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Subject: Re: [OMPI users] Strange Segfault in mpirun: orterun.c:486
From: devendra rai (rai.devendra_at_[hidden])
Date: 2012-01-05 15:37:18


Hello Ralph, I finally solved the problem. My OS had installed another version of openmpi, which I removed. Also, I did not try 'make clean' before 'make'.  I found the problem by doing a verbose build of my application, and noticed that it was referring to libraries from /usr/lib64/mpi/, which was not correct. This was even when I had set the paths of mpic++ in my make file to /home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2/ . I had set the paths of libraries and include files in my makefile to specifically point to my custom MPI installation. So, I am curious as to why open-mpi was trying to refer to libraries in /usr/lib64. I reinstalled everything fresh, and now it seems to work :) Thanks for your help. Best, Devendra ________________________________ From: Ralph Castain <rhc_at_[hidden]> To: devendra rai <rai.devendra_at_[hidden]> Sent: Thursday, 5 January 2012, 20:09 Subject: Re: [OMPI users] Strange Segfault in mpirun: orterun.c:486 Hmm....well, I'm at a bit of a loss. It all certainly looks okay. Can you send the output from configure - should be in config.out? Did you do a "make clean" after your configure and before rebuilding OMPI? On Jan 5, 2012, at 11:25 AM, devendra rai wrote:   Hello Ralph, > > >Here is the command that I use to run my application: > > >/home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2/bin/mpirun -np 2 -v --timestamp-output --tag-output --d kdbg ./MPIDerivedDataTypes > >where MPIDerivedDataTypes is the sample application. > > >Best, > >Devendra > > > > >________________________________ > From: Ralph Castain <rhc_at_[hidden]> >To: devendra rai <rai.devendra_at_[hidden]> >Sent: Thursday, 5 January 2012, 19:14 >Subject: Re: [OMPI users] Strange Segfault in mpirun: orterun.c:486 > > >That is indeed rather strange. The failure occurs at a rather trivial point in the code, well before anything useful can happen. What does your cmd line look like? > > > > >On Jan 5, 2012, at 11:07 AM, devendra rai wrote: > >   Hello Ralph, >> >> >>This time, rebuilding with the configure line that I showed did not fix the problem. And, I am mighty clueless (with some desperation thrown in). >> >> >>Any ideas would be awesome. >> >> >>Best, >> >>Devendra >> >> >> >> >>________________________________ >> From: Ralph Castain <rhc_at_[hidden]> >>To: devendra rai <rai.devendra_at_[hidden]>; Open MPI Users <users_at_[hidden]> >>Sent: Thursday, 5 January 2012, 18:49 >>Subject: Re: [OMPI users] Strange Segfault in mpirun: orterun.c:486 >> >> >>Guess I'm still confused a bit - are you saying that the rebuild no longer fixes the problem? >> >> >>Otherwise, I don't see a ready solution. If your system undergoes a significant change, then rebuilding is not an unexpected requirement. >> >> >> >> >>On Jan 5, 2012, at 10:39 AM, devendra rai wrote: >> >>Hello Ralph, >>> >>> >>>Yes, historically, the rebuild fixed the problem. But, now, how do I rebuild against a new libc? And doesn't mpi build process automatically pick up whatever libc version I have? >>> >>> >>> >>>I cant seem to google this solution. I already included my configure line for building open-mpi. >>> >>> >>> >>>Thanks a lot. >>> >>> >>>Devendra Rai >>> >>> >>> >>> >>>________________________________ >>> From: Ralph Castain <rhc_at_[hidden]> >>>To: devendra rai <rai.devendra_at_[hidden]>; Open MPI Users <users_at_[hidden]> >>>Sent: Thursday, 5 January 2012, 18:32 >>>Subject: Re: [OMPI users] Strange Segfault in mpirun: orterun.c:486 >>> >>> >>>Let me see if I understand correctly. You performed some upgrades on Linux, and then orterun fails. Rebuilding OMPI resolved the problem. >>> >>> >>>Is that correct? If so, then I'm not terribly surprised - it depends on what got upgraded. For example, if the default libc changed due to a revision upgrade, then you probably do need to rebuild against it. >>> >>> >>> >>> >>>On Jan 5, 2012, at 10:28 AM, devendra rai wrote: >>> >>>Hello All, >>>> >>>> >>>>This has happened to me many times, but a simple rebuild of the Open-MPI generally fixed it. >>>> >>>> >>>>I had a perfectly working (and tested) MPI application till a few days ago. Since then, there has been some upgrades on my Linux OS (basically, the ones which the system picks up automatically). >>>> >>>> >>>> >>>>Now, I rebuild and rerun the same application, I get this: >>>> >>>> >>>>mpirun: orterun.c:486: orterun: Assertion `((0xdeafbeedULL << 32) + 0xdeafbeedULL) == ((opal_object_t *) (&cmd_line))->obj_magic_id' failed. >>>>[Morpheus:24572] *** Process received signal *** >>>>[Morpheus:24572] Signal: Aborted (6) >>>>[Morpheus:24572] Signal code:  (-6) >>>>[Morpheus:24572] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7fd23c9312d0] >>>>[Morpheus:24572] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7fd23c5e7ab5] >>>>[Morpheus:24572] [ 2] /lib64/libc.so.6(abort+0x186) [0x7fd23c5e8fb6] >>>>[Morpheus:24572] [ 3] /lib64/libc.so.6(__assert_fail+0xf5) [0x7fd23c5e0385] >>>>[Morpheus:24572] [ 4] /home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2/bin/mpirun() [0x4037ed] >>>>[Morpheus:24572] [ 5] /home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2/bin/mpirun() [0x4032a4] >>>>[Morpheus:24572] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7fd23c5d3bfd] >>>>[Morpheus:24572] [ 7] /home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2/bin/mpirun() [0x4031c9] >>>>[Morpheus:24572] *** End of error message *** >>>> >>>> >>>> >>>> >>>> >>>>I have a custom installation of open-mpi, with the configure script looking like this: >>>> >>>> >>>>./configure --enable-mpi-threads=yes -prefix=/home/Morpheus/CustomInstalledPrograms/OpenMPI-1.4.2 --enable-mem-profile --enable-mem-debug --enable-debug --enable-trace --enable-memchecker --with-valgrind=/usr --with-threads=posix  >>>> >>>> >>>>The rebuild of my application was successful. >>>> >>>> >>>>Where should I fix it? and How? >>>> >>>> >>>>Thanks for ideas. >>>> >>>> >>>>Best >>>> >>>> >>>>Devendra >>>>_______________________________________________ >>>>users mailing list >>>>users_at_[hidden] >>>>http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>>_______________________________________________ >>>users mailing list >>>users_at_[hidden] >>>http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> > > >