dolfin team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

On Wed, Nov 16, 2011 at 10:59 PM, Anders Logg <logg@xxxxxxxxx> wrote:
> The Oneiric buildbot is timing out. It has happened at least twice
> today. Johannes, can you check if it is really stalling on the
> Cahn-Hilliard demo in parallel or if it's just slow?

No, it is stalling, probably because of the known OpenMPI bug on
Oneiric. I thought I had disabled parallel testing on this buildbot,
but I must have accidentally enabled it again recently. I have
disabled it again now.

BTW, the OS X buildbot is stalling on the C++ eigenvalue demo. When I
run this demo manually on the buildbot I get the error below. Any
ideas?

Johannes


buildbot@buildbotmac:cpp$ mpirun -np 3 ./demo_eigenvalue
Small graph
Process 0: Partitioned mesh, edge cut is 69.
Process 2: Partitioned mesh, edge cut is 69.
Process 1: Partitioned mesh, edge cut is 69.
Largest eigenvalue: 10.0279
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Invalid argument!
[1]PETSC ERROR: Vector is not ghosted!
[1]PETSC ERROR: Largest eigenvalue: 10.0279
Process 0: Plotting u (a function).
Process 0: *** Warning: Plotting disabled when running in parallel;
see https://bugs.launchpad.net/dolfin/+bug/427534
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: Vector is not ghosted!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[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: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[0]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[0]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[0]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: VecGhostUpdateBegin() line 453 in src/vec/vec/impls/mpi/pbvec.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: Vector is not ghosted!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[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: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu NoLargest eigenvalue: 10.0279
Process 2: Plotting u (a function).
Process 2: *** Warning: Plotting disabled when running in parallel;
see https://bugs.launchpad.net/dolfin/+bug/427534
------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[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: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[1]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[1]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[1]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: VecGhostUpdateBegin() line 453 in src/vec/vec/impls/mpi/pbvec.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Invalid argument!
[1]PETSC ERROR: Vector is not ghosted!
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[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: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[1]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[1]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[1]PETSC ERROR: Config[2]PETSC ERROR: --------------------- Error
Message ------------------------------------
[2]PETSC ERROR: Invalid argument!
[2]PETSC ERROR: Vector is not ghosted!
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[2]PETSC ERROR: See docs/changes/index.html for recent updates.
[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[2]PETSC ERROR: See docs/index.html for manual pages.
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[2]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[2]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[2]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: VecGhostUpdateBegin() line 453 in src/vec/vec/impls/mpi/pbvec.c
[2]PETSC ERROR: --------------------- Error Message
------------------------------------
[2]PETSC ERROR: Invalid argument!
[2]PETSC ERROR: Vector is not ghosted!
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[2]PETSC ERROR: See docs/changes/index.html for recent updates.
[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[2]PETSC ERROR: See docs/index.html for manual pages.
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[0]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[0]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[0]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: VecGhostUpdateEnd() line 515 in src/vec/vec/impls/mpi/pbvec.c
ure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: VecGhostUpdateEnd() line 515 in src/vec/vec/impls/mpi/pbvec.c
[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/petsc-as/documentation/troubleshooting.html#Signal[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 Release Version 3.1.0, Patch 8, Thu Mar 17
13:37:48 CDT 2011
[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: Unknown Name on a darwin10. named
buildbotmac.simula.no by buildbot Thu Nov 17 07:25:27 2011
[1]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[1]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[1]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxxv 17 07:25:27 2011
[2]PETSC ERROR: Libraries linked from /Users/buildbot/buildbots/main/local/lib
[2]PETSC ERROR: Configure run at Thu Oct 13 10:31:00 2011
[2]PETSC ERROR: Configure options COPTFLAGS=-O2
--prefix=/Users/buildbot/buildbots/main/local --with-debugging=0
--with-shared=1 --with-clanguage=cxx --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[2]PETSC ERROR:
------------------------------------------------------------------------
[2]PETSC ERROR: VecGhostUpdateEnd() line 515 in src/vec/vec/impls/mpi/pbvec.c
 --with-fc=0 --with-parmetis=1
--with-parmetis-dir=/Users/buildbot/buildbots/main/local
--download-umfpack=1 --download-spooles=1
--prefix=/Users/buildbot/buildbots/main/local
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[buildbotmac.simula.no:88290] MPI_ABORT invoked on rank 1 in
communicator MPI_COMM_WORLD with errorcode 59