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

Re: [petsc-dev] Error during KSPDestroy
by Matthew Knepley 06 May '12

06 May '12

On Sun, May 6, 2012 at 8:42 AM, Alexander Grayver <agrayver(a)gfz-potsdam.de>wrote: > ** > On 06.05.2012 14:27, Matthew Knepley wrote: > > On Sun, May 6, 2012 at 7:28 AM, Alexander Grayver <agrayver(a)gfz-potsdam.de > > wrote: > >> Hello, >> >> I use KSP and random rhs to compute largest singular value: >> > > 1) Is this the whole program? If not, this can be caused by memory > corruption somewhere else. This is what I suspect. > > > Matt, > > I can reproduce error using attached test programm and this matrix (7 mb): > http://dl.dropbox.com/u/60982984/A.dat > I run it fine with the latest petsc-dev: 1.405802e+00 Can you valgrind it on your machine? Matt > > > 2) You can put in CHKMEMQ; throughout the code to find exactly where the > memory corruption happens. > > Matt > > >> ! create solver and set options for singular value estimation >> call KSPCreate(MPI_COMM_WORLD,ksp,ierr);CHKERRQ(ierr) >> call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr) >> call >> KSPSetTolerances(ksp,solvertol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,its,ierr);CHKERRQ(ierr) >> call KSPGMRESSetRestart(ksp, its, ierr);CHKERRQ(ierr) >> call KSPSetComputeSingularValues(ksp, flg, ierr);CHKERRQ(ierr) >> call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr) >> >> ! generate random RHS >> call PetscRandomCreate(PETSC_COMM_WORLD,rctx,ierr) >> call PetscRandomSetFromOptions(rctx,ierr) >> call VecSetRandom(b,rctx,ierr) >> >> !no preconditioning >> call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr) >> call PCSetType(pc,PCNONE,ierr);CHKERRQ(ierr) >> call KSPSetOperators(ksp,A,A,SAME_PRECONDITIONER,ierr);CHKERRQ(ierr) >> !solve system >> call KSPSolve(ksp,b,x,ierr);CHKERRQ(ierr) >> call KSPComputeExtremeSingularValues(ksp, smax, smin, ierr);CHKERRQ(ierr) >> >> call KSPDestroy(ksp,ierr);CHKERRQ(ierr) >> >> However it crashes: >> >> [1]PETSC ERROR: >> ------------------------------------------------------------------------ >> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >> probably memory access out of range >> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> [1]PETSC ERROR: or see >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSCERROR: or try >> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory >> corruption errors >> [1]PETSC ERROR: PetscMallocValidate: error detected at >> PetscDefaultSignalHandler() line 157 in >> /home/lib/petsc-dev1/src/sys/error/signal.c >> [1]PETSC ERROR: Memory at address 0x4aa3f00 is corrupted >> [1]PETSC ERROR: Probably write past beginning or end of array >> [1]PETSC ERROR: Last intact block allocated in KSPSetUp_GMRES() line 73 >> in /home/lib/petsc-dev1/src/ksp/ksp/impls/gmres/gmres.c >> [1]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> [1]PETSC ERROR: Memory corruption! >> [1]PETSC ERROR: ! >> [1]PETSC ERROR: >> ------------------------------------------------------------------------ >> [1]PETSC ERROR: Petsc Development HG revision: >> f3c119f7ddbfee243b51907a90acab15127ccb39 HG Date: Sun Apr 29 21:37:29 2012 >> -0500 >> [1]PETSC ERROR: See docs/changes/index.html for recent updates. >> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [1]PETSC ERROR: See docs/index.html for manual pages. >> [1]PETSC ERROR: >> ------------------------------------------------------------------------ >> [1]PETSC ERROR: /home/prog on a openmpi-i named node207 by user Sun May >> 6 12:58:24 2012 >> [1]PETSC ERROR: Libraries linked from >> /home/lib/petsc-dev1/openmpi-intel-complex-debug-f/lib >> [1]PETSC ERROR: Configure run at Mon Apr 30 10:20:49 2012 >> [1]PETSC ERROR: Configure options >> --with-blacs-include=/opt/intel/Compiler/11.1/072/mkl/include >> --with-blacs-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a >> --with-blas-lapack-lib="[/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a,/opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.a]" >> --with-fortran-interfaces=1 --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2 >> --with-petsc-arch=openmpi-intel-complex-debug-f --with-precision=double >> --with-scalapack-include=/opt/intel/Compiler/11.1/072/mkl/include >> --with-scalapack-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_scalapack_lp64.a >> --with-scalar-type=complex --with-x=0 >> PETSC_ARCH=openmpi-intel-complex-debug-f >> [1]PETSC ERROR: >> ------------------------------------------------------------------------ >> [1]PETSC ERROR: PetscMallocValidate() line 138 in >> /home/lib/petsc-dev1/src/sys/memory/mtr.c >> [1]PETSC ERROR: PetscDefaultSignalHandler() line 157 in >> /home/lib/petsc-dev1/src/sys/error/signal.c >> >> >> Call stack from debugger: >> >> opal_memory_ptmalloc2_int_free, FP=7fffd4765300 >> opal_memory_ptmalloc2_free_hook, FP=7fffd4765330 >> PetscFreeAlign, FP=7fffd4765370 >> PetscTrFreeDefault, FP=7fffd4765520 >> KSPReset_GMRES, FP=7fffd4765740 >> KSPReset, FP=7fffd4765840 >> KSPDestroy, FP=7fffd47659a0 >> kspdestroy_, FP=7fffd47659d0 >> >> >> Any ideas? >> >> Thanks. >> >> -- >> Regards, >> Alexander >> >> > > > -- > 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 > > > > -- > Regards, > Alexander > > -- 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: [petsc-dev] Error during KSPDestroy
by Alexander Grayver 06 May '12

