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

Sat Apr 25 10:05:29 CDT 2020

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
> 