On Mon, Apr 06, 2009 at 03:39:13PM +0200, Johannes Ring wrote: > On Mon, April 6, 2009 15:14, Anders Logg wrote: > > On Mon, Apr 06, 2009 at 01:41:59PM +0200, Johannes Ring wrote: > >> On Mon, April 6, 2009 13:35, Anders Logg wrote: > >> > The buildbot is still not happy on all platforms. The MPI fixes by > >> > Johan seem to have helped some but there are still problems. > >> > > >> > For mac-osx, the tests seem to hang when running the submesh demo: > >> > > >> > command timed out: 1200 seconds without output, killing pid 12857 > >> > process killed by signal 9 > >> > program finished with exit code -1 > >> > >> I think the macbot has crashed. I will try to restart it. > > It didn't help with a restart. It was hanging on the submesh demo again. > The output contains an PETSc error. I guess it's related with the mpi fix: > > Updating mesh coordinates using transfinite mean value interpolation > (Hermite). > Plotting mesh (DOLFIN mesh), press 'q' to continue... > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal > memory access > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC > ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to > find memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 15, Tue Sep 23 10:02:49 > CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760 > [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 darwin9.2 named Amira-iMac.local by > fenicsslave Mon Apr 6 15:13:16 2009 > [0]PETSC ERROR: Libraries linked from > /usr/local/src/petsc-2.3.3-p15/lib/darwin9.2.2-cxx-debug > [0]PETSC ERROR: Configure run at Thu Mar 5 10:40:39 2009 > [0]PETSC ERROR: Configure options --with-clanguage=cxx --with-shared=1 > --with-x=0 --with-x11=0 --with-fortran=0 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > [Amira-iMac.local:09565] MPI_ABORT invoked on rank 0 in communicator > MPI_COMM_WORLD with errorcode 59 > > ^C > Program received signal SIGINT, Interrupt. > 0x963b54ba in wait4 () > (gdb) where > #0 0x963b54ba in wait4 () > #1 0x963b3007 in system$UNIX2003 () > #2 0x00eb3fd2 in plot_object<dolfin::Mesh> (t...@0xbfffeb7c, > mo...@0xbfffea58) at dolfin/plot/plot.cpp:35 > #3 0x00eb2d30 in std::string::_M_rep () at basic_string.h:48 > #4 0x00eb2d30 in ~basic_string [inlined] () at dolfin/plot/plot.cpp:472 > #5 ~basic_string [inlined] () at basic_string.h:472 > #6 dolfin::plot (me...@0xbfffeb7c) at dolfin/plot/plot.cpp:48 > #7 0x00003323 in main () at demo/mesh/submesh/cpp/main.cpp:53 > (gdb) > > > >> > For linux64-exp, most tests seem to fail. > >> > >> We thought that our fixes would make this slave green but now we got a > >> strange error: > >> > >> ./../../demo/fem/simple/python (Python) > >> > >> Traceback (most recent call last): > >> File "./demo.py", line 19, in <module> > >> V = FunctionSpace(mesh, "CG", 1) > >> File > >> "/work/jhbuildbot/fenics/lib/python2.5/site-packages/dolfin/functionspace.py", > >> line 184, in __init__ > >> FunctionSpaceBase.__init__(self, mesh, element) > >> File > >> "/work/jhbuildbot/fenics/lib/python2.5/site-packages/dolfin/functionspace.py", > >> line 46, in __init__ > >> ufc_element, ufc_dofmap = jit(self._element) > >> File > >> "/work/jhbuildbot/fenics/lib/python2.5/site-packages/dolfin/jit.py", > >> line 30, in jit > >> if not check_swig_version(cpp.__swigversion__,same=True): > >> File > >> "/work/jhbuildbot/fenics/lib/python2.5/site-packages/instant/config.py", > >> line 35, in check_swig_version > >> installed_version = map(int, get_swig_version().split('.')) > >> File > >> "/work/jhbuildbot/fenics/lib/python2.5/site-packages/instant/config.py", > >> line 14, in get_swig_version > >> r = re.search(pattern, output) > >> File "/usr/lib/python2.5/re.py", line 142, in search > >> return _compile(pattern, flags).search(string) > >> TypeError: expected string or buffer > >> > >> Johannes > > > > This error appears when the second argument to re.search is wrong. > > > > So the output variable returned from Instant's get_status_output > > is wrong. > > Yes, the output variable was None. It is strangely related with todays mpi > fixes. When I reverted the changes the output variable contained the > correct string. > > > Why does Instant require its own get_status_output instead of using > > commands.getstatusoutput? > > Because commands.getstatusoutput is not available on Windows.
I see. As far as I understand, the problems we see now are related to some intricate problems loading MPI in Python on Mac with Trilinos. Is this combination (MPI + Mac + Trilinos) common enough that we need to solve it right now? I only use one of the three myself (MPI). Would it be an option to for example disable MPI support when building for Trilinos on Mac? There are quite a few items in the queue both for DOLFIN and FFC that will break both functionality and interfaces and it would be good to release now so we can get started. -- Anders
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