06 May '12

On 06.05.2012 14:27, Matthew Knepley wrote: > On Sun, May 6, 2012 at 7:28 AM, Alexander Grayver > <agrayver(a)gfz-potsdam.de <mailto:[email protected]>> wrote: > > Hello, > > I use KSP and random rhs to compute largest singular value: > > > 1) Is this the whole program? If not, this can be caused by memory > corruption somewhere else. This is what I suspect. Matt, I can reproduce error using attached test programm and this matrix (7 mb): http://dl.dropbox.com/u/60982984/A.dat > > 2) You can put in CHKMEMQ; throughout the code to find exactly where > the memory corruption happens. > > Matt > > ! create solver and set options for singular value estimation > call KSPCreate(MPI_COMM_WORLD,ksp,ierr);CHKERRQ(ierr) > call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr) > call > KSPSetTolerances(ksp,solvertol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,its,ierr);CHKERRQ(ierr) > call KSPGMRESSetRestart(ksp, its, ierr);CHKERRQ(ierr) > call KSPSetComputeSingularValues(ksp, flg, ierr);CHKERRQ(ierr) > call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr) > > ! generate random RHS > call PetscRandomCreate(PETSC_COMM_WORLD,rctx,ierr) > call PetscRandomSetFromOptions(rctx,ierr) > call VecSetRandom(b,rctx,ierr) > > !no preconditioning > call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr) > call PCSetType(pc,PCNONE,ierr);CHKERRQ(ierr) > call KSPSetOperators(ksp,A,A,SAME_PRECONDITIONER,ierr);CHKERRQ(ierr) > !solve system > call KSPSolve(ksp,b,x,ierr);CHKERRQ(ierr) > call KSPComputeExtremeSingularValues(ksp, smax, smin, > ierr);CHKERRQ(ierr) > > call KSPDestroy(ksp,ierr);CHKERRQ(ierr) > > However it crashes: > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > [1]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > [1]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X > to find memory corruption errors > [1]PETSC ERROR: PetscMallocValidate: error detected at > PetscDefaultSignalHandler() line 157 in > /home/lib/petsc-dev1/src/sys/error/signal.c > [1]PETSC ERROR: Memory at address 0x4aa3f00 is corrupted > [1]PETSC ERROR: Probably write past beginning or end of array > [1]PETSC ERROR: Last intact block allocated in KSPSetUp_GMRES() > line 73 in /home/lib/petsc-dev1/src/ksp/ksp/impls/gmres/gmres.c > [1]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [1]PETSC ERROR: Memory corruption! > [1]PETSC ERROR: ! > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: Petsc Development HG revision: > f3c119f7ddbfee243b51907a90acab15127ccb39 HG Date: Sun Apr 29 > 21:37:29 2012 -0500 > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [1]PETSC ERROR: See docs/index.html for manual pages. > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: /home/prog on a openmpi-i named node207 by user > Sun May 6 12:58:24 2012 > [1]PETSC ERROR: Libraries linked from > /home/lib/petsc-dev1/openmpi-intel-complex-debug-f/lib > [1]PETSC ERROR: Configure run at Mon Apr 30 10:20:49 2012 > [1]PETSC ERROR: Configure options > --with-blacs-include=/opt/intel/Compiler/11.1/072/mkl/include > --with-blacs-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a > --with-blas-lapack-lib="[/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a,/opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.a]" > --with-fortran-interfaces=1 > --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2 > --with-petsc-arch=openmpi-intel-complex-debug-f > --with-precision=double > --with-scalapack-include=/opt/intel/Compiler/11.1/072/mkl/include > --with-scalapack-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_scalapack_lp64.a > --with-scalar-type=complex --with-x=0 > PETSC_ARCH=openmpi-intel-complex-debug-f > [1]PETSC ERROR: > ------------------------------------------------------------------------ > [1]PETSC ERROR: PetscMallocValidate() line 138 in > /home/lib/petsc-dev1/src/sys/memory/mtr.c > [1]PETSC ERROR: PetscDefaultSignalHandler() line 157 in > /home/lib/petsc-dev1/src/sys/error/signal.c > > > Call stack from debugger: > > opal_memory_ptmalloc2_int_free, FP=7fffd4765300 > opal_memory_ptmalloc2_free_hook, FP=7fffd4765330 > PetscFreeAlign, FP=7fffd4765370 > PetscTrFreeDefault, FP=7fffd4765520 > KSPReset_GMRES, FP=7fffd4765740 > KSPReset, FP=7fffd4765840 > KSPDestroy, FP=7fffd47659a0 > kspdestroy_, FP=7fffd47659d0 > > > Any ideas? > > Thanks. > > -- > Regards, > Alexander > > > > > -- > 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 -- Regards, Alexander

