May 2008 - petsc-dev - mailman3.cels.anl.gov

Re: now impossible to debug code that uses PETSc shared libraries?
by Satish Balay 03 May '08

03 May '08

On Sat, 3 May 2008, Satish Balay wrote: > On Fri, 2 May 2008, Barry Smith wrote: > > > apple > > Appears to work fine on 10.4 ppc machine - I have access to. Also works on 10.4 Intel machine Satish -------------------------------------------- videh:~/petsc-dev/src/ksp/ksp/examples/tutorials balay$ ls $PETSC_DIR/$PETSC_ARCH/lib foo libpetsc.dylib libpetscdm.dylib libpetscmat.dylib libpetscts.dylib libmpiuni.a libpetsccontrib.dylib libpetscksp.dylib libpetscsnes.dylib libpetscvec.dylib videh:~/petsc-dev/src/ksp/ksp/examples/tutorials balay$ make ex2 gcc -o ex2.o -c -fPIC -Wall -Wwrite-strings -Wno-long-double -Wno-strict-aliasing -g3 -I/Users/balay/petsc-dev/src/dm/mesh/sieve -I/Users/balay/petsc-dev -I/Users/balay/petsc-dev/darwin8.11.1-c-debug/include -I/Users/balay/petsc-dev/include -I/Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/include -I/Users/balay/petsc-dev/include/mpiuni -D__SDIR__="src/ksp/ksp/examples/tutorials/" ex2.c gcc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -fPIC -Wall -Wwrite-strings -Wno-long-double -Wno-strict-aliasing -g3 -o ex2 ex2.o -L/Users/balay/petsc-dev/darwin8.11.1-c-debug/lib -L/Users/balay/petsc-dev/darwin8.11.1-c-debug/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -L/usr/X11R6/lib -lX11 -L/Users/balay/petsc-dev/darwin8.11.1-c-debug/lib -L/Users/balay/petsc-dev/darwin8.11.1-c-debug/lib -lmpiuni -llapack -lblas /bin/rm -f ex2.o videh:~/petsc-dev/src/ksp/ksp/examples/tutorials balay$ gdb ex2 GNU gdb 6.3.50-20050815 (Apple version gdb-573) (Fri Oct 20 15:50:43 GMT 2006) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-apple-darwin"...Reading symbols for shared libraries .......... done (gdb) b MatMult Breakpoint 1 at 0x184cfe: file matrix.c, line 1687. (gdb) r Starting program: /Users/balay/petsc-dev/src/ksp/ksp/examples/tutorials/ex2 Reading symbols for shared libraries ..+.+++++ done Breakpoint 1 at 0x118cd0c: file matrix.c, line 1690. Breakpoint 1, MatMult (mat=0x1808f30, x=0x180b930, y=0x180fb30) at matrix.c:1690 1690 PetscFunctionBegin; (gdb) where #0 MatMult (mat=0x1808f30, x=0x180b930, y=0x180fb30) at matrix.c:1690 #1 0x00002746 in main (argc=1, args=0xbffffae0) at ex2.c:141 (gdb) list 1685 @*/ 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) 1687 { 1688 PetscErrorCode ierr; 1689 1690 PetscFunctionBegin; 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); 1692 PetscValidType(mat,1); 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); (gdb)

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Re: now impossible to debug code that uses PETSc shared libraries?
by Satish Balay 03 May '08

