Satish, The script that pulled petsc-dev uses:
export PETSC_DIR=/home/augspurger/NumericalLibraries/petsc git clone https://bitbucket.org/petsc/petsc cd petsc export PETSC_ARCH=gnu-opt ./config/configure.py --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" make all make test This is somehow not pulling with git? John On Thu, Dec 12, 2013 at 1:57 PM, Satish Balay <[email protected]> wrote: > [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]PETSCERROR: > > 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]PETSCERROR: > > 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]PETSCERROR: > > 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]PETSCERROR: > > 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 > > > >