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Re: [petsc-dev] Error during KSPDestroy
by Matthew Knepley 06 May '12

06 May '12

On Sun, May 6, 2012 at 7:28 AM, Alexander Grayver <agrayver(a)gfz-potsdam.de>wrote: > Hello, > > I use KSP and random rhs to compute largest singular value: > 1) Is this the whole program? If not, this can be caused by memory corruption somewhere else. This is what I suspect. 2) You can put in CHKMEMQ; throughout the code to find exactly where the memory corruption happens. Matt > ! create solver and set options for singular value estimation > call KSPCreate(MPI_COMM_WORLD,ksp,**ierr);CHKERRQ(ierr) > call KSPSetType(ksp,KSPGMRES,ierr);**CHKERRQ(ierr) > call KSPSetTolerances(ksp,**solvertol,PETSC_DEFAULT_** > DOUBLE_PRECISION,PETSC_**DEFAULT_DOUBLE_PRECISION,its,** > ierr);CHKERRQ(ierr) > call KSPGMRESSetRestart(ksp, its, ierr);CHKERRQ(ierr) > call KSPSetComputeSingularValues(**ksp, flg, ierr);CHKERRQ(ierr) > call KSPSetFromOptions(ksp,ierr);**CHKERRQ(ierr) > > ! generate random RHS > call PetscRandomCreate(PETSC_COMM_**WORLD,rctx,ierr) > call PetscRandomSetFromOptions(**rctx,ierr) > call VecSetRandom(b,rctx,ierr) > > !no preconditioning > call KSPGetPC(ksp,pc,ierr);CHKERRQ(**ierr) > call PCSetType(pc,PCNONE,ierr);**CHKERRQ(ierr) > call KSPSetOperators(ksp,A,A,SAME_**PRECONDITIONER,ierr);CHKERRQ(**ierr) > !solve system > call KSPSolve(ksp,b,x,ierr);**CHKERRQ(ierr) > call KSPComputeExtremeSingularValue**s(ksp, smax, smin, > ierr);CHKERRQ(ierr) > > call KSPDestroy(ksp,ierr);CHKERRQ(**ierr) > > However it crashes: > > [1]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/** > documentation/faq.html#**valgrind[1]PETSC<http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC>ERROR: or try > http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > corruption errors > [1]PETSC ERROR: PetscMallocValidate: error detected at > PetscDefaultSignalHandler() line 157 in /home/lib/petsc-dev1/src/sys/** > error/signal.c > [1]PETSC ERROR: Memory at address 0x4aa3f00 is corrupted > [1]PETSC ERROR: Probably write past beginning or end of array > [1]PETSC ERROR: Last intact block allocated in KSPSetUp_GMRES() line 73 in > /home/lib/petsc-dev1/src/ksp/**ksp/impls/gmres/gmres.c > [1]PETSC ERROR: --------------------- Error Message > ------------------------------**------ > [1]PETSC ERROR: Memory