03 May '08

On Fri, 2 May 2008, Barry Smith wrote: > apple Appears to work fine on 10.4 ppc machine - I have access to. Satish ---------------------------------------------- [icrunch:ksp/examples/tutorials] petsc% ls $PETSC_DIR/$PETSC_ARCH/lib foo/ libmpichf90.a libpetscdm.dylib libpetscsnes.dylib libpmpich.a libfmpich.a libpetsc.dylib* libpetscksp.dylib libpetscts.dylib mpich2-ch3.pc libmpich.a libpetsccontrib.dylib libpetscmat.dylib libpetscvec.dylib pkgconfig/ [icrunch:ksp/examples/tutorials] petsc% make ex2 /sandbox/petsc/petsc-dev/macosx-gnu/bin/mpicc -o ex2.o -c -fPIC -Wall -Wwrite-strings -Wno-long-double -Wno-strict-aliasing -g3 -I/sandbox/petsc/petsc-dev/src/dm/mesh/sieve -I/sandbox/petsc/petsc-dev -I/sandbox/petsc/petsc-dev/macosx-gnu/include -I/sandbox/petsc/petsc-dev/include -I/usr/X11R6/include -I/sandbox/petsc/petsc-dev/macosx-gnu/include -I. -I/sandbox/petsc/petsc-dev/macosx-gnu/include -I/sandbox/petsc/petsc-dev/macosx-gnu/include -D__SDIR__="src/ksp/ksp/examples/tutorials/" ex2.c /sandbox/petsc/petsc-dev/macosx-gnu/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -fPIC -Wall -Wwrite-strings -Wno-long-double -Wno-strict-aliasing -g3 -o ex2 ex2.o -L/sandbox/petsc/petsc-dev/macosx-gnu/lib -L/sandbox/petsc/petsc-dev/macosx-gnu/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -L/usr/X11R6/lib -lX11 /System/Library/Frameworks/vecLib.framework/vecLib -L/sandbox/petsc/petsc-dev/macosx-gnu/lib -L/usr/lib/gcc/powerpc-apple-darwin8/4.0.1 -ldl -lpmpich -lmpich -lSystemStubs -lSystem -lmpichf90 -lgfortranbegin -lgfortran -L/usr/local/gfortran/lib/gcc/powerpc-apple-darwin7.9.0/4.2.0 -L/usr/local/gfortran/lib -lgcc_s.10.4 -lmx -ldl -lpmpich -lmpich -lSystemStubs -lSystem -ldl /usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding may result in errors or different symbols being used symbol _MPI_Comm_rank used from dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetsc.dylib(single module) not from earlier dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetscdm.dylib(single module) symbol _MPI_Comm_size used from dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetsc.dylib(single module) not from earlier dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetscdm.dylib(single module) symbol _MPI_Comm_size used from dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetsc.dylib(single module) not from earlier dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetscvec.dylib(single module) symbol _MPI_Allreduce used from dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetsc.dylib(single module) not from earlier dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetscvec.dylib(single module) symbol _MPI_Comm_compare used from dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetsc.dylib(single module) not from earlier dynamic library /sandbox/petsc/petsc-dev/macosx-gnu/lib/libpetscdm.dylib(single module) /bin/rm -f ex2.o [icrunch:ksp/examples/tutorials] petsc% gdb ex2 GNU gdb 6.1-20040303 (Apple version gdb-434) (Wed Nov 2 17:28:16 GMT 2005) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "powerpc-apple-darwin"...Reading symbols for shared libraries ............ done (gdb) b MatMult Breakpoint 1 at 0x1a9798: file matrix.c, line 1687. (gdb) r Starting program: /sandbox/petsc/petsc-dev/src/ksp/ksp/examples/tutorials/ex2 Reading symbols for shared libraries .++.+....+++++ done Breakpoint 1 at 0x11b17c0: file matrix.c, line 1690. Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Breakpoint 1, MatMult (mat=0x200d130, x=0x2017d30, y=0x2018930) at matrix.c:1690 1690 PetscFunctionBegin; (gdb) where #0 MatMult (mat=0x200d130, x=0x2017d30, y=0x2018930) at matrix.c:1690 #1 0x00002ff8 in main (argc=1, args=0xbffff8a8) at ex2.c:141 (gdb) list 1685 @*/ 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) 1687 { 1688 PetscErrorCode ierr; 1689 1690 PetscFunctionBegin; 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); 1692 PetscValidType(mat,1); 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); (gdb)

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Re: now impossible to debug code that uses PETSc shared libraries?
by Aron Ahmadia 02 May '08

