[petsc-users] VecAssembly gets stuck

[Zhang, Junchao]

When processes get stuck, you can attach gdb to one process and back trace its call stack to see what it is doing, so we can have better understanding.

--Junchao Zhang


On Fri, Sep 13, 2019 at 11:31 AM José Lorenzo via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Hello,

I am solving a finite element problem with Dirichlet boundary conditions using PETSC. In the boundary conditions there are two terms: a first one that is known before hand (normally zero) and a second term that depends linearly on the unknown variable itself in the whole domain. Therefore, at every time step I need to iterate as the boundary condition depends on the field and the latter depends on the BC. Moreover, the problem is nonlinear and I use a ghosted vector to represent the field.

Every processor manages a portion of the domain and a portion of the boundary (if not interior). At every Newton iteration within the time loop the way I set the boundary conditions is as follows:

First, each processor computes the known term of the BC (first term) and inserts the values into the vector

call VecSetValues(H, nedge_own, edglocglo(diredg_loc) - 1, Hdir, INSERT_VALUES, ierr)
call VecAssemblyBegin(H, ierr)
call VecAssemblyEnd(H, ierr)

As far as I understand, at this stage VecAssembly will not need to communicate to other processors as each processor only sets values to components that belong to it.

Then, each processor computes its own contribution to the field-dependent term of the BC for the whole domain boundary as

call VecSetValues(H, nedge_all, edgappglo(diredg_app) - 1, Hself, ADD_VALUES, ierr)
call VecAssemblyBegin(H, ierr)
call VecAssemblyEnd(H, ierr)

In this case communication will be needed as each processor will add values to vector components that are not stored by it, and I guess it might get very busy as all the processors will need to communicate with each other.

When using this strategy I don't find any issue for problems using a small amount of processors, but recently I've been solving using 90 processors and the simulation always hangs at the second VecSetValues at some random time step. It works fine for some time steps but at some point it just gets stuck and I have to cancel the simulation.

I have managed to overcome this by making each processor contribute to its own components using first MPI_Reduce and then doing

call VecSetValues(H, nedge_own, edgappglo(diredg_app_loc), Hself_own, ADD_VALUES, ierr)
call VecAssemblyBegin(H, ierr)
call VecAssemblyEnd(H, ierr)

However I would like to understand whether there is something wrong in the code above.

Thank you.

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