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. Johannes _______________________________________________ DOLFIN-dev mailing list [email protected] http://www.fenics.org/mailman/listinfo/dolfin-dev
