On Tue, 2011-07-19 at 09:49 -0500, Ataollah Mesgarnejad wrote:
> 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!
That is the expected behavior. The code cannot know, a priori, how many
vecs you have in your file. The first pass reads the first vec, and the
second pass tries to read a second PETSc object but gets an empty file.
This is expected to error. Line 119, the except line that I asked you
to change, is supposed to catch that error and tell the program that the
file is empty.
However, I screwed up the line in my last email -- it should read:
except (MemoryError, IndexError):
That should fix your problem, and will be fixed in dev.
Ethan
> 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/
> > ------------------------------------
> >
>
--
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
------------------------------------
