[mpich-discuss] A problem of carrying out mpich2

Dr. Qian-Lin Tang qltang at xidian.edu.cn
Tue Jun 15 21:24:58 CDT 2010 

Hi, Yuriy and Dave,

I use the command of "ulimit -c unlimited" beforhand to eliminate memory stacking. The same error message pops up when performing parallel version of VASP. How to resolve my problem? Thanks.

Best regards,

Qian-Lin                                                                       

======= 2010-06-16 02:21:32 您在来信中写道：=======                      

>Signal 9 is SIGKILL, and in the context of MPI (or at least MPICH2+mpd) usually means that the process manager killed the application because of some other problem.  The  problem is often another process crashing, such as from a signal 11 (SIGSEGV).  Unfortunately, the other failing process does not always show up in the output.  If you enable  core dumps (usually "ulimit -c unlimited") then sometimes you'll get a core dump for the offending process.
>
>Our new process manager, hydra, does a better job with the error reporting and process cleanup.  However you need to use a fairly modern version of MPICH2 in order to use hydra: http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager
>
>-Dave
>
>On Jun 15, 2010, at 10:45 AM PDT, Yuriy Khalak wrote:
> e
>> Dear Qianlin,
>> 
>> Signal 9, which seems to be causing the crash, usually indicates a segmentation fault in the code bing run by mpiexec. I had something similar happen to me recently under c++ and mpich. Turned out I was trying to delete the contents of a pointer twice.
>> 
>> In my case Linux did a core dump, which I could trace with gdb and determine approximately where the segmentation fault occurred. So if you can find a core dump in your program's working directory, the problem is probably in the VASP code, not in mpich2.
>> 
>> Keep in mind that I'm just a user of mpich2 and very well could be wrong.
>> 
>> Regards,
>>              Yuriy
>> 
>> > Dear mpich2-support,
>> >
>> > Based on mpif90, I have installed the parallel version of a commercilal code VASP . Sometimes mpich2 can work well with vasp, but it also failed for some VASP-treated jobs with the following error messages:
>> > ------------------------------
>> -----
>> > running on    8 nodes
>> > distr:  one band on    1 nodes,    8 groups
>> > vasp.4.6.21  23Feb03 complex
>> > POSCAR found :  3 types and   30 ions
>> > LDA part: xc-table for Ceperly-Alder, Vosko type interpolation para-ferro
>> > POSCAR, INCAR and KPOINTS ok, starting setup
>> > WARNING: wrap around errors must be expected
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > FFT: planning ...            2
>> > reading WAVECAR
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > mpiexec_qltang1 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
>> > mpiexec_qltang1 (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &
>> > WARNING: random wavefunctions but no delay for mixing, default for NELMDL
>> > entering main loop
>> >       N       E                     dE             d eps       ncg     rms          rms(c)
>> > rank 6 in job 36  qltang1_54199   caused collective abort of all ranks
>> >  exit status of rank 6: killed by signal 9
>> > rank 3 in job 36  qltang1_54199   caused collective abort of all ranks
>> >  exit status of rank 3: killed by signal 9
>> > -----------------------------
>> > I want to know how to solve the above question. Thank you alot.
>> >
>> > Best regards,
>> > Qianlin
>> _______________________________________________
>> mpich-discuss mailing list
>> mpich-discuss at mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>
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= = = = = = = = = = = = = = = = = = = =
			

　　　　　　　　致
礼！
 
				 
　　　　　　　　Dr. Qian-Lin Tang
　　　　　　　　qltang at xidian.edu.cn
　　　　　　　　　　2010-06-16

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