{"action":"created","issue":{"url":"https://api.github.com/repos/firemodels/fds/issues/6056","repository_url":"https://api.github.com/repos/firemodels/fds","labels_url":"https://api.github.com/repos/firemodels/fds/issues/6056/labels{/name}","comments_url":"https://api.github.com/repos/firemodels/fds/issues/6056/comments","events_url":"https://api.github.com/repos/firemodels/fds/issues/6056/events","html_url":"https://github.com/firemodels/fds/issues/6056","id":299622541,"number":6056,"title":"Solver glmat error at the begining of the fds simulation","user":{"login":"MarjanLukezic","id":13114287,"avatar_url":"https://avatars1.githubusercontent.com/u/13114287?v=4","gravatar_id":"","url":"https://api.github.com/users/MarjanLukezic","html_url":"https://github.com/MarjanLukezic","followers_url":"https://api.github.com/users/MarjanLukezic/followers","following_url":"https://api.github.com/users/MarjanLukezic/following{/other_user}","gists_url":"https://api.github.com/users/MarjanLukezic/gists{/gist_id}","starred_url":"https://api.github.com/users/MarjanLukezic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MarjanLukezic/subscriptions","organizations_url":"https://api.github.com/users/MarjanLukezic/orgs","repos_url":"https://api.github.com/users/MarjanLukezic/repos","events_url":"https://api.github.com/users/MarjanLukezic/events{/privacy}","received_events_url":"https://api.github.com/users/MarjanLukezic/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"marcosvanella","id":7450069,"avatar_url":"https://avatars1.githubusercontent.com/u/7450069?v=4","gravatar_id":"","url":"https://api.github.com/users/marcosvanella","html_url":"https://github.com/marcosvanella","followers_url":"https://api.github.com/users/marcosvanella/followers","following_url":"https://api.github.com/users/marcosvanella/following{/other_user}","gists_url":"https://api.github.com/users/marcosvanella/gists{/gist_id}","starred_url":"https://api.github.com/users/marcosvanella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcosvanella/subscriptions","organizations_url":"https://api.github.com/users/marcosvanella/orgs","repos_url":"https://api.github.com/users/marcosvanella/repos","events_url":"https://api.github.com/users/marcosvanella/events{/privacy}","received_events_url":"https://api.github.com/users/marcosvanella/received_events","type":"User","site_admin":false},"assignees":[{"login":"marcosvanella","id":7450069,"avatar_url":"https://avatars1.githubusercontent.com/u/7450069?v=4","gravatar_id":"","url":"https://api.github.com/users/marcosvanella","html_url":"https://github.com/marcosvanella","followers_url":"https://api.github.com/users/marcosvanella/followers","following_url":"https://api.github.com/users/marcosvanella/following{/other_user}","gists_url":"https://api.github.com/users/marcosvanella/gists{/gist_id}","starred_url":"https://api.github.com/users/marcosvanella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcosvanella/subscriptions","organizations_url":"https://api.github.com/users/marcosvanella/orgs","repos_url":"https://api.github.com/users/marcosvanella/repos","events_url":"https://api.github.com/users/marcosvanella/events{/privacy}","received_events_url":"https://api.github.com/users/marcosvanella/received_events","type":"User","site_admin":false}],"milestone":null,"comments":23,"created_at":"2018-02-23T07:31:15Z","updated_at":"2018-03-19T14:24:54Z","closed_at":null,"author_association":"NONE","body":"Problem with solver glmat in fds, \r\nFDS SMV ver.:\r\n\r\n Current Date     : February 11, 2018  20:47:53\r\n Version          : FDS 6.6.0\r\n Revision         : FDS6.6.0-131-g88ae75a-HEAD\r\n Revision Date    : Wed Nov 1 16:03:29 2017 -0400\r\n Compiler         : Intel ifort 17.0.4\r\n Compilation Date : Nov 01, 2017 21:03:34\r\n\r\nMy HW info:\r\nAMD Ryzen Threadripper 1950X 16-Core Processor\r\nMemTotal:       16353488 kB\r\n\r\nSoftware:\r\nOS: CentOS 7.4 (64 bit)\r\n\r\nWhen I run  ulimit -a I got this set of info.:\r\n[mlukezic@localhost ~]$ ulimit -a\r\ncore file size          (blocks, -c) 0\r\ndata seg size           (kbytes, -d) unlimited\r\nscheduling priority             (-e) 0\r\nfile size               (blocks, -f) unlimited\r\npending signals                 (-i) 63490\r\nmax locked memory       (kbytes, -l) 64\r\nmax memory size         (kbytes, -m) unlimited\r\nopen files                      (-n) 1024\r\npipe size            (512 bytes, -p) 8\r\nPOSIX message queues     (bytes, -q) 819200\r\nreal-time priority              (-r) 0\r\nstack size              (kbytes, -s) 8192\r\ncpu time               (seconds, -t) unlimited\r\nmax user processes              (-u) 4096\r\nvirtual memory          (kbytes, -v) unlimited\r\nfile locks                      (-x) unlimited\r\n\r\nPlease, don't do anything else. First,  paste these lines into your .bashrc file.\r\n\r\n#============= FDS environment =======\r\nexport PATH=/home/mlukezic/FDS/FDS6/bin:$PATH\r\nexport LD_LIBRARY_PATH=/usr/lib64:/home/mlukezic/FDS/FDS6/bin/LIB64:$LD_LIBRARY$\r\nexport OMP_NUM_THREADS=8 \r\n\r\nulimit -s unlimited  \r\n\r\nSalah Benkorichi adviced this code for bash \r\nI_MPI_SHM_LMT=shm\r\n#============= FDS environment ======= \r\n\r\n Don't put the nbr of threads to 16, to me that appears you are having hyperthreadening, and this will only slow the run instead of increasing it.\r\nIf you want to run single MPI, then keep it to 8, if you want use MPI, then reduce it to 1, or 2 depending on how many MPI processes you're intending to use.\r\n\r\nlog off and login again. Run the case again and report what you get.\r\n\r\nWhen I run:\r\n$ fds glmat.fds\r\nI got notice:\r\nMesh 1 is assigned to MPI Process 0\r\n OpenMP thread   0 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   5 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   7 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   3 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   1 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   2 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   4 of   7 assigned to MPI process      0 of      0\r\n OpenMP thread   6 of   7 assigned to MPI process      0 of      0\r\n Completed Initialization Step  1\r\n Completed Initialization Step  2\r\n Completed Initialization Step  3\r\n Completed Initialization Step  4\r\n \r\n Using GLMAT as pressure solver. List of H unknown numbers per proc:\r\n MYID=       0, NUNKH_LOCAL=  256000\r\n\r\nforrtl: severe (174): SIGSEGV, segmentation fault occurred\r\nImage              PC                Routine            Line        Source            \r\nfds                00000000059AAB24  Unknown               Unknown  Unknown\r\nlibpthread-2.17.s  00002B99466B45E0  Unknown               Unknown  Unknown\r\nlibc-2.17.so       00002B99481204FC  cfree                 Unknown  Unknown\r\nld-2.17.so         00002B99460E2F22  Unknown               Unknown  Unknown\r\nld-2.17.so         00002B99460E5712  Unknown               Unknown  Unknown\r\nld-2.17.so         00002B99460F0964  Unknown               Unknown  Unknown\r\nld-2.17.so         00002B99460EC2D4  Unknown               Unknown  Unknown\r\nld-2.17.so         00002B99460F02CB  Unknown               Unknown  Unknown\r\nlibdl-2.17.so      00002B9946BC3FBB  Unknown               Unknown  Unknown\r\nld-2.17.so         00002B99460EC2D4  Unknown               Unknown  Unknown\r\nlibdl-2.17.so      00002B9946BC45BD  Unknown               Unknown  Unknown\r\nlibdl-2.17.so      00002B9946BC4051  dlopen                Unknown  Unknown\r\n\r\nfds                000000000044D9A7  Unknown               Unknown  Unknown\r\nfds                000000000044DCBD  Unknown               Unknown  Unknown\r\nfds                00000000005404EB  Unknown               Unknown  Unknown\r\nfds                000000000045BC37  Unknown               