02 May '08

this fixed yet? I can test out a petsc-dev build on my MBP and see if I've got the same issues. ~A On Fri, May 2, 2008 at 2:21 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > apple > > > On May 1, 2008, at 11:23 AM, Satish Balay wrote: > > What machine is this? > > > > Its been working forever for me on linux. > > > > Satish > > > > --------------------------------------------------- > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ls > > /home/balay/spetsc/asterix/lib/ > > foo libpetscdm.so libpetscmat.so libpetsc.so > > libpetscvec.so > > libpetsccontrib.so libpetscksp.so libpetscsnes.so libpetscts.so > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials> > > > > <removed .a files> > > > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ldd ex2 > > linux-gate.so.1 => (0x00110000) > > libpetscksp.so => /home/balay/spetsc/asterix/lib/libpetscksp.so > > (0x00111000) > > libpetscdm.so => /home/balay/spetsc/asterix/lib/libpetscdm.so > > (0x00374000) > > libpetscmat.so => /home/balay/spetsc/asterix/lib/libpetscmat.so > > (0x00493000) > > libpetscvec.so => /home/balay/spetsc/asterix/lib/libpetscvec.so > > (0x00838000) > > libpetsc.so => /home/balay/spetsc/asterix/lib/libpetsc.so > > (0x00a55000) > > libX11.so.6 => /usr/lib/libX11.so.6 (0x00bf9000) > > liblapack.so.3 => /usr/lib/atlas/liblapack.so.3 (0x00cf5000) > > libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x02a29000) > > libm.so.6 => /lib/libm.so.6 (0x009a0000) > > libpthread.so.0 => /lib/libpthread.so.0 (0x009c9000) > > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00a0e000) > > libgfortran.so.1 => /usr/lib/libgfortran.so.1 (0x0600e000) > > libc.so.6 => /lib/libc.so.6 (0x078a3000) > > libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x009e2000) > > libxcb.so.1 => /usr/lib/libxcb.so.1 (0x009e4000) > > libdl.so.2 => /lib/libdl.so.2 (0x00a00000) > > /lib/ld-linux.so.2 (0x00a38000) > > libXau.so.6 => /usr/lib/libXau.so.6 (0x00a05000) > > libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00a08000) > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>gdb ex2 > > GNU gdb Red Hat Linux (6.6-45.fc8rh) > > Copyright (C) 2006 Free Software Foundation, Inc. > > GDB is free software, covered by the GNU General Public License, and you > > are > > welcome to change it and/or distribute copies of it under certain > > conditions. > > Type "show copying" to see the conditions. > > There is absolutely no warranty for GDB. Type "show warranty" for > > details. > > This GDB was configured as "i386-redhat-linux-gnu"... > > Using host libthread_db library "/lib/libthread_db.so.1". > > (gdb) b MatMult > > Function "MatMult" not defined. > > Make breakpoint pending on future shared library load? (y or [n]) y > > Breakpoint 1 (MatMult) pending. > > (gdb) r > > Starting program: > > /home/balay/hg-repo/petsc-dev/src/ksp/ksp/examples/tutorials/ex2 > > [Thread debugging using libthread_db enabled] > > Breakpoint 2 at 0x6250f3: file matrix.c, line 1690. > > Pending breakpoint "MatMult" resolved > > [New Thread -1208318272 (LWP 30748)] > > [Switching to Thread -1208318272 (LWP 30748)] > > > > Breakpoint 2, MatMult (mat=0x9aabc58, x=0x9a9c888, y=0x9a9d698) at > > matrix.c:1690 > > 1690 PetscFunctionBegin; > > Missing separate debuginfos, use: debuginfo-install atlas.i386 gcc.i386 > > glibc.i686 libX11.i386 libXau.i386 libXdmcp.i386 libxcb.i386 > > (gdb) list > > 1685 @*/ > > 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) > > 1687 { > > 1688 PetscErrorCode ierr; > > 1689 > > 1690 PetscFunctionBegin; > > 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); > > 1692 PetscValidType(mat,1); > > 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); > > 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); > > (gdb) > > > > On Thu, 1 May 2008, Barry Smith wrote: > > > > > > > It seems to now be impossible to debug in code that uses PETSc shared > > > libraries > > > > > > fi; \ > > > if [ "$$flag" != "" ]; then \ > > > echo "building $$LIBNAME.${SL_LINKER_SUFFIX}"; \ > > > ${RM} -f ${INSTALL_LIB_DIR}/tmp-petsc-shlib/*; \ > > > cd ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > > > ${AR} x > > > ${INSTALL_LIB_DIR}/$$LIBNAME.${AR_LIB_SUFFIX}; \ > > > cd $$cwd;\ > > > ${OMAKE} LIBNAME=$$LIBNAME > > > SHARED_LIBRARY_TMPDIR=${INSTALL_LIB_DIR}/tmp-petsc-shlib shared_arch; > > > \ > > > fi; \ > > > fi; \ > > > done; \ > > > ${RM} -rf ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > > > fi > > > > > > > > > In the debugger, of course, one gets > > > warning: Could not find object file > > > "/Users/bsmith/Src/petsc-dev-for-fixes/shit/lib/tmp-petsc-shlib/bvec2.o" > > > - no > > > debug information available for "bvec2.c". > > > > > > > > > since the .o files are removed the debugger cannot find any debug > > > information. > > > > > > Is this intentional? Seems pretty terrible to give up debugging just > > > to use > > > shared libraries. > > > > > > Barry > > > > > > > > > > > > > > >

