Hi,
Thanks for your answers.
However, I got the error message from nohup.out. That is to say, I have
used nohup to run Ray.
This is my command:
nohup mpiexec -n 16 Ray Col.conf &
And the Col.conf contains:
-k 55 # this is a comment
-p /s/oak/a/nobackup/lin/Art/Col_illumina_art/Col_il1.fastq
/s/oak/a/nobackup/lin/Art/Col_illumina_art/Col_il2.fastq
-o RayOutputOfCol
On Mon, Jun 10, 2013 at 2:02 PM, Sébastien Boisvert <
[email protected]> wrote:
> 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--
>
>
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