corruption! > [1]PETSC ERROR: ! > [1]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [1]PETSC ERROR: Petsc Development HG revision: > f3c119f7ddbfee243b51907a90acab**15127ccb39 HG Date: Sun Apr 29 21:37:29 > 2012 -0500 > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [1]PETSC ERROR: See docs/index.html for manual pages. > [1]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [1]PETSC ERROR: /home/prog on a openmpi-i named node207 by user Sun May 6 > 12:58:24 2012 > [1]PETSC ERROR: Libraries linked from /home/lib/petsc-dev1/openmpi-** > intel-complex-debug-f/lib > [1]PETSC ERROR: Configure run at Mon Apr 30 10:20:49 2012 > [1]PETSC ERROR: Configure options --with-blacs-include=/opt/** > intel/Compiler/11.1/072/mkl/**include --with-blacs-lib=/opt/intel/** > Compiler/11.1/072/mkl/lib/**em64t/libmkl_blacs_openmpi_**lp64.a > --with-blas-lapack-lib="[/opt/**intel/Compiler/11.1/072/mkl/** > lib/em64t/libmkl_intel_lp64.a,**/opt/intel/Compiler/11.1/072/** > mkl/lib/em64t/libmkl_intel_**thread.a,/opt/intel/Compiler/** > 11.1/072/mkl/lib/em64t/libmkl_**core.a,/opt/intel/Compiler/11.**1/072/lib/intel64/libiomp5.a]" > --with-fortran-interfaces=1 --with-mpi-dir=/opt/mpi/intel/**openmpi-1.4.2 > --with-petsc-arch=openmpi-**intel-complex-debug-f --with-precision=double > --with-scalapack-include=/opt/**intel/Compiler/11.1/072/mkl/**include > --with-scalapack-lib=/opt/**intel/Compiler/11.1/072/mkl/** > lib/em64t/libmkl_scalapack_**lp64.a --with-scalar-type=complex --with-x=0 > PETSC_ARCH=openmpi-intel-**complex-debug-f > [1]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [1]PETSC ERROR: PetscMallocValidate() line 138 in > /home/lib/petsc-dev1/src/sys/**memory/mtr.c > [1]PETSC ERROR: PetscDefaultSignalHandler() line 157 in > /home/lib/petsc-dev1/src/sys/**error/signal.c > > > Call stack from debugger: > > opal_memory_ptmalloc2_int_**free, FP=7fffd4765300 > opal_memory_ptmalloc2_free_**hook, FP=7fffd4765330 > PetscFreeAlign, FP=7fffd4765370 > PetscTrFreeDefault, FP=7fffd4765520 > KSPReset_GMRES, FP=7fffd4765740 > KSPReset, FP=7fffd4765840 > KSPDestroy, FP=7fffd47659a0 > kspdestroy_, FP=7fffd47659d0 > > > Any ideas? > > Thanks. > > -- > Regards, > Alexander > > -- 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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Error during KSPDestroy
by Alexander Grayver 06 May '12