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Re: now impossible to debug code that uses PETSc shared libraries?
by Barry Smith 02 May '08

02 May '08

apple On May 1, 2008, at 11:23 AM, Satish Balay wrote: > What machine is this? > > Its been working forever for me on linux. > > Satish > > --------------------------------------------------- > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ls /home/ > balay/spetsc/asterix/lib/ > foo libpetscdm.so libpetscmat.so libpetsc.so > libpetscvec.so > libpetsccontrib.so libpetscksp.so libpetscsnes.so libpetscts.so > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials> > > <removed .a files> > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ldd ex2 > linux-gate.so.1 => (0x00110000) > libpetscksp.so => /home/balay/spetsc/asterix/lib/ > libpetscksp.so (0x00111000) > libpetscdm.so => /home/balay/spetsc/asterix/lib/libpetscdm.so > (0x00374000) > libpetscmat.so => /home/balay/spetsc/asterix/lib/ > libpetscmat.so (0x00493000) > libpetscvec.so => /home/balay/spetsc/asterix/lib/ > libpetscvec.so (0x00838000) > libpetsc.so => /home/balay/spetsc/asterix/lib/libpetsc.so > (0x00a55000) > libX11.so.6 => /usr/lib/libX11.so.6 (0x00bf9000) > liblapack.so.3 => /usr/lib/atlas/liblapack.so.3 (0x00cf5000) > libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x02a29000) > libm.so.6 => /lib/libm.so.6 (0x009a0000) > libpthread.so.0 => /lib/libpthread.so.0 (0x009c9000) > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00a0e000) > libgfortran.so.1 => /usr/lib/libgfortran.so.1 (0x0600e000) > libc.so.6 => /lib/libc.so.6 (0x078a3000) > libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x009e2000) > libxcb.so.1 => /usr/lib/libxcb.so.1 (0x009e4000) > libdl.so.2 => /lib/libdl.so.2 (0x00a00000) > /lib/ld-linux.so.2 (0x00a38000) > libXau.so.6 => /usr/lib/libXau.so.6 (0x00a05000) > libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00a08000) > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>gdb ex2 > GNU gdb Red Hat Linux (6.6-45.fc8rh) > Copyright (C) 2006 Free Software Foundation, Inc. > GDB is free software, covered by the GNU General Public License, and > you are > welcome to change it and/or distribute copies of it under certain > conditions. > Type "show copying" to see the conditions. > There is absolutely no warranty for GDB. Type "show warranty" for > details. > This GDB was configured as "i386-redhat-linux-gnu"... > Using host libthread_db library "/lib/libthread_db.so.1". > (gdb) b MatMult > Function "MatMult" not defined. > Make breakpoint pending on future shared library load? (y or [n]) y > Breakpoint 1 (MatMult) pending. > (gdb) r > Starting program: /home/balay/hg-repo/petsc-dev/src/ksp/ksp/examples/ > tutorials/ex2 > [Thread debugging using libthread_db enabled] > Breakpoint 2 at 0x6250f3: file matrix.c, line 1690. > Pending breakpoint "MatMult" resolved > [New Thread -1208318272 (LWP 30748)] > [Switching to Thread -1208318272 (LWP 30748)] > > Breakpoint 2, MatMult (mat=0x9aabc58, x=0x9a9c888, y=0x9a9d698) at > matrix.c:1690 > 1690 PetscFunctionBegin; > Missing separate debuginfos, use: debuginfo-install atlas.i386 > gcc.i386 glibc.i686 libX11.i386 libXau.i386 libXdmcp.i386 libxcb.i386 > (gdb) list > 1685 @*/ > 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) > 1687 { > 1688 PetscErrorCode ierr; > 1689 > 1690 PetscFunctionBegin; > 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); > 1692 PetscValidType(mat,1); > 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); > 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); > (gdb) > > On Thu, 1 May 2008, Barry Smith wrote: > >> >> It seems to now be impossible to debug in code that uses PETSc shared >> libraries >> >> fi; \ >> if [ "$$flag" != "" ]; then \ >> echo "building $$LIBNAME.${SL_LINKER_SUFFIX}"; \ >> ${RM} -f ${INSTALL_LIB_DIR}/tmp-petsc-shlib/*; \ >> cd ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ >> ${AR} x ${INSTALL_LIB_DIR}/$$LIBNAME.${AR_LIB_SUFFIX}; \ >> cd $$cwd;\ >> ${OMAKE} LIBNAME=$$LIBNAME >> SHARED_LIBRARY_TMPDIR=${INSTALL_LIB_DIR}/tmp-petsc-shlib >> shared_arch; \ >> fi; \ >> fi; \ >> done; \ >> ${RM} -rf ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ >> fi >> >> >> In the debugger, of course, one gets >> warning: Could not find object file >> "/Users/bsmith/Src/petsc-dev-for-fixes/shit/lib/tmp-petsc-shlib/ >> bvec2.o" - no >> debug information available for "bvec2.c". >> >> >> since the .o files are removed the debugger cannot find any debug >> information. >> >> Is this intentional? Seems pretty terrible to give up debugging >> just to use >> shared libraries. >> >> Barry >> >> >> >

