Hi,
Yes, they are. When I run "top" or "ps". There are exactly 16 Ray ranks
and one mpiexec process in the oak machine.
But this problem does not always happen because I have gotten some good
results from Ray when I ran it for other datasets.
Thanks
Lin
On Wed, Jun 12, 2013 at 8:00 AM, Sébastien Boisvert <
[email protected]> wrote:
> On 10/06/13 05:26 PM, Lin wrote:
>
>> 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 &
>>
>
> Are all your MPI ranks running on the "oak" machine ?
>
>
>> 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 <
>> sebastien.boisvert.3@ulaval.**ca <[email protected]><mailto:
>> sebastien.boisvert.3@**ulaval.ca <[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--
>>
>>
>> ------------------------------**__----------------------------**
>> --__------------------
>>
>> 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<http://p.sf.net/sfu/__servicenow-d2d-j><
>> http://p.sf.net/sfu/**servicenow-d2d-j<http://p.sf.net/sfu/servicenow-d2d-j>
>> >
>> ______________________________**___________________
>> Denovoassembler-users mailing list
>>
>> Denovoassembler-users@lists.__**sourceforge.net<http://sourceforge.net><mailto:
>> Denovoassembler-users@**lists.sourceforge.net<[email protected]>
>> >
>> https://lists.sourceforge.net/**__lists/listinfo/__**
>> denovoassembler-users<https://lists.sourceforge.net/__lists/listinfo/__denovoassembler-users><
>> https://lists.sourceforge.**net/lists/listinfo/**denovoassembler-users<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
