[petsc-users] Error while reading/writing petsc file

[Matthew Knepley]

On Mon, Mar 5, 2018 at 1:52 PM, Nelson David Rufus <nelrufus at umich.edu>
wrote:

> Hello,
>
> I am writing a vector on a petsc binary file and subsequently reading the
> same in another part of the code.
> This works well for smaller vector sizes but fails for a large vector
> (vectorsize=2048000000 <(204)%20800-0000>; PetscScalar=PetscComplex). For
> a large vector, when the read vector is probed for values, I seems to me
> that it is populated with uninitialized values.
>

The number of bytes written will not fit in a 32-bit integer. We do not
exhaustively check for problems. I recommend
reconfiguring with 64-bit ints and retrying.

  Thanks,

     Matt


> This size is close to the int32 limit (2^31 -1) but does not really breach
> it. Hence i am nt using 64 bit integer. Can you please help me figure out
> what might be going wrong here.? I'm appending with this mail snippets of
> the code which read wnd write the petsc file.
> //**********************************************************
> ************************************************************
> ***********************
> //
> // Snippet which writes v (a vector constructed using global size) to  the
> file. Note that this snippet is part of a parallel code
> //
>       PetscViewer viewer;
>       error = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileName.c_str(),
> FILE_MODE_WRITE,&viewer);
>       checkPETScError(error, "unbale to open binary file");
>
>       error = VecView(v,viewer);
>       checkPETScError(error, "unable to use VecView");
>
>       error = PetscViewerDestroy(&viewer);
>       checkPETScError(error,"unable to destry viewer");
>
>       //
>       // cleanup
>       //
>       error = VecDestroy(&v);
>       checkPETScError(error,"unable to destroy vector");
>
>
>       error = PetscOptionsSetValue(NULL,"-viewer_binary_mpiio","");
>       checkPETScError(error, "error in PetscOptionsSetValue");
>
> //**********************************************************
> *********************************************************************
> //
> // Snippet which reads v (this is part of a serial code)
> //
> PetscViewer viewer;
>   error = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileName.c_str(),
> FILE_MODE_READ,&viewer);
>   checkPETScError(error, "unbale to open binary file");
>
>   error = VecLoad(v,viewer);
>   checkPETScError(error, "unable to use VecView");
>
>   error = PetscViewerDestroy(&viewer);
>   checkPETScError(error,"unable to destry viewer");
>
>    //
>   // write to console
>   //
>   //error = VecView(v,PETSC_VIEWER_STDOUT_WORLD);
>   //checkPETScError(error, "unable to write to console");
>
>   //
>   // copy petsc vec to stl vector
>   //
>   std::vector<std::complex<double> > dummy(vecSize);
>   PetscScalar *pointerX;
>   VecGetArray(v, &pointerX);
>   std::copy(&(pointerX[0]),&(pointerX[vecSize]),dummy.begin());
>   VecRestoreArray(v, &pointerX);
>
>   // subsequently dummy is written to an stl vector.
> //**********************************************************
> ************************************************************
> ***********************
>
>
> Thanks,
> -
> Nelson David Rufus
> PhD Student
> Computational Materials Physics Group
> Mechanical Engineering
> University of Michigan
>



-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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