[petsc-dev] [petsc-maint #135017] Re: petsc-dev/buildsystem is broken on OS X.6+openmpi-nofortran
Aron Ahmadia
aron at ahmadia.net
Sun Oct 7 11:32:24 CDT 2012
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).
> > >
> >
> >
>
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