[petsc-dev] Installation crash on test
Satish Balay
balay at mcs.anl.gov
Thu Dec 12 13:57:25 CST 2013
[posting compressed logs would bypass the moderation on this list. Or
one can send logs to petsc-maint]
================================================================================
TEST configureInstallationMethod from PETSc.utilities.petscdir(/home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/config/PETSc/utilities/petscdir.py:82)
TESTING: configureInstallationMethod from PETSc.utilities.petscdir(config/PETSc/utilities/petscdir.py:82)
This is a Mercurial clone
Defined "VERSION_HG" to ""ae1852fa137384c3044d6feae2ef8a7da2eceaf8""
Defined "VERSION_DATE_HG" to ""Tue Oct 09 18:04:34 2012 -0500""
Defined "VERSION_BS_HG" to ""1a63457bc7b1d283c8380ea48550851ce1bc3091""
Defined "VERSION_BS_DATE_HG" to ""Mon Oct 08 16:33:25 2012 -0500""
================================================================================
This petsc-dev snapshot is a 'mercurial clone' - and is more than a year old.
Could you try using latest petsc-dev [via git]?
http://www.mcs.anl.gov/petsc/developers/index.html#obtaining
thanks,
Satish
On Thu, 12 Dec 2013, Augspurger, Mike wrote:
> I just pulled and installed petsc-dev and bombed the tests with the error
> message below. I've attached configure.log.
>
> Now to check if the libraries are working do:
> make PETSC_DIR=/home/augspurger/NumericalLibraries/petsc PETSC_ARCH=gnu-opt
> test
> =========================================
> Running test examples to verify correct installation
> Using PETSC_DIR=/home/augspurger/NumericalLibraries/petsc and
> PETSC_ARCH=gnu-opt
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR:
> or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development GIT revision:
> 58e0e1d1cef173c8daf844a24cdc569afb7a2817 GIT Date: 2013-12-11 15:53:51
> -0600
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./ex19 on a gnu-opt named lan.iihr.uiowa.edu by augspurger
> Thu Dec 12 10:48:23 2013
> [0]PETSC ERROR: Libraries linked from
> /home/augspurger/NumericalLibraries/petsc/gnu-opt/lib
> [0]PETSC ERROR: Configure run at Thu Dec 12 10:46:20 2013
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-openmpi --download-metis --download-parmetis
> --download-f-blas-lapack --download-cmake=1 --download-scalapack
> --download-mumps --download-superlu_dist -with-debugging=0 COPTFLAGS=-O2
> FOPTFLAGS=-O2
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> 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 has exited due to process rank 0 with PID 26691 on
> node lan.iihr.uiowa.edu exiting improperly. There are two reasons this
> could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
> processes
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [1]PETSC ERROR: [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR:
> or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development GIT revision:
> 58e0e1d1cef173c8daf844a24cdc569afb7a2817 GIT Date: 2013-12-11 15:53:51
> -0600
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./ex19 on a gnu-opt named lan.iihr.uiowa.edu by augspurger
> Thu Dec 12 10:48:24 2013
> [0]PETSC ERROR: Libraries linked from
> /home/augspurger/NumericalLibraries/petsc/gnu-opt/lib
> [0]PETSC ERROR: Configure run at Thu Dec 12 10:46:20 2013
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-openmpi --download-metis --download-parmetis
> --download-f-blas-lapack --download-cmake=1 --download-scalapack
> --download-mumps --download-superlu_dist -with-debugging=0 COPTFLAGS=-O2
> FOPTFLAGS=-O2
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown file
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> 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.
> --------------------------------------------------------------------------
> [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: configure using --with-debugging=yes, recompile, link, and
> run
> [1]PETSC ERROR: to get more information on the crash.
> [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [1]PETSC ERROR: Signal received!
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Development GIT revision:
> 58e0e1d1cef173c8daf844a24cdc569afb7a2817 GIT Date: 2013-12-11 15:53:51
> -0600
> [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: ./ex19 on a gnu-opt named lan.iihr.uiowa.edu by augspurger
> Thu Dec 12 10:48:24 2013
> [1]PETSC ERROR: Libraries linked from
> /home/augspurger/NumericalLibraries/petsc/gnu-opt/lib
> [1]PETSC ERROR: Configure run at Thu Dec 12 10:46:20 2013
> [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-openmpi --download-metis --download-parmetis
> --download-f-blas-lapack --download-cmake=1 --download-scalapack
> --download-mumps --download-superlu_dist -with-debugging=0 COPTFLAGS=-O2
> FOPTFLAGS=-O2
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: User provided function() line 0 in unknown file
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
> batch system) has told this process to end
> [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: configure using --with-debugging=yes, recompile, link, and
> run
> [1]PETSC ERROR: to get more information on the crash.
> [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [1]PETSC ERROR: Signal received!
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Development GIT revision:
> 58e0e1d1cef173c8daf844a24cdc569afb7a2817 GIT Date: 2013-12-11 15:53:51
> -0600
> [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: ./ex19 on a gnu-opt named lan.iihr.uiowa.edu by augspurger
> Thu Dec 12 10:48:24 2013
> [1]PETSC ERROR: Libraries linked from
> /home/augspurger/NumericalLibraries/petsc/gnu-opt/lib
> [1]PETSC ERROR: Configure run at Thu Dec 12 10:46:20 2013
> [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-openmpi --download-metis --download-parmetis
> --download-f-blas-lapack --download-cmake=1 --download-scalapack
> --download-mumps --download-superlu_dist -with-debugging=0 COPTFLAGS=-O2
> FOPTFLAGS=-O2
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: User provided function() line 0 in unknown file
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 0 with PID 26695 on
> node lan.iihr.uiowa.edu exiting improperly. There are two reasons this
> could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
> [lan.iihr.uiowa.edu:26694] 1 more process has sent help message
> help-mpi-api.txt / mpi-abort
> [lan.iihr.uiowa.edu:26694] Set MCA parameter "orte_base_help_aggregate" to
> 0 to see all help / error messages
> Fortran example src/snes/examples/tutorials/ex5f run successfully with 1
> MPI process
> Completed test examples
>
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