On 09/06/13 11:35 AM, Lin wrote: > Hi, Sébastien > > I changed the Max Kmer to 64. And set it as 55 in a run. > But it always end up with a problem like this. > "mpiexec noticed that process rank 11 with PID 25012 on node oak exited on > signal 1(Hangup)" > Could you help me figure it out?
The signal 1 is SIGHUP according to this list: $ kill -l 1) SIGHUP 2) SIGINT 3) SIGQUIT 4) SIGILL 5) SIGTRAP 6) SIGABRT 7) SIGBUS 8) SIGFPE 9) SIGKILL 10) SIGUSR1 11) SIGSEGV 12) SIGUSR2 13) SIGPIPE 14) SIGALRM 15) SIGTERM 16) SIGSTKFLT 17) SIGCHLD 18) SIGCONT 19) SIGSTOP 20) SIGTSTP 21) SIGTTIN 22) SIGTTOU 23) SIGURG 24) SIGXCPU 25) SIGXFSZ 26) SIGVTALRM 27) SIGPROF 28) SIGWINCH 29) SIGIO 30) SIGPWR 31) SIGSYS 34) SIGRTMIN 35) SIGRTMIN+1 36) SIGRTMIN+2 37) SIGRTMIN+3 38) SIGRTMIN+4 39) SIGRTMIN+5 40) SIGRTMIN+6 41) SIGRTMIN+7 42) SIGRTMIN+8 43) SIGRTMIN+9 44) SIGRTMIN+10 45) SIGRTMIN+11 46) SIGRTMIN+12 47) SIGRTMIN+13 48) SIGRTMIN+14 49) SIGRTMIN+15 50) SIGRTMAX-14 51) SIGRTMAX-13 52) SIGRTMAX-12 53) SIGRTMAX-11 54) SIGRTMAX-10 55) SIGRTMAX-9 56) SIGRTMAX-8 57) SIGRTMAX-7 58) SIGRTMAX-6 59) SIGRTMAX-5 60) SIGRTMAX-4 61) SIGRTMAX-3 62) SIGRTMAX-2 63) SIGRTMAX-1 64) SIGRTMAX This signal is not related to the compilation option MAXKMERLENGTH=64. You are gettig this signal because the parent process of your mpiexec process dies (probably because you are closing your terminal) and this causes the SIGHUP that is being sent to your Ray processes. There are several solutions to this issue (pick up on solution in the list below): 1. Use nohup^(i.e.: nohup mpiexec -n 999 Ray -p data1.fastq.gz data2.fastq.gz 2. Launch your work inside a screen session (the screen command) 3. Launch your work inside a tmux session (the tmux command) 4. Use a job scheduler (like Moab, Grid Engine, or another). --SÉB-- > > ------------------------------------------------------------------------------ > How ServiceNow helps IT people transform IT departments: > 1. A cloud service to automate IT design, transition and operations > 2. Dashboards that offer high-level views of enterprise services > 3. A single system of record for all IT processes > http://p.sf.net/sfu/servicenow-d2d-j > _______________________________________________ > Denovoassembler-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
