July 2012 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] How To: petsc binary to matrix market format
by Dave Nystrom 01 Jul '12

01 Jul '12

Jed Brown writes: > On Sat, Jun 30, 2012 at 9:32 PM, Dave Nystrom <dnystrom1(a)comcast.net> wrote: > > > Thanks. I don't have access or experience with Matlab so that seems not a > > good option. I'm fairly new to Python and have never done anything with > > the > > petsc python interface. But that could be an option. Once python reads > > in a > > petsc binary matrix, does it then have a function to write out the matrix > > in > > matrix market format? Or would I need to write the python code to do that? > > > > Scipy has routines to write matrix market files. > > PETSc intentionally does not provide this routine because MatrixMarket is > such a terrible format. We will give you the gun, but if you want to bolt > it to your foot, you have to find your own bolts. Can't really relate to the last comment. My interest in MatrixMarket format is not to shoot myself in the foot. Rather, it is because of 2 different reasons. One is that 2 different vendors have asked for some sample matrices from the problems I solve and their format preference is MatrixMarket. Second is that I would like to test some of my matrices with the new version of cholmod that has gpu support since I have seen good performance with other matrices and I have not been able to get cholmod to work with cublas in petsc yet. Petsc crashes when I try to call cholmod with its cublas support. However, cholmod has a test program that can read and solve systems which are input via MatrixMarket format. I certainly don't want to shoot myself in the foot or use MatrixMarket format for any sort of production scenario. Thanks for the suggestions. I'll look into exploring python for this task. Dave

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Re: [petsc-dev] simple way to use --db-attach with valgrind in parallel with mpiexec
by Jed Brown 01 Jul '12

01 Jul '12

Seems that way, it works for me on Linux. On Sat, Jun 30, 2012 at 7:40 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Both windows just disappear and program ends if I hit y or Y. Maybe a > Mac thing. > > Barry > > On Jun 30, 2012, at 7:51 PM, Jed Brown wrote: > > > Did you try this? > > > > mpiexec -n 2 xterm -e valgrind --db-attach=yes ./ex -args > > > > On Sat, Jun 30, 2012 at 4:33 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > > > Has anyone documented a simple way to run parallel programs with > mpiexec and valgrind and use the --db-attach=yes option to use the debugger > on a process to see what is going on? > > > > My simple minded attempt leads to uselessness; it tries to ask me > about using the debugger but seems to be in tty hell. > > > > Thanks > > > > Barry > > > > > > barry-smiths-macbook-pro:LuLu barrysmith$ > ~/Src/petsc-dev/arch-gnu/bin/mpiexec -n 2 valgrind --tool=memcheck > --db-attach=yes --dsymutil=yes --num-callers=20 -q ./ex26 -ts_type beuler > > --55788-- run: /usr/bin/dsymutil "./ex26" > > --55789-- run: /usr/bin/dsymutil "./ex26" > > error: No such file or directory - old dSYM file cannot be overwritten: > old: './ex26.dSYM/Contents/Resources/DWARF/ex26' > > new:'./ex26.dSYM/Contents/Resources/DWARF/ex26.x86_64'. > > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > > error: No such file or directory - old dSYM file cannot be overwritten: > old: > '/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib' > > > new:'/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib.x86_64'. > > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > > > > warning: (x86_64) > /Users/barrysmith/Src/petsc-dev/externalpackages/mpich2-1.4.1p1/lib/.tmp/wtimef.o > unable to open object file > > warning: no debug symbols in executable (-arch x86_64) > > 4x4 grid, water viscosity = 1, oil vescosity # = 1, > > connate water saturation # = 0 irreducible oil saturation # =0 > > timestep 0 time 0 > > ==55789== Use of uninitialised value of size 8 > > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== > > ==55789== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- > ==55789== Invalid read of size 8 > > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== Address 0x8 is not stack'd, malloc'd or (recently) free'd > > ==55789== > > ==55789== Conditional jump or move depends on uninitialised value(s) > > ==55789== at 0x102738F7B: signal__ (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== Conditional jump or move depends on uninitialised value(s) > > ==55789== at 0x102738FD7: sigaction (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== Conditional jump or move depends on uninitialised value(s) > > ==55789== at 0x102738FDC: sigaction (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== Conditional jump or move depends on uninitialised value(s) > > ==55789== at 0x102738FE1: sigaction (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== Syscall param sigaction(signum) contains uninitialised byte(s) > > ==55789== at 0x102739032: __sigaction (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55789== > > ==55789== > > ==55789== Process terminating with default action of signal 11 (SIGSEGV) > > ==55789== General Protection Fault > > ==55789== at 0x1027F0FC1: dyld_stub_binder (in > /usr/lib/libSystem.B.dylib) > > ==55789== by 0x101C4549F: ??? (in > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib) > > ==55789== by 0x100181B31: PetscDefaultSignalHandler (signal.c:144) > > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > > ==55789== by 0x138048EF3: ??? > > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55789== by 0x1000047A8: main (ex26.c:327) > > ==55788== Invalid read of size 8 > > ==55788== at 0x100006443: FormIFunctionLocal (ex26.c:581) > > ==55788== by 0x100007791: FormIFunction (ex26.c:680) > > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55788== by 0x1000047A8: main (ex26.c:327) > > ==55788== Address 0x1045cf920 is 1,936 bytes inside a block of size > 1,940 alloc'd > > ==55788== at 0x1000251EF: malloc (vg_replace_malloc.c:236) > > ==55788== by 0x1000CC71B: PetscMallocAlign (mal.c:37) > > ==55788== by 0x1000CDF89: PetscTrMallocDefault (mtr.c:190) > > ==55788== by 0x1002B338B: VecGetArray2d (rvector.c:1759) > > ==55788== by 0x1009430B0: DMDAVecGetArray (dagetarray.c:72) > > ==55788== by 0x100007536: FormIFunction (ex26.c:673) > > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > > ==55788== by 0x1000047A8: main (ex26.c:327) > > ==55788== > > ==55788== > > ==55788== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- > > > ===================================================================================== > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = EXIT CODE: 11 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > ================================================================================= > > > > > >

