On Tue, 7 Oct 2014 10:23:21 +0100 "Garth N. Wells" <[email protected]> wrote:
> > On 6 Oct 2014, at 16:38, Martin Sandve Alnæs <[email protected]> > wrote: > > > I think this is the best solution: > > > > 1) Require the user to close file objects deterministically. > > Relying on the del operator is not deterministic, we need to support > > .close() and/or __enter__/__exit__ for the with statement in dolfin. > > > > Sounds good. We can print a warning message from the File object > destructors if a file is not closed (this can later become an error). Good idea, but maybe warning could be issued from __del__ operator if object was not properly destroyed/closed. In C++ layer everything is OK. Maybe we should also check how petsc4py deals with the issue and get eventually inspired. Jan > > > 2) Recommend users to throw in some gc.collect() calls in their > > code if objects go out of scope in their code. This doesn't seem to > > be a big problem, but it's a lingering non-deterministic mpi > > deadlock waiting to happen and very hard to debug. > > > > What about insisting that objects that require collective calls > during destruction must have a collective ‘clear’ or ‘destroy' > function that cleans up the object. > > Related to this discussion, we really need to to starting marking > (logically) collective functions in the docstrings. > > Garth > > > Martin > > > > > > On 6 October 2014 15:05, Martin Sandve Alnæs <[email protected]> > > wrote: Yes. The difference is that mpi initialization / destruction > > happens at beginning / end of the process while the destructors > > happen all the time anywhere. I think that makes this a harder > > problem to solve. > > > > Anyway I was replying to "would it help if MPI is initialised > > explicitly in the setup" and the answer is still no because mpi > > init is not the problem in the tests, although it is of similar > > nature. > > > > I'm pondering if its possible (if necessary) to add a > > dolfin.mpi_gc() function and overload __del__ in some classes to > > handle this deterministically. > > > > 6. okt. 2014 14:54 skrev "Garth N. Wells" <[email protected]> > > følgende: > > > > > > > > On Mon, 6 Oct, 2014 at 1:10 PM, Martin Sandve Alnæs > > <[email protected]> wrote: MPI initialization has nothing to do > > with the test problems. The problem is the destructors of objects. > > It is temporarily solved by calling gc collect in pytest fixtures. > > > > > > The core problem is the same. The problem I describe occurs when > > the SubSystemsManager singleton that controls MPI intialisation is > > destroyed (and finalises MPI) before a PETSc object is destroyed. > > It is an issue of destruction order. > > > > Garth > > > > I think we should implement the with statement pattern for all file > > types in dolfin to allow scope management. > > > > If vectors _do_ call mpi in destructors that's a problem for > > nontrivial dolfin python programs. > > > > 6. okt. 2014 13:53 skrev "Garth N. Wells" <[email protected]> > > følgende: > > > > > > On Mon, 6 Oct, 2014 at 12:32 PM, Jan Blechta > > <[email protected]> wrote: 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 > > > > Yes, they are collective but don't necessarily make MPI calls. My > > understanding is that 'collective' is not the issue but whether or > > not MPI calls are made from a destructor. Some functions will only > > make sense if called collectively (e.g., VecDestroy), but might > > not make collective MPI calls. > > > > For the tests, assuming PyTest permits a 'setup' function like > > unittest, would it help if MPI is initialised explicitly in the > > setup function and closed down at the end of a test suite (if > > possible with PyTest)? > > > > Garth > > > > > > > > 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 _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
