[petsc-dev] [petsc-maint #135017] Re: petsc-dev/buildsystem is broken on OS X.6+openmpi-nofortran

Matthew Knepley petsc-maint at mcs.anl.gov
Mon Oct 8 04:08:49 CDT 2012 

On Mon, Oct 8, 2012 at 3:31 AM, Aron Ahmadia <aron at ahmadia.net> wrote:

> Dang, that's almost a perfect match to my gcc:
>
> i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>
> We can definitely reproduce this on two 10.6 systems out here at KAUST.
>  Ketch and I are both using "brew" on these boxen, but this is fairly
> non-invasive with regards to this stack.
>
> Matt, Satish, can you guys get your config and make logs to me somehow?
>  When I get some time I will try to bisect back to the commit in -dev that
> is causing this.
>

I will send it when not in the airport. However, the fastest way to debug
this is
to run with the debugger and see what the SEGV is actually coming from.

   Matt


> A
>
> On Sun, Oct 7, 2012 at 10:16 PM, Matthew Knepley <petsc-maint at mcs.anl.gov
> >wrote:
>
> > On Sun, Oct 7, 2012 at 2:36 PM, Aron Ahmadia <aron.ahmadia at gmail.com
> >wrote:
> >
> >> Please report your gcc compiler versions.
> >>
> >
> > knepley:/PETSc3/petsc/petsc-dev$ mpicc --show
> > mpicc --show
> > gcc -D_REENTRANT -Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi
> > -lopen-rte -lopen-pal
> > knepley:/PETSc3/petsc/petsc-dev$ gcc --version
> > gcc --version
> > i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664)
> > Copyright (C) 2007 Free Software Foundation, Inc.
> > This is free software; see the source for copying conditions.  There is
> NO
> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
> >
> >    Matt
> >
> >
> >> A
> >>
> >> Sent from my iPhone
> >>
> >> On Oct 7, 2012, at 7:49 PM, Matthew Knepley <petsc-maint at mcs.anl.gov>
> >> wrote:
> >>
> >> > On Sun, Oct 7, 2012 at 12:48 PM, Satish Balay <
> petsc-maint at mcs.anl.gov>
> >> wrote:
> >> > My test ran fine again.
> >> >
> >> > Perhaps you can run the example manually in a debugger to get a better
> >> > trace.
> >> >
> >> > Yes, I can't reproduce this either.
> >> >
> >> >   Matt
> >> >
> >> >
> >> > Satish
> >> >
> >> > On Sun, 7 Oct 2012, Satish Balay wrote:
> >> >
> >> > > ok - then the issue is unrelated to fortran. I'll redo the 10.6
> build
> >> > > and see if its reproduceable.
> >> > >
> >> > > and secondly there is some wierd bug where fortran interface is not
> >> > > getting built [you could try 'make all-legacy' and see if it gets
> >> > > built correctly]
> >> > >
> >> > > Also gfortran-4.2* is buggy [wrt some of the f90 interface
> >> > > functionality].  gfortran >= 4.3 is prefered for that. [but if not
> >> > > using f90 interfaces - it doesn't matter]
> >> > >
> >> > > Satish
> >> > >
> >> > > On Sun, 7 Oct 2012, Aron Ahmadia wrote:
> >> > >
> >> > > > reproduced with fortran enabled, additionally:
> >> > > >
> >> > > > /Users/aron/sandbox/petsc/arch-darwin-c-debug/bin/mpif90 -c  -Wall
> >> > > > -Wno-unused-variable -g  -I/Users/aron/sandbox/petsc/include
> >> > > > -I/Users/aron/sandbox/petsc/arch-darwin-c-debug/include    -o
> >> ex5f.o ex5f.F
> >> > > > Warning: Nonconforming tab character in column 1 of line 2757
> >> > > > Warning: Nonconforming tab character in column 1 of line 4937
> >> > > > Warning: Nonconforming tab character in column 1 of line 6914
> >> > > > Warning: Nonconforming tab character in column 1 of line 8887
> >> > > > Warning: Nonconforming tab character in column 1 of line 10901
> >> > > > /Users/aron/sandbox/petsc/arch-darwin-c-debug/bin/mpif90
> >> > > > -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress