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Re: [petsc-dev] How To: petsc binary to matrix market format
by Jed Brown 01 Jul '12

01 Jul '12

On Sat, Jun 30, 2012 at 9:32 PM, Dave Nystrom <dnystrom1(a)comcast.net> wrote: > Thanks. I don't have access or experience with Matlab so that seems not a > good option. I'm fairly new to Python and have never done anything with > the > petsc python interface. But that could be an option. Once python reads > in a > petsc binary matrix, does it then have a function to write out the matrix > in > matrix market format? Or would I need to write the python code to do that? > Scipy has routines to write matrix market files. PETSc intentionally does not provide this routine because MatrixMarket is such a terrible format. We will give you the gun, but if you want to bolt it to your foot, you have to find your own bolts.

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Re: [petsc-dev] How To: petsc binary to matrix market format
by Dave Nystrom 01 Jul '12

01 Jul '12

Jed Brown writes: > On Sat, Jun 30, 2012 at 9:17 PM, Dave Nystrom <dnystrom1(a)comcast.net> wrote: > > > From the FAQ, I see that src/mat/examples/tests/ex72.c provides an example > > of > > reading in a matrix system in matrix market format and then exporting it in > > petsc sparse format for the serial case. > > > > Is there an example of how to read in a matrix system in kspviewbinary > > format > > and then write it out in matrix market format for the serial case? > > > > I suggest doing it with Python or Matlab, either of which can read PETSc > binary matrices. Thanks. I don't have access or experience with Matlab so that seems not a good option. I'm fairly new to Python and have never done anything with the petsc python interface. But that could be an option. Once python reads in a petsc binary matrix, does it then have a function to write out the matrix in matrix market format? Or would I need to write the python code to do that?

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Re: [petsc-dev] How To: petsc binary to matrix market format
by Jed Brown 01 Jul '12

01 Jul '12

On Sat, Jun 30, 2012 at 9:17 PM, Dave Nystrom <dnystrom1(a)comcast.net> wrote: > From the FAQ, I see that src/mat/examples/tests/ex72.c provides an example > of > reading in a matrix system in matrix market format and then exporting it in > petsc sparse format for the serial case. > > Is there an example of how to read in a matrix system in kspviewbinary > format > and then write it out in matrix market format for the serial case? > I suggest doing it with Python or Matlab, either of which can read PETSc binary matrices.

