[petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

[Yuyun Yang]

It's simply for visualization purposes. I wasn't sure if HDF5 would perform better than binary, and what specific functions are needed to load the PETSc vectors/matrices, so wanted to ask for some advice here. Since Matt mentioned it's not likely to be much faster than binary, I guess there is no need to make the change?

So running h5read will load the vector from the hdf5 file directly to a Matlab vector? And similarly so for matrices?

Thanks,
Yuyun

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________________________________
From: petsc-users <petsc-users-bounces at mcs.anl.gov> on behalf of zakaryah via petsc-users <petsc-users at mcs.anl.gov>
Sent: Tuesday, March 19, 2019 11:54:02 AM
To: petsc-users at mcs.anl.gov
Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

Hi Yuyun,

I'm not sure exactly what you want to do but I use Matlab to work with and visualize HDF5 files from PETSc all the time.  Matlab has h5info and h5read routines, then I visualize with my own routines.  Is there something specific you need from Matlab?

On Tue, Mar 19, 2019 at 1:18 PM Yuyun Yang via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Got it, thanks!

From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Sent: Tuesday, March 19, 2019 10:10 AM
To: Yuyun Yang <yyang85 at stanford.edu<mailto:yyang85 at stanford.edu>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab

On Tue, Mar 19, 2019 at 11:58 AM Yuyun Yang via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
Hello team,

Currently we’re using the PETSc binary file format to save Vecs and Mats and visualize them in Matlab. It looks like HDF5 works more efficiently with large data sets (faster I/O), and we’re wondering if PETSc Vecs/Mats saved in HDF5 viewer can be visualized in Matlab as well?

We do not have code for that. I am using Paraview to look at HDF5 since everything I do is on 2D and 3D meshes. Note that HDF5 is not likely to have faster I/O than the PETSc binary.

  Thanks,

    Matt


Thanks for your help,
Yuyun


--
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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