[mpich-discuss] Abnormal termination on Linux

Tue Apr 7 03:37:02 CDT 2020

As long as you use a standard MPI implementation, there is no resilience 
and the MPI job will not survive a segfault or any other MPI error. 
Probably you should target your question towards "Why does my 
application segfault in the first place?"

If it's only one process, that segfaults probably use the core file for 
debugging. By default I assume corefile size is limited on most 
clusters, so increase it in your batch job:
ulimit -c unlimited

gdb a.out -c corefile.hostname.timestamp
backtrace
quit

Am 07.04.20 um 00:23 schrieb Zhou, Hui via discuss:
> I see. MPICH doesn’t trap any signal as I checked 😊.  So back to your issue, let’s assume your trap did work, but after the signal handler, which after it called `MPI_Finalize`, the code is still going to run the same code that causes segfault in the first place, right? Wouldn’t that endup in infinite signal loop or maybe the kernel smart out and by-passed your handler? Just a thought experiment.
> 

Calling MPI_Finalize would not help, because MPI_Finalize is a 
collective call and will not finish before all other processes have 
called MPI_Finalize.
Furthermore, in such error situation you won't have any guarantees, that 
the process does not have any open blocking or non-blocking 
communication. Such communication would need to be completed before 
calling MPI_Finalize.

- Joachim

> Beside, MPICH is thread-safe but not interrupt safe. So you should not really call MPI functions inside signal handlers.
> 
> --
> Hui Zhou
> 
> 
> From: "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov>
> Date: Monday, April 6, 2020 at 4:50 PM
> To: "Zhou, Hui" <zhouh at anl.gov>, "discuss at mpich.org" <discuss at mpich.org>
> Subject: RE: [mpich-discuss] Abnormal termination on Linux
> 
> Hui,
> 
> I’d like to trap segfaults so that the process that raised them can be shut down gracefully/finalized without taking down the whole MPI job.   Maybe you are right and  I shouldn’t trap them.
> 
> However, when I install my signal handlers, I check if MPI already has a signal handler installed for each of them.   It isn’t reporting that MPI has done so.  Perhaps my code is incorrect?
> 
> setUpOneHandler(const int signum)
> {
>      struct sigaction sa_new, sa_old;
> 
>      sa_new.sa_handler = mpiSignalHandler;
>      sa_new.sa_flags = 0;
>      sigemptyset(&sa_new.sa_mask);
> 
>      if (sigaction(signum, NULL, &sa_old) < 0)
>      {
>            // ERROR: could not query old handler
> 
>      } else if (sa_old.sa_handler == SIG_IGN ||
>                    sa_old.sa_handler == SIG_DFL)
>      {
>          // MPI hasn't set its own handler for this signal, so we
>          // will install our own.
> 
>          if (sigaction(signum, &sa_new, NULL) < 0)
>          {
>              // ERROR: could not set new handler
>          }
>      } else
>      {
>          // MPI already has a handler installed for this signal.  Do nothing
>      }
> }
> 
> 
> 
> 
> From: Zhou, Hui <zhouh at anl.gov>
> Sent: Monday, April 6, 2020 2:08 PM
> To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
> Subject: [EXTERNAL] Re: [mpich-discuss] Abnormal termination on Linux
> 
> Thanks, Kurt. I think the reason your signal trap didn’t work is because `mpiexec` is trapping it first. Segfault is code error. Why would you want to trap it?
> 
> --
> Hui Zhou
> 
> 
> From: "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
> Date: Monday, April 6, 2020 at 1:52 PM
> To: "Zhou, Hui" <zhouh at anl.gov<mailto:zhouh at anl.gov>>, "discuss at mpich.org<mailto:discuss at mpich.org>" <discuss at mpich.org<mailto:discuss at mpich.org>>
> Subject: RE: [mpich-discuss] Abnormal termination on Linux
> 
> Hui,
> 
> Sorry for not mentioning that.  MPICH 3.3.2 compiled with pgc++ 19.5.
> 
> Kurt
> 
> From: Zhou, Hui <zhouh at anl.gov<mailto:zhouh at anl.gov>>
> Sent: Monday, April 6, 2020 12:58 PM
> To: discuss at mpich.org<mailto:discuss at mpich.org>
> Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
> Subject: [EXTERNAL] Re: [mpich-discuss] Abnormal termination on Linux
> 
> Which version of MPICH were you running?
> 
> --
> Hui Zhou
> 
> 
> From: "Mccall, Kurt E. (MSFC-EV41) via discuss" <discuss at mpich.org<mailto:discuss at mpich.org>>
> Reply-To: "discuss at mpich.org<mailto:discuss at mpich.org>" <discuss at mpich.org<mailto:discuss at mpich.org>>
> Date: Monday, April 6, 2020 at 12:45 PM
> To: "discuss at mpich.org<mailto:discuss at mpich.org>" <discuss at mpich.org<mailto:discuss at mpich.org>>
> Cc: "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
> Subject: Re: [mpich-discuss] Abnormal termination on Linux
> 
> I should mention that I am unable to predict in which node or process the abnormal termination occurs, so I can’t practically attach a debugger and try to intercept the error.
> 
> Kurt
> 
> From: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
> Sent: Monday, April 6, 2020 11:50 AM
> To: discuss at mpich.org<mailto:discuss at mpich.org>
> Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
> Subject: Abnormal termination on Linux
> 
> I have a couple of questions about abnormal termination.   The EXIT CODE below is 11, which could be signal SIGSEGV, or is it something defined by MPICH?  If it is SIGSEGV, it is strange because my signal handler isn’t catching it and cleaning up properly (the signal handler calls MPI_Finalize()).   Is there any way to get more information about the location of the error?
> 
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 14385 RUNNING AT n020.cluster.com
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> 
> Thanks,
> Kurt
> 
> 
> _______________________________________________
> discuss mailing list     discuss at mpich.org
> To manage subscription options or unsubscribe:
> https://lists.mpich.org/mailman/listinfo/discuss
> 

-- 
Dipl.-Inf. Joachim Protze

IT Center
Group: High Performance Computing
Division: Computational Science and Engineering
RWTH Aachen University
Seffenter Weg 23
D 52074  Aachen (Germany)
Tel: +49 241 80- 24765
Fax: +49 241 80-624765
protze at itc.rwth-aachen.de
www.itc.rwth-aachen.de

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 5327 bytes
Desc: S/MIME Cryptographic Signature
URL: <http://lists.mpich.org/pipermail/discuss/attachments/20200407/f8e0184f/attachment-0001.p7s>