from dolfin import *
set_log_level(10000)
if MPI.process_number() == 0:
print "%10s --- %10s" %("Cells", "Time (s)")
for i in range(5,250, 20):
mesh = UnitCubeMesh(i,i,i)
tic()
mesh.hash()
t = toc()
if MPI.process_number() == 0:
print "%10d --- %.10f" %(mesh.size_global(3), t)
del mesh
2013/9/29 Garth N. Wells <[email protected]>
> On 29 September 2013 17:46, Øyvind Evju <[email protected]> wrote:
> > From a quad core @ 2.20ghz, calling the mesh.hash() function.
> >
>
> Please post test code.
>
> Garth
>
> > One process:
> > Cells --- Time (s)
> > 750 --- 0.0001020432
> > 93750 --- 0.0019581318
> > 546750 --- 0.0110230446
> > 1647750 --- 0.0335328579
> > 3684750 --- 0.0734529495
> > 6945750 --- 0.1374619007
> > 11718750 --- 0.2321729660
> > 18291750 --- 0.3683109283
> > 26952750 --- 0.5321540833
> > 37989750 --- 0.7479040623
> > 51690750 --- 1.0299670696
> > 68343750 --- 1.3440520763
> > 88236750 --- 1.7490680218
> >
> > Two processes:
> > Cells --- Time (s)
> > 750 --- 0.0002639294
> > 93750 --- 0.0011038780
> > 546750 --- 0.0128669739
> > 1647750 --- 0.0124230385
> > 3684750 --- 0.0274820328
> > 6945750 --- 0.0780282021
> > 11718750 --- 0.1386530399
> > (Out of memory)
> >
> >
> > -Øyvind
> >
> >
> >
> >
> > 2013/9/29 Garth N. Wells <[email protected]>
> >
> >> On 29 September 2013 17:12, Øyvind Evju <[email protected]> wrote:
> >> > Wouldn't it be quite messy to suddenly have several vectors associated
> >> > with
> >> > a Function?
> >> >
> >>
> >> No. It's very natural for a time-dependent Function.
> >>
> >> > Creating a hash of the mesh and finite element and storing cells,
> >> > cell_dofs
> >> > and x_cell_dofs there, we could keep the same structure for Functions
> as
> >> > today with links (instead of actual data sets) within each Function to
> >> > cells, cell_dofs and x_cell_dofs.
> >> >
> >> > When writing a Function a check is done to see if the cells, cell_dofs
> >> > and
> >> > x_cell_dofs exist under the relevant hash. If the hash (mesh,
> >> > distribution
> >> > or function space) changes, we need to write these data sets under the
> >> > new
> >> > hash.
> >> >
> >> > Have I misunderstood this hashing? It does seem to be very efficient,
> >> > more
> >> > efficient than rewriting those three datasets.
> >> >
> >>
> >> Can you post a benchmark for testing the speed of hashing?
> >>
> >> Garth
> >>
> >> >
> >> > -Øyvind
> >> >
> >> >
> >> >
> >> > 2013/9/28 Chris Richardson <[email protected]>
> >> >>
> >> >> On 28/09/2013 13:29, Garth N. Wells wrote:
> >> >>>
> >> >>> On 28 September 2013 12:56, Chris Richardson <[email protected]>
> >> >>> wrote:
> >> >>>>
> >> >>>> On 28/09/2013 11:31, Garth N. Wells wrote:
> >> >>>>>
> >> >>>>>
> >> >>>>> On 28 September 2013 10:42, Chris Richardson <[email protected]
> >
> >> >>>>> wrote:
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>>> This is a continuation of the discussion at:
> >> >>>>>>
> >> >>>>>> https://bitbucket.org/fenics-project/dolfin/pull-request/52
> >> >>>>>>
> >> >>>>>> The question is how best to save a time-series of Function in
> HDF5,
> >> >>>>>> when
> >> >>>>>> the
> >> >>>>>> cell and dof layout remains constant.
> >> >>>>>>
> >> >>>>>> It has been suggested to use:
> >> >>>>>>
> >> >>>>>> u = Function(V)
> >> >>>>>> h0 = HDF5File('Timeseries_of_Function.h5', 'w')
> >> >>>>>> h0.write(u, '/Function')
> >> >>>>>> # Then later
> >> >>>>>> h0.write(u.vector(), "/Vector/0")
> >> >>>>>> h0.write(u.vector(), "/Vector/1")
> >> >>>>>>
> >> >>>>>
> >> >>>>> Shouldn't this be
> >> >>>>>
> >> >>>>> h0.write(u.vector(), "/Function/Vector/0")
> >> >>>>> h0.write(u.vector(), "/Function/Vector/1")
> >> >>>>>
> >> >>>>
> >> >>>> In the HDF5File model, the user is free to put vectors etc wherever
> >> >>>> they
> >> >>>> want. There is no explicit meaning
> >> >>>> to dumping extra vectors inside the "group" of a Function.
> >> >>>>
> >> >>>>
> >> >>>>>
> >> >>>>>> and to read back:
> >> >>>>>>
> >> >>>>>> u = Function(V)
> >> >>>>>> h0 = HDF5File('Timeseries_of_Function.h5', 'r')
> >> >>>>>> h0.read(u, "/Function")
> >> >>>>>> h0.read(u.vector(), "/Function/vector")
> >> >>>>>>
> >> >>>>
> >> >>>> OK, this probably should have been
> >> >>>>
> >> >>>> h0.read(u.vector(), "/Vector/1")
> >> >>>>
> >> >>>> When reading in a vector, it is just read directly, and
> >> >>>> not reordered in any way. If the vector was saved from a different
> >> >>>> set
> >> >>>> of
> >> >>>> processors, with different partitioning, the order could be quite
> >> >>>> different.
> >> >>>>
> >> >>>> When reading a Function, the vector is reordered to take this into
> >> >>>> account.
> >> >>>>
> >> >>>> If the vector is already associated with a Function (not all
> vectors
> >> >>>> are)
> >> >>>> then it should be possible to reorder it when reading... maybe that
> >> >>>> should
> >> >>>> be an option.
> >> >>>>
> >> >>>
> >> >>> A solution seems very simple - use the HDF5 hierarchal structure to
> >> >>> associate Vectors with a Function. This is the advantage of using a
> >> >>> hierarchal storage format.
> >> >>>
> >> >>> If a user reads a Vector that is not already associated with a
> >> >>>
> >> >>> Function, then it should be the user's responsibility to take care
> of
> >> >>> things.
> >> >>>
> >> >>
> >> >> It could work like this:
> >> >>
> >> >> At present, when writing a Function, it creates a group and populates
> >> >> it
> >> >> with
> >> >> dofmap, cells, and vector. Writing again with the same name will
> cause
> >> >> an
> >> >> error.
> >> >> We could allow writes to the same name, but create more vectors
> (maybe
> >> >> checking that the cells/dofs are still compatible) in the same HDF5
> >> >> group.
> >> >> Or, a user could just manually dump more vectors in the group (as
> >> >> described
> >> >> above by Garth).
> >> >>
> >> >> For read, reading a Function will still behave the same, but we could
> >> >> have
> >> >> the additional option of reading a Function by just giving the vector
> >> >> dataset name - and assuming that cell/dof information exists in the
> >> >> same
> >> >> HDF5 group. This should be fairly easy to implement.
> >> >>
> >> >>
> >> >> Chris
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >
>
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