On Wed, Nov 26, 2014 at 10:25 AM, Martin Sandve Alnæs <[email protected]> wrote:
> My understanding of groups is that they allow running different code on > different processes. Thus I don't see any use for creation of a mesh > object, expression object, etc. outside of the group it is defined on. Is > there any reason to do that? > Not that I am aware of. > "Why wouldn't it?" - it shouldn't. Exactly why it's a good check. If the > user runs different code on different processes however, things like meshes > and functions may be created in a different order, destroying the form > uniqueness. If that happens I would like to know early. > Ok, so assuming all objects determining the signature has been created in the same order in the same group it should be fine. But in general that might not be the case. On one rank a used might want to create a local mesh, screwing the id (counter) for domains. Then he decides to construct a form using a mesh constructed after the local mesh. Johan > Martin > 26. nov. 2014 10:11 skrev "Johan Hake" <[email protected]>: > > On Wed, Nov 26, 2014 at 10:05 AM, Martin Sandve Alnæs <[email protected]> >> wrote: >> >>> Surely the group_comm object does not exist on processes outside the >>> group, and the Expression object construction can only happen within the >>> group? >>> >> There is nothing that prevent you to construct an mpi group on all >> processes. However it seems one cannot do anything with it on ranks that is >> not included in the group. >> >>> I don't see how anything else makes sense. But clear docstring is always >>> good. >>> >> Sure. >> >> >>> Btw, can we assert that the jit signatures match across the group? >>> >> >> Why wouldn't it? >> >> Johan >> >> >> >>> I'm a bit nervous about bugs in nonuniform mpi programs, and that would >>> be a good early indicator of something funny happening. >>> >>> Martin >>> 26. nov. 2014 09:43 skrev "Garth N. Wells" <[email protected]>: >>> >>>> On Wed, 26 Nov, 2014 at 8:32 AM, Johan Hake <[email protected]> wrote: >>>> >>>>> On Wed, Nov 26, 2014 at 9:22 AM, Garth N. Wells <[email protected]> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Wed, 26 Nov, 2014 at 7:50 AM, Johan Hake <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> On Wed, Nov 26, 2014 at 8:34 AM, Garth N. Wells <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 25 Nov, 2014 at 9:48 PM, Johan Hake <[email protected]> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hello! >>>>>>>>> >>>>>>>>> I just pushed some fixes to the jit interface of DOLFIN. Now one >>>>>>>>> can jit on different mpi groups. >>>>>>>>> >>>>>>>> >>>>>>>> Nice. >>>>>>>> >>>>>>>> Previously jiting was only done on rank 1 of the mpi_comm_world. >>>>>>>>> Now it is done on rank 1 of any passed group communicator. >>>>>>>>> >>>>>>>> >>>>>>>> Do you mean rank 0? >>>>>>>> >>>>>>> >>>>>>> Yes, of course. >>>>>>> >>>>>>> >>>>>>> There is no demo atm showing this but a test has been added: >>>>>>>>> >>>>>>>>> test/unit/python/jit/test_jit_with_mpi_groups.py >>>>>>>>> >>>>>>>>> Here an expression, a subdomain, and a form is constructed on >>>>>>>>> different ranks using group. It is somewhat tedious as one need to >>>>>>>>> initialize PETSc with the same group, otherwise PETSc will deadlock >>>>>>>>> during >>>>>>>>> initialization (the moment a PETSc la object is constructed). >>>>>>>>> >>>>>>>> >>>>>>>> This is ok. It's arguably a design flaw that we don't make the user >>>>>>>> handle MPI initialisation manually. >>>>>>>> >>>>>>> >>>>>>> Sure, it is just somewhat tedious. You cannot start your typical >>>>>>> script with importing dolfin. >>>>>>> >>>>>>> The procedure in Python for this is: >>>>>>>>> >>>>>>>>> 1) Construct mpi groups using mpi4py >>>>>>>>> 2) Initalize petscy4py using the groups >>>>>>>>> 3) Wrap groups to petsc4py comm (dolfin only support petsc4py not >>>>>>>>> mpi4py) >>>>>>>>> 4) import dolfin >>>>>>>>> 5) Do group specific stuff: >>>>>>>>> a) Function and forms no change needed as communicator >>>>>>>>> is passed via mesh >>>>>>>>> b) domain = CompiledSubDomain("...", mpi_comm=group_comm) >>>>>>>>> c) e = Expression("...", mpi_comm=group_comm) >>>>>>>>> >>>>>>>> >>>>>>>> It's not so clear whether passing the communicator means that the >>>>>>>> Expression is only defined/available on group_comm, or if group_comm is >>>>>>>> simply to control who does the JIT. Could you clarify this? >>>>>>>> >>>>>>> >>>>>>> My knowledge is not that good in MPI. I have only tried to access >>>>>>> (and construct) the Expression on ranks included in that group. Also >>>>>>> when I >>>>>>> tried construct one using a group communicator on a rank that is not >>>>>>> included in the group, I got an when calling MPI_size on it. There is >>>>>>> probably a perfectly reasonable explaination to this. >>>>>>> >>>>>> >>>>>> Could you clarify what goes on behind-the-scenes with the >>>>>> communicator? Is it only used in a call to get the process rank? What do >>>>>> the ranks other than zero do? >>>>>> >>>>> >>>>> Not sure what you want to know. Instead of using mpi_comm_world to >>>>> construct meshes you use the group communicator. This communicator has its >>>>> own local group of ranks. JITing is still done on rank 0 of the local >>>>> group, which might and most often is different from rank 0 process of the >>>>> mpi_comm_word. >>>>> >>>> >>>> I just want to be clear (and have in the docstring) that >>>> >>>> e = Expression("...", mpi_comm=group_comm) >>>> >>>> is valid only on group_comm (if this is the case), or make clear that >>>> the communicator only determines the process that does the JIT. >>>> >>>> If we required all Expressions to have a domain/mesh, as Martin >>>> advocates, things would be clearer. >>>> >>>> The group communicator works exactly like the world communicator but >>>>> now on just a subset of the processes. There were some sharp edges with >>>>> deadlocks as a consequence, when barriers were taken on the world >>>>> communicator. This is done by default when dolfin is imported and petcs >>>>> gets initialized with the world communicator. So we need to initialized >>>>> petsc using the group communicator. Other than that there are not real >>>>> differences. >>>>> >>>> >>>> That doesn't sound right. PETSc initialisation does not take a >>>> communicator. It is collective on MPI_COMM_WORLD, but each PETSc object >>>> takes a communicator at construction, which can be something other than >>>> MPI_COMM_WORLD or MPI_COMM_SELF. >>>> >>>> Garth >>>> >>>> >>>>> Johan >>>>> >>>>> >>>>> >>>>>> Garth >>>>>> >>>>>> >>>>>> >>>>>> Please try it out and report any sharp edges. A demo would also be >>>>>>>>> fun to include :) >>>>>>>>> >>>>>>>> >>>>>>>> We could run tests on different communicators to speed them up on >>>>>>>> machines with high core counts! >>>>>>>> >>>>>>> >>>>>>> True! >>>>>>> >>>>>>> Johan >>>>>>> >>>>>>> >>>>>>> Garth >>>>>>>> >>>>>>>> >>>>>>>> Johan >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> _______________________________________________ >>>> fenics mailing list >>>> [email protected] >>>> http://fenicsproject.org/mailman/listinfo/fenics >>>> >>> >>
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