[petsc-users] Skipping data when reading from binary file

[Barry Smith]

  To minimize code changes you could add a PETSc viewer format that caused skipping reading in an object. Then each object load would need a skip-read method that mimicked the reading but actually just skipped over the parts of the data of the object (using the correct sizes). For vectors this is trivial since you just skip the single known array. For sparse matrices it is not difficult but you will need to read in the number of nonzeros so you know how much to skip etc.

  Barry


> On Oct 4, 2021, at 9:58 AM, Peder Jørgensgaard Olesen via petsc-users <petsc-users at mcs.anl.gov> wrote:
> 
> Thank you for your quick reply.
> 
> I've had to change away from HDF5 to Binary format at an earlier stage in my work due to the former not working well with what I needed, so I would prefer to stick with the binary format.
> I had a quick view at the code for some of the Viewer-routines, but I'm not well versed in gleaning information about header sizes from that. Hints about what I'm looking for there would be appreciated. 
> 
> Best regards
> Peder
> Fra: Matthew Knepley <knepley at gmail.com>
> Sendt: 4. oktober 2021 15:37:08
> Til: Peder Jørgensgaard Olesen
> Cc: petsc-users at mcs.anl.gov
> Emne: Re: [petsc-users] Skipping data when reading from binary file
>  
> On Mon, Oct 4, 2021 at 9:26 AM Peder Jørgensgaard Olesen via petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
> Hello
> I have a binary file in which a mix of different objects is stored (Vecs, Mats, PetscInts). I can read each element just fine using VecLoad, MatLoad, and PetscIntView, provided they're read in the order in which they were put in the binary. What I would like to do is to skip the reading of any unneeded element, instead proceeding directly to the next one. I tried using PetscBinarySeek() for this, as shown in the attached code. This produces segmentation faults, suggesting that the file pointer isn't going where I want it to.
> There is header information you also have to skip for each object.
> 
> We can go over the sizes  for that (it is best just to look at the code), but that is fragile. A more robust way to achieve this random
> access is to use HDF5 and name the objects.
> 
>   Thanks,
> 
>      Matt
> Any suggestions as to what I'm doing wrong here?
> 
> Best regards,
> Peder
> 
> 
> 
> Peder Jørgensgaard Olesen
> PhD student
> Department of Mechanical Engineering
>  
> pjool at mek.dtu.dk <mailto:pjool at mek.dtu.dk>
> Koppels Allé
> Building 403, room 105
> 2800 Kgs. Lyngby
> www.dtu.dk/english <https://www.dtu.dk/english>
> 
> 
> 
> -- 
> 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.cse.buffalo.edu/~knepley/>

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