> >> > > > -Wl,-commons,use_dylibs -Wl,-search_paths_first
> >> > > > -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress
> >> > > > -Wl,-commons,use_dylibs -Wl,-search_paths_first   -Wall
> >> > > > -Wno-unused-variable -g  -o ex5f ex5f.o
> >> > > > -L/Users/aron/sandbox/petsc/arch-darwin-c-debug/lib  -lpetsc
> >> > > > -L/usr/X11R6/lib -lX11 -lpthread -llapack -lblas
> >> > > > -L/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64
> >> > > > -L/usr/lib/i686-apple-darwin10/4.2.1
> >> > > > -L/usr/lib/gcc/i686-apple-darwin10/4.2.1 -lmpichf90 -lgfortran
> >> > > >
> >>
> -L/usr/local/Cellar/gfortran/4.2.4-5664/lib/gcc/i686-apple-darwin10/4.2.1/x86_64
> >> > > >
> >>
> -L/usr/local/Cellar/gfortran/4.2.4-5664/lib/gcc/i686-apple-darwin10/4.2.1
> >> > > > -L/usr/local/Cellar/gfortran/4.2.4-5664/lib/gcc
> >> > > > -L/usr/local/Cellar/gfortran/4.2.4-5664/lib -ldl -lpmpich -lmpich
> >> -lopa
> >> > > > -lmpl -lpthread -lSystem -ldl
> >> > > > Undefined symbols:
> >> > > >   "_dmlocaltoglobalbegin_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > >   "_dmgetlocalvector_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > >   "_matassemblybegin_", referenced from:
> >> > > >       _formjacobianlocal_ in ex5f.o
> >> > > >   "_dmdestroy_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_snessolve_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_vecrestorearray_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > >   "_vecdestroy_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_matsetvalueslocal_", referenced from:
> >> > > >       _formjacobianlocal_ in ex5f.o
> >> > > >       _formjacobianlocal_ in ex5f.o
> >> > > >   "_matassemblyend_", referenced from:
> >> > > >       _formjacobianlocal_ in ex5f.o
> >> > > >   "_dmdagetcorners_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmdasetlocaljacobian_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_petscinitialize_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmcreateglobalvector_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_petscfinalize_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_snessetdm_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_snessetfromoptions_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_snescreate_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_snesdestroy_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmdacreate2d_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_vecduplicate_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_petsclogflops_", referenced from:
> >> > > >       _formfunctionlocal_ in ex5f.o
> >> > > >   "_dmdagetghostcorners_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmrestorelocalvector_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > >   "_snesgetiterationnumber_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmlocaltoglobalend_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > >   "_dmdasetlocalfunction_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_dmdagetinfo_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_petscoptionsgetreal_", referenced from:
> >> > > >       _MAIN__ in ex5f.o
> >> > > >   "_vecgetarray_", referenced from:
> >> > > >       _forminitialguess_ in ex5f.o
> >> > > > ld: symbol(s) not found
> >> > > > collect2: ld returned 1 exit status
> >> > > > make[3]: [ex5f] Error 1 (ignored)
> >> > > >
> >> > > > On Sun, Oct 7, 2012 at 7:29 PM, Satish Balay <
> >> petsc-maint at mcs.anl.gov>wrote:
> >> > > >
> >> > > > > Hm - nightlybuilds use --download-mpich=1 - but I don't see this
> >> error
