On Mon, 06 Oct 2014 11:53:58 +0100 "Garth N. Wells" <[email protected]> wrote:
> On Mon, 6 Oct, 2014 at 11:23 AM, Martin Sandve Alnæs > <[email protected]> wrote: > > All collective destructors must be managed explicitly in python, > > preferably via with statement. Are there any apart from file > > objects? Vectors? Matrices? Meshes? > > > > Off the top of my head I can't think of any cases, apart from IO, in > which a (collective) MPI call needs to be made inside a destructor. > For IO, we could insist on a user closing or flushing a file > explicitly. We cannot guarantee that 3rd party linear algebra > backends do not call MPI when objects are destroyed. VecDestroy and MatDestroy (called by PESTcVector and PETScBaseMatrix destructors) are claimed to be collective by PETSc doc: http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecDestroy.html http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDestroy.html Jan > > We have had this problem in the past with the 'automatic' > finalisation of MPI, which is a problem if MPI is shutdown before > PETSc. > > Garth > > > > 6. okt. 2014 12:18 skrev "Jan Blechta" <[email protected]> > > følgende: > >> On Mon, 6 Oct 2014 12:07:02 +0200 > >> Martin Sandve Alnæs <[email protected]> wrote: > >> > >> > The problem is that gc is nondeterministic and in particular not > >> > running with equal timing and ordering on each mpi process. > >> > > >> > We can't use the with statement to handle the scope of every > >> > single dolfin object in a program. > >> > >> Most of the DOLFIN destructors are not collective. So the moral is > >> that > >> we should avoid collective destructors as possible and document it > >> like > >> it is in PETSc doc. > >> > >> Jan > >> > >> > > >> > We can change all file handling to use with, and require the > >> > user > >> to > >> > use that in parallel. > >> > 6. okt. 2014 11:41 skrev "Jan Blechta" > >> <[email protected]> > >> > følgende: > >> > > >> > > On Mon, 6 Oct 2014 09:48:29 +0200 > >> > > Martin Sandve Alnæs <[email protected]> wrote: > >> > > > >> > > > The 'fix' that's in the branch now was to trigger python > >> garbage > >> > > > collection (suggested by Øyvind Evju) before each test. > >> > > > > >> > > > This probably means we have a general problem in dolfin with > >> > > > non-deterministic destruction order of objects in parallel. > >> > > > Any destructor that uses MPI represents a potential deadlock. > >> > > > >> > > To understand the issue, is the problem that garbage > >> > > collection > >> does > >> > > not ensure when the object is destroyed which is the problem? > >> > > > >> > > Here http://stackoverflow.com/a/5071376/1796717 the distinction > >> > > between variable scoping and object cleanup is discussed. > >> Quoting it > >> > > > >> > > Deterministic cleanup happens through the with statement. > >> > > > >> > > which might be a proper solution to the problem. > >> > > > >> > > Jan > >> > > > >> > > > > >> > > > On 19 September 2014 12:52, Jan Blechta > >> > > > <[email protected]> wrote: > >> > > > > >> > > > > On Fri, 19 Sep 2014 00:27:50 +0200 > >> > > > > Jan Blechta <[email protected]> wrote: > >> > > > > > >> > > > > > Yes, after many trials using > >> > > > > > > >> > > > > > $ cd test/unit/io/python > >> > > > > > $ while true; do git clean -fdx && mpirun -n 3 xterm -e > >> > > > > > gdb -ex r -ex q -args python -m pytest -sv; done > >> > > > > > # when it hangs and you interrupt it, it asks for > >> > > > > > confirmation for # quitting, so you type n and enjoy > >> > > > > > gdb... > >> > > > > > > >> > > > > > I've seen a situation when 2 processes deadlocked on > >> > > > > > HDF5Interface::close_file() in DOLFIN with backtrace like > >> > > > > > > >> > > > > > # MPI barrier > >> > > > > > ... > >> > > > > > # MPI close > >> > > > > > # HDF5 lib calls > >> > > > > > H5FClose() > >> > > > > > dolfin::HDF5Interface::close_file() > >> > > > > > dolfin::HDF5File::close() > >> > > > > > dolfin::HDF5File::~HDF5File() > >> > > > > > dolfin::HDF5File::~HDF5File() > >> > > > > > # smart ptr management > >> > > > > > # garbage collection > >> > > > > > > >> > > > > > while 3rd process is waiting far away. Isn't it strange > >> that > >> > > > > > destructor is there twice in stacktrace? (The upper one > >> > > > > > is > >> on > >> > > > > > '}' line which I don't get.) What does it mean? > >> > > > > > >> > > > > Probably just code generation artifact - nothing harmful, > >> > > > > see http://stackoverflow.com/a/15244091/1796717 > >> > > > > > >> > > > > Jan > >> > > > > > >> > > > > > > >> > > > > > Jan > >> > > > > > > >> > > > > > > >> > > > > > On Thu, 18 Sep 2014 16:20:51 +0200 > >> > > > > > Martin Sandve Alnæs <[email protected]> wrote: > >> > > > > > > >> > > > > > > I've added the mpi fixes for temppath fixture and fixed > >> > > > > > > some other related issues while at it: When > >> parameterizing > >> > > > > > > a test that uses a temppath fixture, there is a need > >> > > > > > > for separate directories for each parameter combo. > >> > > > > > > A further improvement would be automatic cleaning of > >> > > > > > > old tempdirs, but I leave that for now. > >> > > > > > > > >> > > > > > > I've pushed these changes to the branch > >> > > > > > > aslakbergersen/topic-change-unittest-to-pytest > >> > > > > > > > >> > > > > > > The tests still hang though, in the closing of > >> > > > > > > HDF5File. > >> > > > > > > > >> > > > > > > Here's now to debug if someone wants to give it a shot: > >> > > > > > > Just run: > >> > > > > > > mpirun -np 3 python -m pytest -s -v > >> > > > > > > With gdb: > >> > > > > > > mpirun -np 3 xterm -e gdb --args python -m pytest > >> > > > > > > then enter 'r' in each of the three xterms. > >> > > > > > > > >> > > > > > > You may have to try a couple of times to get the > >> > > > > > > hanging behaviour. > >> > > > > > > > >> > > > > > > Martin > >> > > > > > > > >> > > > > > > On 18 September 2014 13:23, Martin Sandve Alnæs > >> > > > > > > <[email protected]> wrote: > >> > > > > > > > >> > > > > > > > Good spotting both of you, thanks. > >> > > > > > > > > >> > > > > > > > Martin > >> > > > > > > > > >> > > > > > > > On 18 September 2014 13:01, Lawrence Mitchell < > >> > > > > > > > [email protected]> wrote: > >> > > > > > > > > >> > > > > > > >> On 18/09/14 11:42, Jan Blechta wrote: > >> > > > > > > >> > Some problems (when running in a clean dir) are > >> avoided > >> > > > > > > >> > using this (although incorrect) patch. There are > >> race > >> > > > > > > >> > conditions in creation of temp dir. It should be > >> done > >> > > > > > > >> > using atomic operation. > >> > > > > > > >> > > >> > > > > > > >> > Jan > >> > > > > > > >> > > >> > > > > > > >> > > >> > > > > > > >> > > >> > > > >> ================================================================== > >> > > > > > > >> > diff --git a/test/unit/io/python/test_XDMF.py > >> > > > > > > >> > b/test/unit/io/python/test_XDMF.py index > >> > > > > > > >> > 9ad65a4..31471f1 100755 --- > >> > > > > > > >> > a/test/unit/io/python/test_XDMF.py +++ > >> > > > > > > >> > b/test/unit/io/python/test_XDMF.py @@ -28,8 +28,9 > >> > > > > > > >> > @@ def temppath(): filedir = > >> > > > > > > >> > os.path.dirname(os.path.abspath(__file__)) > >> > > > > > > >> > basename > >> = > >> > > > > > > >> > os.path.basename(__file__).replace(".py", "_data") > >> > > > > > > >> > temppath = os.path.join(filedir, basename, "") > >> > > > > > > >> > - if not os.path.exists(temppath): > >> > > > > > > >> > - os.mkdir(temppath) > >> > > > > > > >> > + if MPI.rank(mpi_comm_world()) == 0: > >> > > > > > > >> > + if not os.path.exists(temppath): > >> > > > > > > >> > + os.mkdir(temppath) > >> > > > > > > >> > return temppath > >> > > > > > > >> > >> > > > > > > >> There's still a race condition here because ranks > >> other > >> > > > > > > >> than zero might try and use temppath before it's > >> > > > > > > >> created. I think you want something like the below: > >> > > > > > > >> > >> > > > > > > >> if MPI.rank(mpi_comm_world()) == 0: > >> > > > > > > >> if not os.path.exists(temppath): > >> > > > > > > >> os.mkdir(temppath) > >> > > > > > > >> MPI.barrier(mpi_comm_world()) > >> > > > > > > >> return temppath > >> > > > > > > >> > >> > > > > > > >> If you're worried about the OS not creating files > >> > > > > > > >> atomically, you can always mkdir into a tmp > >> > > > > > > >> directory > >> and > >> > > > > > > >> then os.rename(tmp, temppath), since posix > >> > > > > > > >> guarantees that renames are atomic. > >> > > > > > > >> > >> > > > > > > >> Lawrence > >> > > > > > > >> _______________________________________________ > >> > > > > > > >> fenics mailing list > >> > > > > > > >> [email protected] > >> > > > > > > >> http://fenicsproject.org/mailman/listinfo/fenics > >> > > > > > > >> > >> > > > > > > > > >> > > > > > > > > >> > > > > > > >> > > > > > _______________________________________________ > >> > > > > > fenics mailing list > >> > > > > > [email protected] > >> > > > > > http://fenicsproject.org/mailman/listinfo/fenics > >> > > > > > >> > > > > > >> > > > >> > > > >> _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
