> On 26 Jan 2015, at 11:53, Jan Blechta <[email protected]> wrote: > > On Mon, 26 Jan 2015 11:42:42 +0100 > Mikael Mortensen <[email protected] > <mailto:[email protected]>> wrote: > >> Hi, >> >> With recent (today) hashdist installation I run the following test.py >> script >> >> from dolfin import * >> >> mesh = UnitSquareMesh(4, 4) >> V = VectorFunctionSpace(mesh, 'CG', 1) >> u = interpolate(Expression(('x[0]', 'x[1]')), V) >> print “Hi" >> >> >> [mikael@ubuntu tests (master)]$ python test.py >> Hi >> >> and then it just hangs there without exiting. Same thing in ipython. >> I am currently using host python, but I got the same when I compiled >> with hashdist python. Anyone else experiencing this weirdness? Any >> idea what is going on? I’m on Ubuntu 14.04 and I’ve done >> instant-clean. > > To debug it, you could try attaching debugger (if it is allowed on your > system) > > gdb python <pid> > > hit ^C, and print stacktrace > > (gdb) bt > > Jan
Thanks for the tip. Not really familiar with gdb so I tried pdb first python -m pdb test_GaussDivergence.py > /home/mikael/MySoftware/fenicstools/tests/test.py(5)<module>() -> from dolfin import * (Pdb) continue Hi The program finished and will be restarted and then it just hangs there. Ctrl+C does nothing. With gdb I am getting somewhere though: gdb python Reading symbols from python...(no debugging symbols found)...done. (gdb) run test.py Starting program: /home/mikael/.hashdist/bld/profile/6axink4nal3d/bin/python test.py process 16999 is executing new program: /home/mikael/.hashdist/bld/python/qlvjlzdbishm/bin/python2.7 [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". [New Thread 0x7fffdc7e3700 (LWP 17005)] Hi ^C Program received signal SIGINT, Interrupt. __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135 135 ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file or directory. (gdb) bt #0 __lll_lock_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135 #1 0x00007ffff7bc6657 in _L_lock_909 () from /lib/x86_64-linux-gnu/libpthread.so.0 #2 0x00007ffff7bc6480 in __GI___pthread_mutex_lock (mutex=0x7ffff063fa10 <attribute_lock+16>) at ../nptl/pthread_mutex_lock.c:79 #3 0x00007ffff03a140c in ompi_attr_get_c () from /home/mikael/.hashdist/bld/mpi/vrn4awnke2cx/lib/libmpi.so.1 #4 0x00007ffff03cba27 in MPI_Attr_get () from /home/mikael/.hashdist/bld/mpi/vrn4awnke2cx/lib/libmpi.so.1 #5 0x00007ffff07b2afb in Petsc_DelComm_Outer () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #6 0x00007ffff03a1e88 in ompi_attr_delete () from /home/mikael/.hashdist/bld/mpi/vrn4awnke2cx/lib/libmpi.so.1 #7 0x00007ffff03cb93c in MPI_Attr_delete () from /home/mikael/.hashdist/bld/mpi/vrn4awnke2cx/lib/libmpi.so.1 #8 0x00007ffff07a2baa in PetscCommDestroy () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #9 0x00007ffff07a52bc in PetscHeaderDestroy_Private () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #10 0x00007ffff081372c in ISLocalToGlobalMappingDestroy () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #11 0x00007ffff0819d08 in PetscLayoutDestroy () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #12 0x00007ffff0871718 in VecDestroy () from /home/mikael/.hashdist/bld/petsc/dfw5fwbfp6hl/lib/libpetsc.so.3.5 #13 0x00007ffff22bb15c in dolfin::PETScVector::~PETScVector() () from /home/mikael/.hashdist/bld/dolfin/wt5zll4ojwwy/lib/libdolfin.so.1.5 #14 0x00007ffff22bb229 in dolfin::PETScVector::~PETScVector() () from /home/mikael/.hashdist/bld/dolfin/wt5zll4ojwwy/lib/libdolfin.so.1.5 #15 0x00007ffff221c34a in dolfin::Function::~Function() () from /home/mikael/.hashdist/bld/dolfin/wt5zll4ojwwy/lib/libdolfin.so.1.5 #16 0x00007ffff221c4d9 in dolfin::Function::~Function() () from /home/mikael/.hashdist/bld/dolfin/wt5zll4ojwwy/lib/libdolfin.so.1.5 #17 0x00007ffff308f999 in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release (this=0x19bbc60) at /usr/include/c++/4.8/bits/shared_ptr_base.h:144 #18 0x00007fffdf8093cc in _wrap_delete_Function () from /home/mikael/Software/hashstack/default/lib/python2.7/site-packages/dolfin/cpp/_function.so #19 0x00007fffdf7fc15e in SwigPyObject_dealloc () from /home/mikael/Software/hashstack/default/lib/python2.7/site-packages/dolfin/cpp/_function.so #20 0x00000000005392ff in ?? () #21 0x00000000004d914b in ?? () #22 0x00000000004fdb96 in PyDict_SetItem () #23 0x000000000055a9e1 in _PyModule_Clear () #24 0x00000000004f2ad4 in PyImport_Cleanup () #25 0x000000000042fa89 in Py_Finalize () #26 0x000000000046ac10 in Py_Main () So I’m trying to google this now. I think it’s because I’m using a newer version of openmpi than in the default hashdist script. Default is 1.6.5, but I have compiled with 1.8.2. 1.6.5 gives me problems with h5py, which is why I upgraded it in the first place. So at the moment h5py works, but not fenics:-( M > >> >> Mikael >> >> >> _______________________________________________ >> fenics-support mailing list >> [email protected] <mailto:[email protected]> >> http://fenicsproject.org/mailman/listinfo/fenics-support >> <http://fenicsproject.org/mailman/listinfo/fenics-support>
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