[petsc-users] Configure with precompiled mumps and other packages
san.temporal at gmail.com
san.temporal at gmail.com
Sat Apr 25 08:04:56 CDT 2020
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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