[petsc-users] Load Vec from 1D HDF5 dataset

[Håkon Strandenes]

I'm sorry I didn't include this in the first email. Here is an example 
HDF5-file, together with a sample program that demonstrate the problem.

I have been trying to dig into VecLoad_HDF5() in vecio.c in order to 
suggest a solution myself, however, I do not think I fully understand 
the concept of the Vec block size and how that affects how the Vec is 
stored in memory and on disk (HDF5 file).

Regards,
Håkon Strandenes


On 19. mars 2015 18:17, Barry Smith wrote:
>
>    Please email the file in.h5 so we can try to reproduce the problem and debug it. Are you using petsc version 3.5.?
>
>    Barry
>
>> On Mar 19, 2015, at 4:19 AM, Håkon Strandenes <haakon at hakostra.net> wrote:
>>
>> Hi,
>>
>> I am again in trouble with PETSc and its HDF5-related functions.
>>
>> I have a code in which I want to read a 1D dataset from a HDF5 file into a PETSc Vec. The array are "small", and each MPI process should read the entire dataset and store it in its own sequential Vec.
>>
>> Currently my code is as follows (somewhat simplified):
>>
>> VecCreate(PETSC_COMM_SELF, &v);
>> VecSetType(v, VECSEQ);
>> PetscObjectSetName((PetscObject)v, "x");
>> PetscViewerHDF5Open(PETSC_COMM_WORLD, "in.h5", FILE_MODE_READ, &viewer);
>> VecLoad(v, viewer);
>>
>> This works, but only if the dataset in the HDF5 file is a 2D dataset, of size Nx1, where N is the number of elements I read. If the dataset in the HDF5 file is of size N (i.e. a 1D dataset) this does not work.
>>
>> The error message I get is the following:
>> [0]PETSC ERROR: Unexpected data in file
>> [0]PETSC ERROR: Dimension of array in file 1 not 2 as expected
>> etc. and it points back to the line 296 in file vecio.c, function VecLoad_HDF5().
>>
>> Technically this is not a problem. I could of course just go ahead and "reshape" all my datasets into 2D datasets. I do however find this behaviour very un-logical. Why can't I read a 1D dataset into a Vec?
>>
>> So my question are:
>> 1) Do I do anything wrong when creating my Vec and reading my datasets?
>> 2) Is there anything I can do to read my 1D datasets into Vecs?
>> 3) Could PETSc perhaps be a little less restrictive in these cases?
>>
>> Thanks in advance.
>>
>> Regards,
>> Håkon Strandenes
>
>
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