[petsc-users] reading petsc binary vec in python.

[Ataollah Mesgarnejad]

Dear Ethan,

I started deciphering your code for some reason it tries to read header two times and the error comes from the second try! Is it normal for PetscBinaryRead to try to read header twice?


Best,
Ata
On Jul 18, 2011, at 6:28 PM, Ethan Coon wrote:

> Hi Ata,
> 
> Can you tell me what version of numpy you're using?  In some older
> versions of numpy, a "fromfile" called on a file with no data left to
> read did not error, but instead returned an empty list.  This
> implementation, since it doesn't know how many objects are in the file,
> tries to read objects until it gets an error saying the file is empty.
> Try something for me:
> 
> change line 119 of PetscBinaryRead.py to read:
> 
> except MemoryError, IndexError:
> 
> Does that fix it?  
> 
> Thanks,
> 
> Ethan
> 
> 
> On Mon, 2011-07-18 at 17:56 -0500, Ataollah Mesgarnejad wrote:
>> Thanks Ethan,
>> 
>> I did as you said but when I try to read the file using:
>> 
>> petsc_objs = PetscBinaryRead.readBinaryFile('V-018.bin')
>> 
>> I get the following error:
>> 
>> Traceback (most recent call last):
>>  File "./petscvec.py", line 4, in <module>
>>    petsc_objs = PetscBinaryRead.readBinaryFile('V-018.bin')
>>  File "/Users/ataollahmesgarnejad/Software/petsc-3.1/bin/python/PetscBinaryRead.py", line 118, in readBinaryFile
>>    header = np.fromfile(fid, dtype=IntType, count=1)[0]
>> IndexError: index out of bounds
>> 
>> Which is peculiar since when I try to read the header myself using:
>> 
>> header=numpy.fromfile('V-018.bin',dtype='>i4',count=1) 
>> print header[0]
>> 
>> I get:
>> 
>> 1211214
>> 
>> which is a Vec identifier.
>> 
>> Any thoughts on what goes wrong?
>> 
>> Best,
>> Ata
> 
> -- 
> ------------------------------------
> Ethan Coon
> Post-Doctoral Researcher
> Applied Mathematics - T-5
> Los Alamos National Laboratory
> 505-665-8289
> 
> http://www.ldeo.columbia.edu/~ecoon/
> ------------------------------------
>