[petsc-users] Configure with precompiled mumps and other packages

san.temporal at gmail.com san.temporal at gmail.com
Sun Apr 26 06:58:44 CDT 2020 

Satish,
Thanks.
Santiago

On Sat, Apr 25, 2020 at 12:05 PM Satish Balay <balay at mcs.anl.gov> wrote:

> I have no idea whats different with UBUNTU MUMPS.
>
> You can try debugging it as the error message suggests.
>
> My suggestion is to stick with petsc-3.13 and --download-mumps.
>
> You can use ubuntu packages for software where API is more consistent -
> like blas/lapack, MPICH/OpenMPI
>
> Satish
>
> On Sat, 25 Apr 2020, san.temporal at gmail.com wrote:
>
> > Hi,
> >
> > I am trying to compile PETSc, using the precompiled Mumps in Ubuntu. The
> > available Mumps version is 5.1.2, so I use PETSc 3.11 (for 3.13 I would
> > require mumps 5.2.1, not available as a precompiled package).
> >
> > The packages are:
> >
> >     $ dpkg -l | grep mumps
> >     ii  libmumps-5.1.2:amd64                          5.1.2-4
> >               amd64        Direct linear systems solver - parallel shared
> > libraries
> >     ii  libmumps-dev:amd64                            5.1.2-4
> >               amd64        Direct linear systems solver - parallel
> > development files
> >     ii  libmumps-ptscotch-5.1.2:amd64                 5.1.2-4
> >               amd64        Direct linear systems solver -
> PTScotch-version
> > shared libraries
> >     ii  libmumps-ptscotch-dev:amd64                   5.1.2-4
> >               amd64        Direct linear systems solver -
> PTScotch-version
> > development files
> >     ii  libmumps-scotch-5.1.2:amd64                   5.1.2-4
> >               amd64        Direct linear systems solver - Scotch-version
> > shared libraries
> >     ii  libmumps-scotch-dev:amd64                     5.1.2-4
> >               amd64        Direct linear systems solver - Scotch-version
> > development files
> >     ii  libmumps-seq-5.1.2:amd64                      5.1.2-4
> >               amd64        Direct linear systems solver - non-parallel
> > shared libraries
> >     ii  libmumps-seq-dev:amd64                        5.1.2-4
> >               amd64        Direct linear systems solver - non-parallel
> > development files
> >
> > So I configure with
> >
> >     $ ./configure --with-cc=mpicc --with-fc=mpif90 -with-cxx=mpicxx
> > --prefix=/home/santiago/usr/local --with-make-np=10
> >  --with-shared-libraries
> > --with-packages-download-dir=/home/santiago/Documents/installers/petsc
> > --download-fblaslapack --with-mumps --with-scalapack --with-debugging=0
> > COPTFLAGS='-O -O3 -march=native -mtune=native' FOPTFLAGS='-O -O3
> > -march=native -mtune=native' CXXOPTFLAGS='-O -O3 -march=native
> > -mtune=native' --force
> >
> > works fine. But
> >
> >     $ make PETSC_DIR=/home/santiago/usr/local PETSC_ARCH="" test
> >     Running test examples to verify correct installation
> >     Using PETSC_DIR=/home/santiago/usr/local and PETSC_ARCH=
> >     C/C++ example src/snes/examples/tutorials/ex19 run successfully with
> 1
> > MPI process
> >     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
> >     [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: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > for trouble shooting.
> >     [0]PETSC ERROR: Petsc Release Version 3.11.4, Sep, 28, 2019
> >     [0]PETSC ERROR: ./ex19 on a  named isaiasPrecision-7820 by santiago
> Sat
> > Apr 25 09:52:01 2020
> >     [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: 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: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > for trouble shooting.
> >     [1]PETSC ERROR: Petsc Release Version 3.11.4, Sep, 28, 2019
> >     [1]PETSC ERROR: ./ex19 on a  named isaiasPrecision-7820 by santiago
> Sat
> > Apr 25 09:52:01 2020
> >     [1]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90
> > -with-cxx=mpicxx --prefix=/home/santiago/usr/local --with-make-np=10
> > --with-shared-libraries
> > --with-packages-download-dir=/home/santiago/Documents/installers/petsc
> > --download-fblaslapack --with-mumps --with-scalapack --with-debugging=0
> > COPTFLAGS="-O -O3 -march=native -mtune=native" FOPTFLAGS="-O -O3
> > -march=native -mtune=native" CXXOPTFLAGS="-O -O3 -march=native
> > -mtune=native" --force
> >     [1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> >     [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90
> > -with-cxx=mpicxx --prefix=/home/santiago/usr/local --with-make-np=10
> > --with-shared-libraries
> > --with-packages-download-dir=/home/santiago/Documents/installers/petsc
> > --download-fblaslapack --with-mumps --with-scalapack --with-debugging=0
> > COPTFLAGS="-O -O3 -march=native -mtune=native" FOPTFLAGS="-O -O3
> > -march=native -mtune=native" CXXOPTFLAGS="-O -O3 -march=native
> > -mtune=native" --force
> >     [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> >
> >
> --------------------------------------------------------------------------
> >     MPI_ABORT was invoked on rank 1 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.
> >
> >
> --------------------------------------------------------------------------
> >     [isaiasPrecision-7820:09935] 1 more process has sent help message
> > help-mpi-api.txt / mpi-abort
> >     [isaiasPrecision-7820:09935] Set MCA parameter
> > "orte_base_help_aggregate" to 0 to see all help / error messages
> >
> > fails. As mentioned in
> >
> https://www.mcs.anl.gov/petsc/documentation/faq.html#PetscOptionsInsertFile
> > (even if not the same error) I checked
> >
> >     $ ping `hostname`
> >
> > It works fine.
> > As a reference, a PETSc version that is compiled with ...
> --download-mumps
> > --download-scalapack ... works fine.
> >
> > How can I compile and successfully check PETSc, using the precompiled
> Mumps
> > in Ubuntu?
> >
> > Thanks
> >
>
>
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