Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
Sounds good, thanks for the advice! -Original Message- From: Jed Brown Sent: Tuesday, March 19, 2019 1:23 PM To: Yuyun Yang ; zakaryah ; petsc-users@mcs.anl.gov Subject: Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab Yuyun Yang via petsc-users writes: > 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? There is no speed benefit. The advantage of HDF5 is that it supports better metadata, including the data types and sizes. The PETSc data format is quick, dirty, and fast.
Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
Yuyun Yang via petsc-users writes: > 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? There is no speed benefit. The advantage of HDF5 is that it supports better metadata, including the data types and sizes. The PETSc data format is quick, dirty, and fast.
Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
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 Get Outlook for iOS<https://aka.ms/o0ukef> From: petsc-users on behalf of zakaryah via petsc-users Sent: Tuesday, March 19, 2019 11:54:02 AM To: petsc-users@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 mailto:petsc-users@mcs.anl.gov>> wrote: Got it, thanks! From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Tuesday, March 19, 2019 10:10 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@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 mailto:petsc-users@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/>
Re: [petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
Got it, thanks! From: Matthew Knepley Sent: Tuesday, March 19, 2019 10:10 AM To: Yuyun Yang Cc: petsc-users@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 mailto:petsc-users@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/>
[petsc-users] Saving Vecs/Mats in HDF5 and visualizing in Matlab
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? Thanks for your help, Yuyun
