Subject: [Viper-dev] Plot and MPI

From: "Garth N. Wells" <[email-masked]>
Date: Thu, 10 Jul 2008 15:46:34 +0100

When I have MPI installed and configure DOLFIN with either PETSc or 
Trilinos, I get a bunch of errors when plot() is called (see below).
A plot appears as expected, followed by the error messages. Looks like a 
Viper issue (?).

Garth

Plotting Function, press q to continue...
*** An error occurred in MPI_Attr_get
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[gnw20pc:3330] Abort before MPI_INIT completed successfully; not able to 
guarantee that all other processes were killed!
*** An error occurred in MPI_Comm_rank
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
*** An error occurred in MPI_Type_free
*** after MPI was finalized
*** MPI_ERRORS_ARE_FATAL (goodbye)
Segmentation fault
Unable to plot (PyDOLFIN or Viper plotter not available).
Saved function u (discrete function) to file poisson.pvd in VTK format.

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From: Ola Skavhaug <[email-masked]>
Date: Fri, 11 Jul 2008 10:54:30 +0200

> A plot appears as expected, followed by the error messages. Looks like a 

As far as I know, there shouldn't be any MPI calls in viper/VTK. I have
absolutely no idea what causes this error.

Did you compile VTK with MPI? Could you report the output of this commando on
the shared vtk-libraries:
objdump -R /usr/lib/libvtk*.so  | grep MPI

Ola

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From: "Garth N. Wells" <[email-masked]>
Date: Fri, 11 Jul 2008 09:56:09 +0100

> objdump -R /usr/lib/libvtk*.so  | grep MPI

I didn't build VTK. I'm using the package. From objdump I get

 >objdump -R /usr/lib/libvtk*.so  | grep MPI
000fc960 R_386_JUMP_SLOT 
_ZN24vtkDistributedDataFilter15MPIRedistributeEP10vtkDataSetS1_

Garth

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From: Ola Skavhaug <[email-masked]>
Date: Fri, 11 Jul 2008 11:06:26 +0200

Garth N. Wells skrev den 11/07-2008 følgende:
>>> A plot appears as expected, followed by the error messages. Looks 
>>> like a Viper issue (?).
>>

OK, then we have the vtk. As you can see, no MPI stuff is going on in viper,
and the MPI_Attr_get does not live in vtk. I have a similar problem now when I
try to combine dolfin with petsc bindings and the PyCC bindings to a serial
build of HYPRE. The problems are likely to be caused by some dummy MPI calls
in HYPRE that are mixed with the non-dummy versions of MPI in dolfin/PETSc.
I don't know what causes the problem you describe.

Can you give a more elaborate description of your system build + which
problems that fail?

Ola

>>> [gnw20pc:3330] Abort before MPI_INIT completed successfully; not able 
>>> to guarantee that all other processes were killed!

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From: "Garth N. Wells" <[email-masked]>
Date: Fri, 11 Jul 2008 11:01:06 +0100

> Can you give a more elaborate description of your system build + which

Fresh clone of dolfin-dev

   ./scons.local enablePetsc=yes enableTrilinos=no enableMpi=yes

Running the Poisson demo in demo/pde/poisson/cpp/ and I get the 
MPI-related error messages. I get the same messages running 
demo/pde/poisson/python/demo.py.

I'm using OpenMPI 1.2.6 which I built and installed, and the Ubuntu 8.04 
VTK packages.

Garth

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From: Ola Skavhaug <[email-masked]>
Date: Fri, 11 Jul 2008 13:48:55 +0200

[snip]

> I'm using OpenMPI 1.2.6 which I built and installed, and the Ubuntu 8.04  

It worked just fine here, running the same Ubuntu (64bit) and OpenMPI 1.2.4.

Ola