> >> > > > > on OSX build.
> >> > > > >
> >> > > > > wrt binsection - the following worked - the last time I tried.
> >> > > > >
> >> > > > > http://www.mcs.anl.gov/petsc/documentation/faq.html#bisect
> >> > > > >
> >> > > > > Satish
> >> > > > >
> >> > > > > On Sun, 7 Oct 2012, Aron Ahmadia wrote:
> >> > > > >
> >> > > > > > reproduced with --download-mpich=1
> >> > > > > >
> >> > > > > > how the heck do you guys bisect with two independent repos?
> >> > > > > >
> >> > > > > > A
> >> > > > > >
> >> > > > > > On Sun, Oct 7, 2012 at 6:28 PM, Aron Ahmadia <
> aron at ahmadia.net>
> >> wrote:
> >> > > > > >
> >> > > > > > > I'm able to reproduce with shared libraries enabled and
> >> disabled.  Your
> >> > > > > > > nightly logs aren't indicating failures as far as I can
> tell.
> >> > > > > > >
> >> > > > > > > changeset:   24541:729963bc657c
> >> > > > > > > tag:         tip
> >> > > > > > > user:        Stefano Zampini <stefano.zampini at gmail.com>
> >> > > > > > > date:        Sat Oct 06 13:39:31 2012 +0200
> >> > > > > > > summary:     Rearranged some deallocations when building
> >> FETIDP mat.
> >> > > > > > > (same failure with 2 processes), I'm looking into whether
> any
> >> of the
> >> > > > > > > specific configure options (python/shared libraries)
> triggers
> >> the
> >> > > > > failure.
> >> > > > > > >
> >> > > > > > > ~/s/petsc ❯❯❯ make PETSC_DIR=/Users/aron/sandbox/petsc
> >> > > > > > > PETSC_ARCH=arch-darwin-c-debug test
> >> > > > > > > Running test examples to verify correct installation
> >> > > > > > > Using PETSC_DIR=/Users/aron/sandbox/petsc and
> >> > > > > > > PETSC_ARCH=arch-darwin-c-debug
> >> > > > > > > Possible error running C/C++
> src/snes/examples/tutorials/ex19
> >> with 1
> >> > > > > MPI
> >> > > > > > > process
> >> > > > > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >> > > > > > > [peregrine:31992] *** Process received signal ***
> >> > > > > > > [peregrine:31992] Signal: Segmentation fault (11)
> >> > > > > > > [peregrine:31992] Signal code: Address not mapped (1)
> >> > > > > > > [peregrine:31992] Failing at address: 0x440000b0
> >> > > > > > > [peregrine:31992] [ 0] 2   libSystem.B.dylib
> >> > > > > > > 0x00007fff846391ba _sigtramp + 26
> >> > > > > > > [peregrine:31992] [ 1] 3   ???
> >> > > > > > > 0x0000000101434fd0 0x0 + 4316155856
> >> > > > > > > [peregrine:31992] [ 2] 4   libpetsc.dylib
> >> > > > > > >  0x0000000100118456 PetscInitialize + 1424
> >> > > > > > > [peregrine:31992] [ 3] 5   ex19
> >> > > > > > >  0x000000010000110f main + 43
> >> > > > > > > [peregrine:31992] [ 4] 6   ex19
> >> > > > > > >  0x00000001000010dc start + 52
> >> > > > > > > [peregrine:31992] [ 5] 7   ???
> >> > > > > > > 0x0000000000000007 0x0 + 7
> >> > > > > > > [peregrine:31992] *** End of error message ***
> >> > > > > > > mpiexec noticed that job rank 0 with PID 31992 on node
> >> peregrine.local
> >> > > > > > > exited on signal 11 (Segmentation fault).
> >> > > > > > >
> >> > > > > >
> >> > > > > >
> >> > > > >
> >> > > >
> >> > > >
> >> > >
> >> > >
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > What most experimenters take for granted before they begin their
> >> experiments is infinitely more interesting than any results to which
> their
> >> experiments lead.
> >> > -- Norbert Wiener
> >>
> >>
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> > experiments is infinitely more interesting than any results to which
> their
> > experiments lead.
> > -- Norbert Wiener
> >
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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