06 May '12

Hello, I use KSP and random rhs to compute largest singular value: ! create solver and set options for singular value estimation call KSPCreate(MPI_COMM_WORLD,ksp,ierr);CHKERRQ(ierr) call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr) call KSPSetTolerances(ksp,solvertol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,its,ierr);CHKERRQ(ierr) call KSPGMRESSetRestart(ksp, its, ierr);CHKERRQ(ierr) call KSPSetComputeSingularValues(ksp, flg, ierr);CHKERRQ(ierr) call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr) ! generate random RHS call PetscRandomCreate(PETSC_COMM_WORLD,rctx,ierr) call PetscRandomSetFromOptions(rctx,ierr) call VecSetRandom(b,rctx,ierr) !no preconditioning call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr) call PCSetType(pc,PCNONE,ierr);CHKERRQ(ierr) call KSPSetOperators(ksp,A,A,SAME_PRECONDITIONER,ierr);CHKERRQ(ierr) !solve system call KSPSolve(ksp,b,x,ierr);CHKERRQ(ierr) call KSPComputeExtremeSingularValues(ksp, smax, smin, ierr);CHKERRQ(ierr) call KSPDestroy(ksp,ierr);CHKERRQ(ierr) However it crashes: [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [1]PETSC ERROR: PetscMallocValidate: error detected at PetscDefaultSignalHandler() line 157 in /home/lib/petsc-dev1/src/sys/error/signal.c [1]PETSC ERROR: Memory at address 0x4aa3f00 is corrupted [1]PETSC ERROR: Probably write past beginning or end of array [1]PETSC ERROR: Last intact block allocated in KSPSetUp_GMRES() line 73 in /home/lib/petsc-dev1/src/ksp/ksp/impls/gmres/gmres.c [1]PETSC ERROR: --------------------- Error Message ------------------------------------ [1]PETSC ERROR: Memory corruption! [1]PETSC ERROR: ! [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: Petsc Development HG revision: f3c119f7ddbfee243b51907a90acab15127ccb39 HG Date: Sun Apr 29 21:37:29 2012 -0500 [1]PETSC ERROR: See docs/changes/index.html for recent updates. [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [1]PETSC ERROR: See docs/index.html for manual pages. [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: /home/prog on a openmpi-i named node207 by user Sun May 6 12:58:24 2012 [1]PETSC ERROR: Libraries linked from /home/lib/petsc-dev1/openmpi-intel-complex-debug-f/lib [1]PETSC ERROR: Configure run at Mon Apr 30 10:20:49 2012 [1]PETSC ERROR: Configure options --with-blacs-include=/opt/intel/Compiler/11.1/072/mkl/include --with-blacs-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a --with-blas-lapack-lib="[/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a,/opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.a]" --with-fortran-interfaces=1 --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2 --with-petsc-arch=openmpi-intel-complex-debug-f --with-precision=double --with-scalapack-include=/opt/intel/Compiler/11.1/072/mkl/include --with-scalapack-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_scalapack_lp64.a --with-scalar-type=complex --with-x=0 PETSC_ARCH=openmpi-intel-complex-debug-f [1]PETSC ERROR: ------------------------------------------------------------------------ [1]PETSC ERROR: PetscMallocValidate() line 138 in /home/lib/petsc-dev1/src/sys/memory/mtr.c [1]PETSC ERROR: PetscDefaultSignalHandler() line 157 in /home/lib/petsc-dev1/src/sys/error/signal.c Call stack from debugger: opal_memory_ptmalloc2_int_free, FP=7fffd4765300 opal_memory_ptmalloc2_free_hook, FP=7fffd4765330 PetscFreeAlign, FP=7fffd4765370 PetscTrFreeDefault, FP=7fffd4765520 KSPReset_GMRES, FP=7fffd4765740 KSPReset, FP=7fffd4765840 KSPDestroy, FP=7fffd47659a0 kspdestroy_, FP=7fffd47659d0 Any ideas? Thanks. -- Regards, Alexander

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Re: [petsc-dev] Error in make test
by Stefano Zampini 06 May '12