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Re: now impossible to debug code that uses PETSc shared libraries?
by Matthew Knepley 01 May '08

01 May '08

I can also debug just fine or I would scream bloody murder. Matt On Thu, May 1, 2008 at 10:23 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: > What machine is this? > > Its been working forever for me on linux. > > Satish > > --------------------------------------------------- > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ls /home/balay/spetsc/asterix/lib/ > foo libpetscdm.so libpetscmat.so libpetsc.so libpetscvec.so > libpetsccontrib.so libpetscksp.so libpetscsnes.so libpetscts.so > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials> > > <removed .a files> > > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ldd ex2 > linux-gate.so.1 => (0x00110000) > libpetscksp.so => /home/balay/spetsc/asterix/lib/libpetscksp.so (0x00111000) > libpetscdm.so => /home/balay/spetsc/asterix/lib/libpetscdm.so (0x00374000) > libpetscmat.so => /home/balay/spetsc/asterix/lib/libpetscmat.so (0x00493000) > libpetscvec.so => /home/balay/spetsc/asterix/lib/libpetscvec.so (0x00838000) > libpetsc.so => /home/balay/spetsc/asterix/lib/libpetsc.so (0x00a55000) > libX11.so.6 => /usr/lib/libX11.so.6 (0x00bf9000) > liblapack.so.3 => /usr/lib/atlas/liblapack.so.3 (0x00cf5000) > libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x02a29000) > libm.so.6 => /lib/libm.so.6 (0x009a0000) > libpthread.so.0 => /lib/libpthread.so.0 (0x009c9000) > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00a0e000) > libgfortran.so.1 => /usr/lib/libgfortran.so.1 (0x0600e000) > libc.so.6 => /lib/libc.so.6 (0x078a3000) > libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x009e2000) > libxcb.so.1 => /usr/lib/libxcb.so.1 (0x009e4000) > libdl.so.2 => /lib/libdl.so.2 (0x00a00000) > /lib/ld-linux.so.2 (0x00a38000) > libXau.so.6 => /usr/lib/libXau.so.6 (0x00a05000) > libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00a08000) > asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>gdb ex2 > GNU gdb Red Hat Linux (6.6-45.fc8rh) > Copyright (C) 2006 Free Software Foundation, Inc. > GDB is free software, covered by the GNU General Public License, and you are > welcome to change it and/or distribute copies of it under certain conditions. > Type "show copying" to see the conditions. > There is absolutely no warranty for GDB. Type "show warranty" for details. > This GDB was configured as "i386-redhat-linux-gnu"... > Using host libthread_db library "/lib/libthread_db.so.1". > (gdb) b MatMult > Function "MatMult" not defined. > Make breakpoint pending on future shared library load? (y or [n]) y > Breakpoint 1 (MatMult) pending. > (gdb) r > Starting program: /home/balay/hg-repo/petsc-dev/src/ksp/ksp/examples/tutorials/ex2 > [Thread debugging using libthread_db enabled] > Breakpoint 2 at 0x6250f3: file matrix.c, line 1690. > Pending breakpoint "MatMult" resolved > [New Thread -1208318272 (LWP 30748)] > [Switching to Thread -1208318272 (LWP 30748)] > > Breakpoint 2, MatMult (mat=0x9aabc58, x=0x9a9c888, y=0x9a9d698) at matrix.c:1690 > 1690 PetscFunctionBegin; > Missing separate debuginfos, use: debuginfo-install atlas.i386 gcc.i386 glibc.i686 libX11.i386 libXau.i386 libXdmcp.i386 libxcb.i386 > (gdb) list > 1685 @*/ > 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) > 1687 { > 1688 PetscErrorCode ierr; > 1689 > 1690 PetscFunctionBegin; > 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); > 1692 PetscValidType(mat,1); > 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); > 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); > (gdb) > > > > On Thu, 1 May 2008, Barry Smith wrote: > > > > > It seems to now be impossible to debug in code that uses PETSc shared > > libraries > > > > fi; \ > > if [ "$$flag" != "" ]; then \ > > echo "building $$LIBNAME.${SL_LINKER_SUFFIX}"; \ > > ${RM} -f ${INSTALL_LIB_DIR}/tmp-petsc-shlib/*; \ > > cd ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > > ${AR} x ${INSTALL_LIB_DIR}/$$LIBNAME.${AR_LIB_SUFFIX}; \ > > cd $$cwd;\ > > ${OMAKE} LIBNAME=$$LIBNAME > > SHARED_LIBRARY_TMPDIR=${INSTALL_LIB_DIR}/tmp-petsc-shlib shared_arch; \ > > fi; \ > > fi; \ > > done; \ > > ${RM} -rf ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > > fi > > > > > > In the debugger, of course, one gets > > warning: Could not find object file > > "/Users/bsmith/Src/petsc-dev-for-fixes/shit/lib/tmp-petsc-shlib/bvec2.o" - no > > debug information available for "bvec2.c". > > > > > > since the .o files are removed the debugger cannot find any debug information. > > > > Is this intentional? Seems pretty terrible to give up debugging just to use > > shared libraries. > > > > Barry > > > > > > > > -- 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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Re: now impossible to debug code that uses PETSc shared libraries?
by Satish Balay 01 May '08

