[petsc-dev] elemental fail in master

Mon Mar 2 17:43:53 CST 2015

Well all linux [test] boxes are equivalent. But each of us might have different soft env than whats in petsc account.

I'll check if I can reproduce. Perhaps its because of some inconsistant software env..
[system openmpi + gcc-4.9]

Satish

On Mon, 2 Mar 2015, Barry Smith wrote:

> 
>   Run with valgrind?
> 
>   Run on the same machine as test actually fails on?  Yes, there should be a trivial way for all of us to access all the test machines to debug stuff!
> 
>   Barry
> 
> > On Mar 2, 2015, at 5:36 PM, hong at aspiritech.org wrote:
> > 
> > I cannot reproduce it, even with same configure options on petsc machine:
> > 
> > Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --download-metis --download-openmpich --with-debugging=0 --with-cc=mpicc.openmpi --with-cxx=mpicxx.openmpi --with-fc=mpif90.openmpi --with-mpiexec=mpiexec.openmpi --download-fblaslapack=1 --download-mumps --download-parmetis --download-scalapack --download-elemental --with-cxx-dialect=C++11 --download-cmake PETSC_ARCH=arch-openmpi-o
> > 
> > Any suggestion?
> > 
> > Hong
> > 
> > On Mon, Mar 2, 2015 at 2:34 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2015/03/01/examples_master_arch-linux-pkgs-opt_crank.log
> > 
> > ******* Testing: testexamples_ELEMENTAL *******
> > 0a1,55
> > > [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > > [0]PETSC ERROR: Object is in wrong state
> > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > > [1]PETSC ERROR: Object is in wrong state
> > > [1]PETSC ERROR: C != D
> > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > [1]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2131-g5620d6d  GIT Date: 2015-02-28 21:26:35 -0600
> > > [1]PETSC ERROR: ./ex104 on a arch-linux-pkgs-opt named crank by petsc Sun Mar  1 14:11:43 2015
> > > [1]PETSC ERROR: Configure options --with-debugging=0 --with-cc=mpicc.openmpi --with-cxx=mpicxx.openmpi --with-fc=mpif90.openmpi --with-mpiexec=mpiexec.openmpi --download-fblaslapack=1 --download-hypre=1 --download-cmake=1 --download-metis=1 --download-parmetis=1 --download-ptscotch=1 --download-suitesparse=1 --download-triangle=1 --download-superlu=1 --download-superlu_dist=1 --download-scalapack=1 --download-mumps=1 --download-elemental=1 --with-cxx-dialect=C++11 --download-spai=1 --download-parms=1 --download-moab=1 --download-chaco=1 --download-saws --with-no-output -PETSC_ARCH=arch-linux-pkgs-opt -PETSC_DIR=/sandbox/petsc/petsc.clone
> > > [1]PETSC ERROR: #1 main() line 67 in /sandbox/petsc/petsc.clone/src/mat/examples/tests/ex104.c
> > > [2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > > [2]PETSC ERROR: Object is in wrong state
> > > [2]PETSC ERROR: C != D
> > > [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > [2]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2131-g5620d6d  GIT Date: 2015-02-28 21:26:35 -0600
> > > [2]PETSC ERROR: ./ex104 on a arch-linux-pkgs-opt named crank by petsc Sun Mar  1 14:11:43 2015
> > > [2]PETSC ERROR: Configure options --with-debugging=0 --with-cc=mpicc.openmpi --with-cxx=mpicxx.openmpi --with-fc=mpif90.openmpi --with-mpiexec=mpiexec.openmpi --download-fblaslapack=1 --download-hypre=1 --download-cmake=1 --download-metis=1 --download-parmetis=1 --download-ptscotch=1 --download-suitesparse=1 --download-triangle=1 --download-superlu=1 --download-superlu_dist=1 --download-scalapack=1 --download-mumps=1 --download-elemental=1 --with-cxx-dialect=C++11 --download-spai=1 --download-parms=1 --download-moab=1 --download-chaco=1 --download-saws --with-no-output -PETSC_ARCH=arch-linux-pkgs-opt -PETSC_DIR=/sandbox/petsc/petsc.clone
> > > [2]PETSC ERROR: #1 main() line 67 in /sandbox/petsc/petsc.clone/src/mat/examples/tests/ex104.c
> > > [2]PETSC ERROR: PETSc Option Table entries:
> > > [2]PETSC ERROR: -display 140.221.10.20:0.0
> > > [2]PETSC ERROR: -malloc_dump
> > > C != D
> > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2131-g5620d6d  GIT Date: 2015-02-28 21:26:35 -0600
> > > [0]PETSC ERROR: ./ex104 on a arch-linux-pkgs-opt named crank by petsc Sun Mar  1 14:11:43 2015
> > > [0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=mpicc.openmpi --with-cxx=mpicxx.openmpi --with-fc=mpif90.openmpi --with-mpiexec=mpiexec.openmpi --download-fblaslapack=1 --download-hypre=1 --download-cmake=1 --download-metis=1 --download-parmetis=1 --download-ptscotch=1 --download-suitesparse=1 --download-triangle=1 --download-superlu=1 --download-superlu_dist=1 --download-scalapack=1 --download-mumps=1 --download-elemental=1 --with-cxx-dialect=C++11 --download-spai=1 --download-parms=1 --download-moab=1 --download-chaco=1 --download-saws --with-no-output -PETSC_ARCH=arch-linux-pkgs-opt -PETSC_DIR=/sandbox/petsc/petsc.clone
