19T23:11:10Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\nI'm trying to run a bioinformatics program, spades and it hangs when I try to run it with dmctp_launch\r\n\r\nspades can be downloaded as a binary or as conda package using the bioconda channel\r\nconda install spades\r\nThe following hangs\r\ndmtcp_launch spades.py --test\r\n\r\nTo try and isolate the problem i ran single threaded with strace.\r\nBased on that it is hanging on a read until I manually kill the process.\r\n\r\ntail -20 strace1.thread.err\r\nfcntl(4085, F_SETLKW, {type=F_WRLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nfcntl(4085, F_SETLK, {type=F_UNLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nclose(10)                               = 0\r\ngetppid()                               = 36777\r\nfcntl(4085, F_SETLKW, {type=F_WRLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nfcntl(4085, F_SETLK, {type=F_UNLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nfcntl(4085, F_SETLKW, {type=F_WRLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nfcntl(4085, F_SETLK, {type=F_UNLCK, whence=SEEK_SET, start=0, len=0}) = 0\r\nclose(9)                                = 0\r\nmmap(NULL, 1052672, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2aaab16ef000\r\nread(8, \"\", 1048576)                    = 0\r\nmremap(0x2aaab16ef000, 1052672, 4096, MREMAP_MAYMOVE) = 0x2aaab16ef000\r\nmunmap(0x2aaab16ef000, 4096)            = 0\r\nclose(7)                                = 0\r\nclose(8)                                = 0\r\nfstat(5, {st_mode=S_IFSOCK|0777, st_size=0, ...}) = 0\r\nfcntl(5, F_GETFL)                       = 0x2 (flags O_RDWR)\r\nwait4(36800, 0x7fffffff5240, WNOHANG, NULL) = 0\r\nread(5, Process 36779 detached\r\n <detached ...>\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/dmtcp/dmtcp/issues/comments/440075884","html_url":"https://github.com/dmtcp/dmtcp/issues/710#issuecomment-440075884","issue_url":"https://api.github.com/repos/dmtcp/dmtcp/issues/710","id":440075884,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MDA3NTg4NA==","user":{"login":"rohgarg","id":1672104,"node_id":"MDQ6VXNlcjE2NzIxMDQ=","avatar_url":"https://avatars0.githubusercontent.com/u/1672104?v=4","gravatar_id":"","url":"https://api.github.com/users/rohgarg","html_url":"https://github.com/rohgarg","followers_url":"https://api.github.com/users/rohgarg/followers","following_url":"https://api.github.com/users/rohgarg/following{/other_user}","gists_url":"https://api.github.com/users/rohgarg/gists{/gist_id}","starred_url":"https://api.github.com/users/rohgarg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rohgarg/subscriptions","organizations_url":"https://api.github.com/users/rohgarg/orgs","repos_url":"https://api.github.com/users/rohgarg/repos","events_url":"https://api.github.com/users/rohgarg/events{/privacy}","received_events_url":"https://api.github.com/users/rohgarg/received_events","type":"User","site_admin":false},"created_at":"2018-11-19T23:11:10Z","updated_at":"2018-11-19T23:11:10Z","author_association":"CONTRIBUTOR","body":"@mamelara: Sorry for the delay. Twinkle and I have identified the root cause, and we have a patch that fixes the issue. Twinkle is cleaning up the patch and preparing it to share with you.\r\n\r\nThanks!"}}
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