>> Maybe we should also check how petsc4py deals with the issue and
get
>> eventually inspired.
>
>
> I haven't checked in detail, but I presumed that petsc4py wraps the
PETSc 'FooDestroy' functions. From a quick survey of some of the
petsc4py demos, it appears that some explicitly clean up, e.g.
>
>
https://bitbucket.org/petsc/petsc4py/src/7081705ebf90034163de05034df749fcd50cc288/demo/taosolve/chwirut.py?at=master
>
> and some do not, e.g.
>
>
https://bitbucket.org/petsc/petsc4py/src/7081705ebf90034163de05034df749fcd50cc288/demo/kspsolve/test_mat_cg.py?at=master
>
> I suspect that petsc4py could suffer the same issue that we're
seeing in the case that objects are not explicitly cleaned up.
>
> Garth
>
>
>
>>
>> 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
>>
>>
>
