[petsc-users] PETSc + Julia + MVAPICH2 = Segfault

[Matthew Knepley]

On Mon, Dec 5, 2016 at 10:56 PM, Derek Gaston <friedmud at gmail.com> wrote:

> Please excuse the slightly off-topic post: but I'm pulling my hair out
> here and I'm hoping someone else has seen this before.
>
> I'm calling PETSc from Julia and it's working great on my Mac with MPICH
> but I'm seeing a segfault on my Linux cluster using MVAPICH2.  I get the
> same segfault both with the "official" PETSc.jl and my own smaller wrapper
> MiniPETSc.jl: https://github.com/friedmud/MiniPETSc.jl
>
> Here is the stack trace I'm seeing:
>
> signal (11): Segmentation fault
> while loading /home/gastdr/projects/falcon/julia_mpi.jl, in expression
> starting on line 5
> _int_malloc at /home/gastdr/projects/falcon/root/lib/libmpi.so.12
> (unknown line)
> calloc at /home/gastdr/projects/falcon/root/lib/libmpi.so.12 (unknown
> line)
>

Why is MPI taking over calloc()?

   Matt


> PetscOptionsCreate at /home/gastdr/projects/falcon/
> petsc-3.7.3/src/sys/objects/options.c:2578
> PetscInitialize at /home/gastdr/projects/falcon/
> petsc-3.7.3/src/sys/objects/pinit.c:761
> PetscInitializeNoPointers at /home/gastdr/projects/falcon/
> petsc-3.7.3/src/sys/objects/pinit.c:111
> __init__ at /home/gastdr/.julia/v0.5/MiniPETSc/src/MiniPETSc.jl:14
>
> The script I'm running is simply just run.jl :
>
> using MiniPETSc
>
> It feels like libmpi is not quite loaded correctly yet.  It does get
> loaded by MPI.jl here: https://github.com/JuliaParallel/MPI.jl/blob/
> master/src/MPI.jl#L29 and I've verified that that code is running before
> PETSc is being initialized.
>
> It looks ok to me... and I've tried a few variations on that dlopen() call
> and nothing makes it better.
>
> BTW: MPI.jl is working fine on its own.  I can write pure MPI Julia apps
> and run them in parallel on the cluster.  Just need to get this
> initialization of PETSc straightened out.
>
> Thanks for any help!
>
> Derek
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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