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How To: petsc binary to matrix market format
by Dave Nystrom 01 Jul '12

01 Jul '12

>From the FAQ, I see that src/mat/examples/tests/ex72.c provides an example of reading in a matrix system in matrix market format and then exporting it in petsc sparse format for the serial case. Is there an example of how to read in a matrix system in kspviewbinary format and then write it out in matrix market format for the serial case? Thanks, Dave

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Re: [petsc-dev] simple way to use --db-attach with valgrind in parallel with mpiexec
by Barry Smith 30 Jun '12

30 Jun '12

Both windows just disappear and program ends if I hit y or Y. Maybe a Mac thing. Barry On Jun 30, 2012, at 7:51 PM, Jed Brown wrote: > Did you try this? > > mpiexec -n 2 xterm -e valgrind --db-attach=yes ./ex -args > > On Sat, Jun 30, 2012 at 4:33 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Has anyone documented a simple way to run parallel programs with mpiexec and valgrind and use the --db-attach=yes option to use the debugger on a process to see what is going on? > > My simple minded attempt leads to uselessness; it tries to ask me about using the debugger but seems to be in tty hell. > > Thanks > > Barry > > > barry-smiths-macbook-pro:LuLu barrysmith$ ~/Src/petsc-dev/arch-gnu/bin/mpiexec -n 2 valgrind --tool=memcheck --db-attach=yes --dsymutil=yes --num-callers=20 -q ./ex26 -ts_type beuler > --55788-- run: /usr/bin/dsymutil "./ex26" > --55789-- run: /usr/bin/dsymutil "./ex26" > error: No such file or directory - old dSYM file cannot be overwritten: old: './ex26.dSYM/Contents/Resources/DWARF/ex26' > new:'./ex26.dSYM/Contents/Resources/DWARF/ex26.x86_64'. > --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > error: No such file or directory - old dSYM file cannot be overwritten: old: '/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib' > new:'/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib.x86_64'. > --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > > warning: (x86_64) /Users/barrysmith/Src/petsc-dev/externalpackages/mpich2-1.4.1p1/lib/.tmp/wtimef.o unable to open object file > warning: no debug symbols in executable (-arch x86_64) > 4x4 grid, water viscosity = 1, oil vescosity # = 1, > connate water saturation # = 0 irreducible oil saturation # =0 > timestep 0 time 0 > ==55789== Use of uninitialised value of size 8 > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== > ==55789== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- ==55789== Invalid read of size 8 > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== Address 0x8 is not stack'd, malloc'd or (recently) free'd > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738F7B: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FD7: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FDC: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FE1: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Syscall param sigaction(signum) contains uninitialised byte(s) > ==55789== at 0x102739032: __sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== > ==55789== Process terminating with default action of signal 11 (SIGSEGV) > ==55789== General Protection Fault > ==55789== at 0x1027F0FC1: dyld_stub_binder (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x101C4549F: ??? (in /Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib) > ==55789== by 0x100181B31: PetscDefaultSignalHandler (signal.c:144) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55788== Invalid read of size 8 > ==55788== at 0x100006443: FormIFunctionLocal (ex26.c:581) > ==55788== by 0x100007791: FormIFunction (ex26.c:680) > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55788== by 0x1000047A8: main (ex26.c:327) > ==55788== Address 0x1045cf920 is 1,936 bytes inside a block of size 1,940 alloc'd > ==55788== at 0x1000251EF: malloc (vg_replace_malloc.c:236) > ==55788== by 0x1000CC71B: PetscMallocAlign (mal.c:37) > ==55788== by 0x1000CDF89: PetscTrMallocDefault (mtr.c:190) > ==55788== by 0x1002B338B: VecGetArray2d (rvector.c:1759) > ==55788== by 0x1009430B0: DMDAVecGetArray (dagetarray.c:72) > ==55788== by 0x100007536: FormIFunction (ex26.c:673) > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55788== by 0x1000047A8: main (ex26.c:327) > ==55788== > ==55788== > ==55788== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- > ===================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 11 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > ================================================================================= > >

1 0

Re: [petsc-dev] simple way to use --db-attach with valgrind in parallel with mpiexec
by Jed Brown 30 Jun '12