06 May '12

I've just pulled and make test is broken for me. There's something messed up with PetscThreadCommunicators. Besides, I did not configure petsc-dev to use threads. A revision which works for me is 23244. I'm using openmpi.1.5.5. Here is the traceback of the error [0]PETSC ERROR: PetscCommDuplicate() line 200 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c [0]PETSC ERROR: SNESCreate() line 1293 in /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c 2012/5/5 Stefano Zampini <stefano.zampini(a)gmail.com> > I reverted to 23244. > > 2012/5/5 Shri <abhyshr(a)mcs.anl.gov> > >> I've disabled the threadcomm code temporarily, so hopefully your code >> should run as before now. Please pull and retry. >> >> Thanks, >> Shri >> >> ------------------------------ >> >> Same error on make test. >> >> Moreover, I got some mpi errors running my fortran codes and PETSc >> doesn't show the traceback >> I can only see that the problem occurs in PetscInitialize >> Here is the cryptic output from MPI (openmpi.1.4.5) >> >> [neo155:25438] *** An error occurred in MPI_Attr_get >> [neo155:25438] *** on communicator MPI COMMUNICATOR 3 DUP FROM 1 >> [neo155:25438] *** MPI_ERR_OTHER: known error not in list >> [neo155:25438] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) >> >> >> 2012/5/5 Shri <abhyshr(a)mcs.anl.gov> >> >>> I pushed some changes to fix these errors. Can you please pull and retry. >>> >>> >>> ------------------------------ >>> >>> I had pulled some hours ago from >>> http://petsc.cs.iit.edu/petsc/petsc-dev/rev/61898f35c333 and obtained >>> the following error on make test >>> >>> [0]PETSC ERROR: PetscCommDuplicate() line 200 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c >>> [0]PETSC ERROR: PetscHeaderCreate_Private() line 51 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/inherit.c >>> [0]PETSC ERROR: SNESCreate() line 1293 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/snes/interface/snes.c >>> [0]PETSC ERROR: main() line 102 in src/snes/examples/tutorials/ex19.c >>> >>> I've just pulled and got the following error after typing make test >>> >>> [0]PETSC ERROR: PetscCommDestroy() line 246 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/tagm.c >>> [0]PETSC ERROR: PetscThreadCommFinalizePackage() line 36 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/threadcomm/interface/dlregisthreadcomm.c >>> [0]PETSC ERROR: PetscRegisterFinalizeAll() line 313 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/destroy.c >>> [0]PETSC ERROR: PetscFinalize() line 1080 in >>> /work/adz/zampini/MyWorkingCopyOfPetsc/petsc-dev/src/sys/objects/pinit. >>> >>> I did not configure for a threaded version of PETSc. >>> >>> -- >>> Stefano >>> >>> >>> >> >> >> -- >> Stefano >> >> >> > > > -- > Stefano > -- Stefano

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What needs to be done before a release?
by Sean Farley 05 May '12

05 May '12

On Saturday, May 5, 2012, Barry Smith wrote: > I thought the compiling was fine, only the running was broken. > So, along with not being able to run fortran I am also not able to make a joke about myself.

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Re: [petsc-dev] What needs to be done before a release?
by Barry Smith 05 May '12

05 May '12

On May 5, 2012, at 10:15 PM, Sean Farley wrote: > On Saturday, May 5, 2012, Barry Smith wrote: > Matt is suggesting a code freeze on May 11. That is what his email says. > > So, along with not being able to compile fortran I also am not able to read. I thought the compiling was fine, only the running was broken. Barry

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Re: [petsc-dev] What needs to be done before a release?
by Sean Farley 05 May '12

05 May '12

On Saturday, May 5, 2012, Barry Smith wrote: > Matt is suggesting a code freeze on May 11. That is what his email says. > So, along with not being able to compile fortran I also am not able to read.

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Re: [petsc-dev] What needs to be done before a release?
by Barry Smith 05 May '12

05 May '12

Sean, Matt is suggesting a code freeze on May 11. That is what his email says. Barry On May 5, 2012, at 9:59 PM, Sean Farley wrote: >> Can we commit to a hard deadline? I would like the freeze for testing May >> 11, and clone and release May 14. > > I don't think we can ever commit to a hard deadline until we actually > implement a code freeze. There are too many people that push broken > code to ever have a hard deadline like you suggest.

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Re: [petsc-dev] What needs to be done before a release?
by Sean Farley 05 May '12

05 May '12

> Can we commit to a hard deadline? I would like the freeze for testing May > 11, and clone and release May 14. I don't think we can ever commit to a hard deadline until we actually implement a code freeze. There are too many people that push broken code to ever have a hard deadline like you suggest.

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