01 May '08

What machine is this? Its been working forever for me on linux. Satish --------------------------------------------------- asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ls /home/balay/spetsc/asterix/lib/ foo libpetscdm.so libpetscmat.so libpetsc.so libpetscvec.so libpetsccontrib.so libpetscksp.so libpetscsnes.so libpetscts.so asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials> <removed .a files> asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>ldd ex2 linux-gate.so.1 => (0x00110000) libpetscksp.so => /home/balay/spetsc/asterix/lib/libpetscksp.so (0x00111000) libpetscdm.so => /home/balay/spetsc/asterix/lib/libpetscdm.so (0x00374000) libpetscmat.so => /home/balay/spetsc/asterix/lib/libpetscmat.so (0x00493000) libpetscvec.so => /home/balay/spetsc/asterix/lib/libpetscvec.so (0x00838000) libpetsc.so => /home/balay/spetsc/asterix/lib/libpetsc.so (0x00a55000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00bf9000) liblapack.so.3 => /usr/lib/atlas/liblapack.so.3 (0x00cf5000) libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x02a29000) libm.so.6 => /lib/libm.so.6 (0x009a0000) libpthread.so.0 => /lib/libpthread.so.0 (0x009c9000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00a0e000) libgfortran.so.1 => /usr/lib/libgfortran.so.1 (0x0600e000) libc.so.6 => /lib/libc.so.6 (0x078a3000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x009e2000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x009e4000) libdl.so.2 => /lib/libdl.so.2 (0x00a00000) /lib/ld-linux.so.2 (0x00a38000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00a05000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00a08000) asterix:/home/balay/spetsc/src/ksp/ksp/examples/tutorials>gdb ex2 GNU gdb Red Hat Linux (6.6-45.fc8rh) Copyright (C) 2006 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-redhat-linux-gnu"... Using host libthread_db library "/lib/libthread_db.so.1". (gdb) b MatMult Function "MatMult" not defined. Make breakpoint pending on future shared library load? (y or [n]) y Breakpoint 1 (MatMult) pending. (gdb) r Starting program: /home/balay/hg-repo/petsc-dev/src/ksp/ksp/examples/tutorials/ex2 [Thread debugging using libthread_db enabled] Breakpoint 2 at 0x6250f3: file matrix.c, line 1690. Pending breakpoint "MatMult" resolved [New Thread -1208318272 (LWP 30748)] [Switching to Thread -1208318272 (LWP 30748)] Breakpoint 2, MatMult (mat=0x9aabc58, x=0x9a9c888, y=0x9a9d698) at matrix.c:1690 1690 PetscFunctionBegin; Missing separate debuginfos, use: debuginfo-install