30 Jun '12

Did you try this? mpiexec -n 2 xterm -e valgrind --db-attach=yes ./ex -args On Sat, Jun 30, 2012 at 4:33 PM, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Has anyone documented a simple way to run parallel programs with > mpiexec and valgrind and use the --db-attach=yes option to use the debugger > on a process to see what is going on? > > My simple minded attempt leads to uselessness; it tries to ask me about > using the debugger but seems to be in tty hell. > > Thanks > > Barry > > > barry-smiths-macbook-pro:LuLu barrysmith$ > ~/Src/petsc-dev/arch-gnu/bin/mpiexec -n 2 valgrind --tool=memcheck > --db-attach=yes --dsymutil=yes --num-callers=20 -q ./ex26 -ts_type beuler > --55788-- run: /usr/bin/dsymutil "./ex26" > --55789-- run: /usr/bin/dsymutil "./ex26" > error: No such file or directory - old dSYM file cannot be overwritten: > old: './ex26.dSYM/Contents/Resources/DWARF/ex26' > new:'./ex26.dSYM/Contents/Resources/DWARF/ex26.x86_64'. > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" > error: No such file or directory - old dSYM file cannot be overwritten: > old: > '/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib' > > new:'/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib.x86_64'. > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" > --55788-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > --55789-- run: /usr/bin/dsymutil > "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" > > warning: (x86_64) > /Users/barrysmith/Src/petsc-dev/externalpackages/mpich2-1.4.1p1/lib/.tmp/wtimef.o > unable to open object file > warning: no debug symbols in executable (-arch x86_64) > 4x4 grid, water viscosity = 1, oil vescosity # = 1, > connate water saturation # = 0 irreducible oil saturation # =0 > timestep 0 time 0 > ==55789== Use of uninitialised value of size 8 > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== > ==55789== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- > ==55789== Invalid read of size 8 > ==55789== at 0x100002B3C: Mobility (ex26.c:116) > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== Address 0x8 is not stack'd, malloc'd or (recently) free'd > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738F7B: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FD7: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FDC: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Conditional jump or move depends on uninitialised value(s) > ==55789== at 0x102738FE1: sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== Syscall param sigaction(signum) contains uninitialised byte(s) > ==55789== at 0x102739032: __sigaction (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) > ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55789== > ==55789== > ==55789== Process terminating with default action of signal 11 (SIGSEGV) > ==55789== General Protection Fault > ==55789== at 0x1027F0FC1: dyld_stub_binder (in > /usr/lib/libSystem.B.dylib) > ==55789== by 0x101C4549F: ??? (in > /Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib) > ==55789== by 0x100181B31: PetscDefaultSignalHandler (signal.c:144) > ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) > ==55789== by 0x138048EF3: ??? > ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) > ==55789== by 0x100007791: FormIFunction (ex26.c:680) > ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55789== by 0x1000047A8: main (ex26.c:327) > ==55788== Invalid read of size 8 > ==55788== at 0x100006443: FormIFunctionLocal (ex26.c:581) > ==55788== by 0x100007791: FormIFunction (ex26.c:680) > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55788== by 0x1000047A8: main (ex26.c:327) > ==55788== Address 0x1045cf920 is 1,936 bytes inside a block of size 1,940 > alloc'd > ==55788== at 0x1000251EF: malloc (vg_replace_malloc.c:236) > ==55788== by 0x1000CC71B: PetscMallocAlign (mal.c:37) > ==55788== by 0x1000CDF89: PetscTrMallocDefault (mtr.c:190) > ==55788== by 0x1002B338B: VecGetArray2d (rvector.c:1759) > ==55788== by 0x1009430B0: DMDAVecGetArray (dagetarray.c:72) > ==55788== by 0x100007536: FormIFunction (ex26.c:673) > ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) > ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) > ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) > ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) > ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) > ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) > ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) > ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) > ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) > ==55788== by 0x1000047A8: main (ex26.c:327) > ==55788== > ==55788== > ==55788== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- > > ===================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 11 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > ================================================================================= > >

1 0

simple way to use --db-attach with valgrind in parallel with mpiexec
by Barry Smith 30 Jun '12

