[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
Sun Oct 7 14:16:45 CDT 2012
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
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