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

Sun Oct 7 11:36:44 CDT 2012

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).
> > > >
> > >
> > >
> >
> 
> 