30 Jun '12

Has anyone documented a simple way to run parallel programs with mpiexec and valgrind and use the --db-attach=yes option to use the debugger on a process to see what is going on? My simple minded attempt leads to uselessness; it tries to ask me about using the debugger but seems to be in tty hell. Thanks Barry barry-smiths-macbook-pro:LuLu barrysmith$ ~/Src/petsc-dev/arch-gnu/bin/mpiexec -n 2 valgrind --tool=memcheck --db-attach=yes --dsymutil=yes --num-callers=20 -q ./ex26 -ts_type beuler --55788-- run: /usr/bin/dsymutil "./ex26" --55789-- run: /usr/bin/dsymutil "./ex26" error: No such file or directory - old dSYM file cannot be overwritten: old: './ex26.dSYM/Contents/Resources/DWARF/ex26' new:'./ex26.dSYM/Contents/Resources/DWARF/ex26.x86_64'. --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib" error: No such file or directory - old dSYM file cannot be overwritten: old: '/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib' new:'/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib.dSYM/Contents/Resources/DWARF/libpetsc.dylib.x86_64'. --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libparmetis.dylib" --55788-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" --55789-- run: /usr/bin/dsymutil "/Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libmetis.dylib" warning: (x86_64) /Users/barrysmith/Src/petsc-dev/externalpackages/mpich2-1.4.1p1/lib/.tmp/wtimef.o unable to open object file warning: no debug symbols in executable (-arch x86_64) 4x4 grid, water viscosity = 1, oil vescosity # = 1, connate water saturation # = 0 irreducible oil saturation # =0 timestep 0 time 0 ==55789== Use of uninitialised value of size 8 ==55789== at 0x100002B3C: Mobility (ex26.c:116) ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== ==55789== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- ==55789== Invalid read of size 8 ==55789== at 0x100002B3C: Mobility (ex26.c:116) ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== Address 0x8 is not stack'd, malloc'd or (recently) free'd ==55789== ==55789== Conditional jump or move depends on uninitialised value(s) ==55789== at 0x102738F7B: signal__ (in /usr/lib/libSystem.B.dylib) ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== Conditional jump or move depends on uninitialised value(s) ==55789== at 0x102738FD7: sigaction (in /usr/lib/libSystem.B.dylib) ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== Conditional jump or move depends on uninitialised value(s) ==55789== at 0x102738FDC: sigaction (in /usr/lib/libSystem.B.dylib) ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== Conditional jump or move depends on uninitialised value(s) ==55789== at 0x102738FE1: sigaction (in /usr/lib/libSystem.B.dylib) ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== Syscall param sigaction(signum) contains uninitialised byte(s) ==55789== at 0x102739032: __sigaction (in /usr/lib/libSystem.B.dylib) ==55789== by 0x102738FA6: signal__ (in /usr/lib/libSystem.B.dylib) ==55789== by 0x100181B19: PetscDefaultSignalHandler (signal.c:143) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55789== ==55789== ==55789== Process terminating with default action of signal 11 (SIGSEGV) ==55789== General Protection Fault ==55789== at 0x1027F0FC1: dyld_stub_binder (in /usr/lib/libSystem.B.dylib) ==55789== by 0x101C4549F: ??? (in /Users/barrysmith/Src/petsc-dev/arch-gnu/lib/libpetsc.dylib) ==55789== by 0x100181B31: PetscDefaultSignalHandler (signal.c:144) ==55789== by 0x1001818AE: PetscSignalHandler_Private (signal.c:53) ==55789== by 0x138048EF3: ??? ==55789== by 0x10000637F: FormIFunctionLocal (ex26.c:579) ==55789== by 0x100007791: FormIFunction (ex26.c:680) ==55789== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55789== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55789== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55789== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55789== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55789== by 0x100CBF982: SNESSolve (snes.c:3549) ==55789== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55789== by 0x100DBC4B9: TSStep (ts.c:1827) ==55789== by 0x100DBDA12: TSSolve (ts.c:1951) ==55789== by 0x1000047A8: main (ex26.c:327) ==55788== Invalid read of size 8 ==55788== at 0x100006443: FormIFunctionLocal (ex26.c:581) ==55788== by 0x100007791: FormIFunction (ex26.c:680) ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) ==55788== by 0x1000047A8: main (ex26.c:327) ==55788== Address 0x1045cf920 is 1,936 bytes inside a block of size 1,940 alloc'd ==55788== at 0x1000251EF: malloc (vg_replace_malloc.c:236) ==55788== by 0x1000CC71B: PetscMallocAlign (mal.c:37) ==55788== by 0x1000CDF89: PetscTrMallocDefault (mtr.c:190) ==55788== by 0x1002B338B: VecGetArray2d (rvector.c:1759) ==55788== by 0x1009430B0: DMDAVecGetArray (dagetarray.c:72) ==55788== by 0x100007536: FormIFunction (ex26.c:673) ==55788== by 0x100DACF67: TSComputeIFunction (ts.c:374) ==55788== by 0x100DA3778: SNESTSFormFunction_Theta (theta.c:204) ==55788== by 0x100DC2D27: SNESTSFormFunction (ts.c:2560) ==55788== by 0x100CACE87: SNESComputeFunction (snes.c:1901) ==55788== by 0x100CF7651: SNESSolve_LS (ls.c:161) ==55788== by 0x100CBF982: SNESSolve (snes.c:3549) ==55788== by 0x100DA223F: TSStep_Theta (theta.c:114) ==55788== by 0x100DBC4B9: TSStep (ts.c:1827) ==55788== by 0x100DBDA12: TSSolve (ts.c:1951) ==55788== by 0x1000047A8: main (ex26.c:327) ==55788== ==55788== ==55788== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- ===================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 11 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================

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