Unknown  Unknown\r\nfds                0000000000407C7F  Unknown               Unknown  Unknown\r\nfds                000000000610478B  Unknown               Unknown  Unknown\r\nfds                0000000005A8DEFD  MAIN__                    252  main.f90\r\nfds                000000000040784E  Unknown               Unknown  Unknown\r\nlibc-2.17.so       00002B99480C1C05  __libc_start_main     Unknown  Unknown\r\nfds                0000000000407729  Unknown  \r\n\r\nEven with this code:\r\n&HEAD CHID='glmat', TITLE='Compart_Test'/\r\n&TIME T_END=360.0/\r\n \r\n \r\n&MESH IJK=21,10,10, XB=0.0,2.1,0.0,1.0,0.0,1.0 /\r\n \r\n&REAC ID='React_Methane',\r\n      FUEL='METHANE',\r\n      CO_YIELD=0.1,\r\n      SOOT_YIELD=0.01/\r\n \r\n \r\n&PRES SOLVER='GLMAT'/\r\n \r\n&TAIL /\r\nI got the same notice."},"comment":{"url":"https://api.github.com/repos/firemodels/fds/issues/comments/374229931","html_url":"https://github.com/firemodels/fds/issues/6056#issuecomment-374229931","issue_url":"https://api.github.com/repos/firemodels/fds/issues/6056","id":374229931,"user":{"login":"MarjanLukezic","id":13114287,"avatar_url":"https://avatars1.githubusercontent.com/u/13114287?v=4","gravatar_id":"","url":"https://api.github.com/users/MarjanLukezic","html_url":"https://github.com/MarjanLukezic","followers_url":"https://api.github.com/users/MarjanLukezic/followers","following_url":"https://api.github.com/users/MarjanLukezic/following{/other_user}","gists_url":"https://api.github.com/users/MarjanLukezic/gists{/gist_id}","starred_url":"https://api.github.com/users/MarjanLukezic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MarjanLukezic/subscriptions","organizations_url":"https://api.github.com/users/MarjanLukezic/orgs","repos_url":"https://api.github.com/users/MarjanLukezic/repos","events_url":"https://api.github.com/users/MarjanLukezic/events{/privacy}","received_events_url":"https://api.github.com/users/MarjanLukezic/received_events","type":"User","site_admin":false},"created_at":"2018-03-19T14:24:54Z","updated_at":"2018-03-19T14:24:54Z","author_association":"NONE","body":"Hi Marco,\n\ni installed the latest Intel MKL library without any problems, but I did\nnot know how to modify my .bushrc\nI'm going to try as you suggest. I complied fds-master with gfortran and\nnow with Intel fortran, is it right or I made a mistake.\n\nBest regards,\n\nMarjan L.\n\nOn Mon, Mar 19, 2018 at 3:17 PM, marcosvanella <notifications@github.com>\nwrote:\n\n> Marjan, your compilation hasn't linked the code to the Intel MKL library.\n>\n>    1. Download and install Intel performance libs as explained in the\n>    wiki.\n>    2. Add paths to the lib in your system, on your ~/.bashrc. In my case\n>    I put:\n>\n> # MKL Environment Variables:\n> #export INTEL_COMPILERS_AND_LIBS=/home/marcos/intel/compilers_and_libraries_2017/linux\n> #source $INTEL_COMPILERS_AND_LIBS/mkl/bin/mklvars.sh intel64\n>\n> If you downloaded intel 2018 -> use YOURPATH/intel/compilers_and_libraries_2018/linux\n> in the definitions above. Make sure you see the -DWITH_MKL flag in\n> compilation lines.\n>\n> Intel support hasn't helped much so far. They are releasing an update for\n> intel 2018 this week, which I was told contains several fixes. I'll see if\n> the problem persists.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/firemodels/fds/issues/6056#issuecomment-374227130>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AMgbrwCaQsPdkaR2NDsEXLwWlM6aaOieks5tf73fgaJpZM4SQfOC>\n> .\n>\n\n\n\n-- \n\n\n*_______________________________________________________________________\nMarjan Lukežič*\n\n*\"Excellence is not a singular act, but a habit. You are what you\nrepeatedly do.\" - Shaquille O'Neal*\n\n\n\n*\"The walls between art and engineering exist only in our minds\" - Theo\nJansen“Simplicity is the ultimate form of sophistication.” - Leonardo da\nVinci*\n"}}
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