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

[Matthew Knepley]

On Mon, Mar 5, 2018 at 2:10 PM, Nelson David Rufus <nelrufus at umich.edu>
wrote:

> Thanks Matt. I will try to use a 32 bit integer to see if the problem goes
> away. I had a query about compatibility of while reading and writing files
> compiled with different int varaints. For example, in the past, I've
> noticed that a file written using an int32 petsc installation (using code
> similar to below) had trouble being read by an int64 petsc installation. Is
> this an issue?
>

Yes, definitely. What we write is not intraconvertible. We could write
headers for things that have
the integer size, but right now we do not.

  Thanks,

     Matt


> --
> Nelson David Rufus
> PhD Student
> Computational Materials Physics Group
> Mechanical Engineering
> University of Michigan
>
> On Mon, Mar 5, 2018 at 1:56 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
>> 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_CO
>>> MM_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/>
>>
>
>


-- 
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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