> > > [0]PETSC ERROR: #1 main() line 67 in /sandbox/petsc/petsc.clone/src/mat/examples/tests/ex104.c
> > > [0]PETSC ERROR: PETSc Option Table entries:
> > > [0]PETSC ERROR: -display 140.221.10.20:0.0
> > > [0]PETSC ERROR: -malloc_dump
> > > [0]PETSC ERROR: -mat_type elemental
> > > [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
> > > [1]PETSC ERROR: PETSc Option Table entries:
> > > [1]PETSC ERROR: -display 140.221.10.20:0.0
> > > [1]PETSC ERROR: -malloc_dump
> > > [1]PETSC ERROR: -mat_type elemental
> > > [1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
> > > [2]PETSC ERROR: -mat_type elemental
> > > [2]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
> > > --------------------------------------------------------------------------
> > > MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
> > > with errorcode 73.
> > >
> > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > > You may or may not see output from other processes, depending on
> > > exactly when Open MPI kills them.
> > > --------------------------------------------------------------------------
> > > --------------------------------------------------------------------------
> > > mpiexec.openmpi has exited due to process rank 2 with PID 21714 on
> > > node crank exiting without calling "finalize". This may
> > > have caused other processes in the application to be
> > > terminated by signals sent by mpiexec.openmpi (as reported here).
> > > --------------------------------------------------------------------------
> > > [crank:21711] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
> > > [crank:21711] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> > /sandbox/petsc/petsc.clone/src/mat/examples/tests
> > Possible problem with ex104_elemental_2, diffs above
> > =========================================
> > 6c6,30
> > <  Test LU Solver
> > ---
> > > terminate called after throwing an instance of 'std::logic_error'
> > >   what():  A was not numerically HPD
> > >
> > > [crank:21810] *** Process received signal ***
> > > [crank:21810] Signal: Aborted (6)
> > > [crank:21810] Signal code:  (-6)
> > > [crank:21810] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x2b997a66bcb0]
> > > [crank:21810] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [0x2b997a8af0d5]
> > > [crank:21810] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) [0x2b997a8b283b]
> > > [crank:21810] [ 3] /nfs/software/linux-ubuntu_precise_amd64/apps/packages/gcc-4.9.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x175) [0x2b9976a592d5]
> > > [crank:21810] [ 4] /nfs/software/linux-ubuntu_precise_amd64/apps/packages/gcc-4.9.0/lib64/libstdc++.so.6(+0x5e336) [0x2b9976a57336]
> > > [crank:21810] [ 5] /nfs/software/linux-ubuntu_precise_amd64/apps/packages/gcc-4.9.0/lib64/libstdc++.so.6(+0x5e381) [0x2b9976a57381]
> > > [crank:21810] [ 6] /nfs/software/linux-ubuntu_precise_amd64/apps/packages/gcc-4.9.0/lib64/libstdc++.so.6(+0x5e598) [0x2b9976a57598]
> > > [crank:21810] [ 7] /sandbox/petsc/petsc.clone/arch-linux-pkgs-opt/lib/libEl.so(_ZN2El10LogicErrorIJPKcEEEvDpT_+0xaa) [0x2b9974d9dffa]
> > > [crank:21810] [ 8] /sandbox/petsc/petsc.clone/arch-linux-pkgs-opt/lib/libEl.so(_ZN2El8CholeskyIdEEvNS_14UpperOrLowerNS12UpperOrLowerERNS_6MatrixIT_EE+0x281) [0x2b997557b391]
> > > [crank:21810] [ 9] /sandbox/petsc/petsc.clone/arch-linux-pkgs-opt/lib/libEl.so(_ZN2El8cholesky5UVar3IdEEvRNS_18AbstractDistMatrixIT_EE+0x20c) [0x2b997558460c]
> > > [crank:21810] [10] /sandbox/petsc/petsc.clone/arch-linux-pkgs-opt/lib/libpetsc.so.3.05(+0x56fd37) [0x2b9973546d37]
> > > [crank:21810] [11] /sandbox/petsc/petsc.clone/arch-linux-pkgs-opt/lib/libpetsc.so.3.05(MatCholeskyFactor+0x230) [0x2b99732a79aa]
> > > [crank:21810] [12] ./ex145(main+0x24b7) [0x4044ff]
> > > [crank:21810] [13] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x2b997a89a76d]
> > > [crank:21810] [14] ./ex145() [0x401f59]
> > > [crank:21810] *** End of error message ***
> > > --------------------------------------------------------------------------
> > > mpiexec.openmpi noticed that process rank 5 with PID 21810 on node crank exited on signal 6 (Aborted).
> > > --------------------------------------------------------------------------
> > /sandbox/petsc/petsc.clone/src/mat/examples/tests
> > Possible problem with ex145_2, diffs above
> > =========================================
> > 
> > 
> 
> 