{"action":"opened","issue":{"url":"https://api.github.com/repos/weizhongli/cdhit/issues/28","labels_url":"https://api.github.com/repos/weizhongli/cdhit/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/weizhongli/cdhit/issues/28/comments","events_url":"https://api.github.com/repos/weizhongli/cdhit/issues/28/events","html_url":"https://github.com/weizhongli/cdhit/issues/28","id":129085337,"number":28,"title":"segmentation falut & compipation error","user":{"login":"KamilSJaron","id":8181573,"avatar_url":"https://avatars.githubusercontent.com/u/8181573?v=3","gravatar_id":"","url":"https://api.github.com/users/KamilSJaron","html_url":"https://github.com/KamilSJaron","followers_url":"https://api.github.com/users/KamilSJaron/followers","following_url":"https://api.github.com/users/KamilSJaron/following{/other_user}","gists_url":"https://api.github.com/users/KamilSJaron/gists{/gist_id}","starred_url":"https://api.github.com/users/KamilSJaron/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KamilSJaron/subscriptions","organizations_url":"https://api.github.com/users/KamilSJaron/orgs","repos_url":"https://api.github.com/users/KamilSJaron/repos","events_url":"https://api.github.com/users/KamilSJaron/events{/privacy}","received_events_url":"https://api.github.com/users/KamilSJaron/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-01-27T09:35:31Z","updated_at":"2016-01-27T09:35:31Z","closed_at":null,"body":"First I ve compiled program with max length of sequences suiting my dataset:\r\nmake MAX_SEQ=12000000\r\n, everything went fine during compilation, but every attempt to run resulted in segmentation fault (already reported). Since I have a little C++ experience, I knew that problem will be most likely in paralelization, so I tried to compile program without...\r\n\r\nmake openmp=no MAX_SEQ=12000000\r\ng++  -DNO_OPENMP -O2 -DMAX_SEQ=12000000  cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d\r\ncdhit-common.o: In function `CleanUpTempFiles()':\r\ncdhit-common.c++:(.text+0x1b): undefined reference to `GOMP_critical_start'\r\ncdhit-common.o: In function `OpenTempFile(char const*)':\r\ncdhit-common.c++:(.text+0x1b2): undefined reference to `GOMP_critical_start'\r\ncdhit-common.c++:(.text+0x21a): undefined reference to `GOMP_critical_end'\r\ncdhit-common.o: In function `Options::SetOptionCommon(char const*, char const*)':\r\ncdhit-common.c++:(.text+0x618): undefined reference to `omp_get_num_procs'\r\ncdhit-common.o: In function `SequenceDB::ClusterTo(SequenceDB&, Options const&) [clone ._omp_fn.3]':\r\ncdhit-common.c++:(.text+0x85e0): undefined reference to `GOMP_loop_dynamic_start'\r\ncdhit-common.c++:(.text+0x86ab): undefined reference to `omp_get_thread_num'\r\ncdhit-common.c++:(.text+0x87db): undefined reference to `GOMP_loop_dynamic_next'\r\ncdhit-common.c++:(.text+0x87e8): undefined reference to `GOMP_loop_end_nowait'\r\ncdhit-common.o: In function `SequenceDB::DoClustering(int, Options const&) [clone ._omp_fn.2]':\r\ncdhit-common.c++:(.text+0x8880): undefined reference to `GOMP_loop_dynamic_start'\r\ncdhit-common.c++:(.text+0x88c5): undefined reference to `omp_get_thread_num'\r\ncdhit-common.c++:(.text+0x8931): undefined reference to `GOMP_loop_dynamic_next'\r\ncdhit-common.c++:(.text+0x893e): undefined reference to `GOMP_loop_end_nowait'\r\ncdhit-common.o: In function `SequenceDB::DoClustering(int, Options const&) [clone ._omp_fn.0]':\r\ncdhit-common.c++:(.text+0x8990): undefined reference to `GOMP_loop_dynamic_start'\r\ncdhit-common.c++:(.text+0x89d9): undefined reference to `omp_get_thread_num'\r\ncdhit-common.c++:(.text+0x8a69): undefined reference to `GOMP_loop_dynamic_next'\r\ncdhit-common.c++:(.text+0x8a76): undefined reference to `GOMP_loop_end_nowait'\r\ncdhit-common.o: In function `SequenceDB::DoClustering(int, Options const&) [clone ._omp_fn.1]':\r\ncdhit-common.c++:(.text+0x9447): undefined reference to `GOMP_loop_dynamic_start'\r\ncdhit-common.c++:(.text+0x94c2): undefined reference to `omp_get_thread_num'\r\ncdhit-common.c++:(.text+0x95d1): undefined reference to `omp_get_thread_num'\r\ncdhit-common.c++:(.text+0x970e): undefined reference to `GOMP_loop_dynamic_next'\r\ncdhit-common.c++:(.text+0x971b): undefined reference to `GOMP_loop_end_nowait'\r\ncdhit-common.c++:(.text+0x9731): undefined reference to `GOMP_critical_start'\r\ncdhit-common.c++:(.text+0x973e): undefined reference to `GOMP_critical_end'\r\ncdhit-common.o: In function `SequenceDB::ClusterTo(SequenceDB&, Options const&)':\r\ncdhit-common.c++:(.text+0xb1aa): undefined reference to `omp_set_num_threads'\r\ncdhit-common.c++:(.text+0xb68d): undefined reference to `GOMP_parallel'\r\ncdhit-common.o: In function `SequenceDB::DoClustering(int, Options const&)':\r\ncdhit-common.c++:(.text+0xc5f2): undefined reference to `omp_set_num_threads'\r\ncdhit-common.c++:(.text+0xc967): undefined reference to `GOMP_parallel'\r\ncdhit-common.c++:(.text+0xcf19): undefined reference to `GOMP_parallel'\r\ncdhit-common.c++:(.text+0xd00b): undefined reference to `GOMP_parallel'\r\ncdhit-common.o: In function `CleanUpTempFiles()':\r\ncdhit-common.c++:(.text+0xa6): undefined reference to `GOMP_critical_end'\r\ncdhit-common.o: In function `TempFiles::~TempFiles()':\r\ncdhit-common.c++:(.text._ZN9TempFilesD2Ev[_ZN9TempFilesD5Ev]+0x13): undefined reference to `GOMP_critical_start'\r\ncdhit-common.c++:(.text._ZN9TempFilesD2Ev[_ZN9TempFilesD5Ev]+0x83): undefined reference to `GOMP_critical_end'\r\ncdhit-common.o: In function `TempFiles::Clear()':\r\ncdhit-common.c++:(.text._ZN9TempFiles5ClearEv[_ZN9TempFiles5ClearEv]+0x13): undefined reference to `GOMP_critical_start'\r\ncdhit-common.c++:(.text._ZN9TempFiles5ClearEv[_ZN9TempFiles5ClearEv]+0x8d): undefined reference to `GOMP_critical_end'\r\ncollect2: error: ld returned 1 exit status\r\nmake: *** [cd-hit-est-2d] Error 1\r\n"}}