atlas.i386 gcc.i386 glibc.i686 libX11.i386 libXau.i386 libXdmcp.i386 libxcb.i386 (gdb) list 1685 @*/ 1686 PetscErrorCode PETSCMAT_DLLEXPORT MatMult(Mat mat,Vec x,Vec y) 1687 { 1688 PetscErrorCode ierr; 1689 1690 PetscFunctionBegin; 1691 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); 1692 PetscValidType(mat,1); 1693 PetscValidHeaderSpecific(x,VEC_COOKIE,2); 1694 PetscValidHeaderSpecific(y,VEC_COOKIE,3); (gdb) On Thu, 1 May 2008, Barry Smith wrote: > > It seems to now be impossible to debug in code that uses PETSc shared > libraries > > fi; \ > if [ "$$flag" != "" ]; then \ > echo "building $$LIBNAME.${SL_LINKER_SUFFIX}"; \ > ${RM} -f ${INSTALL_LIB_DIR}/tmp-petsc-shlib/*; \ > cd ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > ${AR} x ${INSTALL_LIB_DIR}/$$LIBNAME.${AR_LIB_SUFFIX}; \ > cd $$cwd;\ > ${OMAKE} LIBNAME=$$LIBNAME > SHARED_LIBRARY_TMPDIR=${INSTALL_LIB_DIR}/tmp-petsc-shlib shared_arch; \ > fi; \ > fi; \ > done; \ > ${RM} -rf ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ > fi > > > In the debugger, of course, one gets > warning: Could not find object file > "/Users/bsmith/Src/petsc-dev-for-fixes/shit/lib/tmp-petsc-shlib/bvec2.o" - no > debug information available for "bvec2.c". > > > since the .o files are removed the debugger cannot find any debug information. > > Is this intentional? Seems pretty terrible to give up debugging just to use > shared libraries. > > Barry > > >

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now impossible to debug code that uses PETSc shared libraries?
by Barry Smith 01 May '08

01 May '08

It seems to now be impossible to debug in code that uses PETSc shared libraries fi; \ if [ "$$flag" != "" ]; then \ echo "building $$LIBNAME.${SL_LINKER_SUFFIX}"; \ ${RM} -f ${INSTALL_LIB_DIR}/tmp-petsc-shlib/*; \ cd ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ ${AR} x ${INSTALL_LIB_DIR}/$$LIBNAME.${AR_LIB_SUFFIX}; \ cd $$cwd;\ ${OMAKE} LIBNAME=$$LIBNAME SHARED_LIBRARY_TMPDIR=$ {INSTALL_LIB_DIR}/tmp-petsc-shlib shared_arch; \ fi; \ fi; \ done; \ ${RM} -rf ${INSTALL_LIB_DIR}/tmp-petsc-shlib; \ fi In the debugger, of course, one gets warning: Could not find object file "/Users/bsmith/Src/petsc-dev-for- fixes/shit/lib/tmp-petsc-shlib/bvec2.o" - no debug information available for "bvec2.c". since the .o files are removed the debugger cannot find any debug information. Is this intentional? Seems pretty terrible to give up debugging just to use shared libraries. Barry

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