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. 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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