On Thu, Sep 14, 2017 at 9:47 AM, Matthew Knepley <knep...@gmail.com> wrote:
> On Thu, Sep 14, 2017 at 11:43 AM, Adriano Côrtes <adrimacor...@gmail.com> > wrote: > >> Dear Matthew, >> >> Thank you for your return. It worked, but this prompts another question. >> So why PetscViewer does not write both files (.h5 and .xmf) directly, >> instead of having to post-proc the .h5 file (in serial)? >> > > 1) Maintenance: Changing the Python is much easier than changing the C you > would add to generate it > > 2) Performance: On big parallel system, writing files is expensive so I > wanted to minimize what I had to do. > > 3) Robustness: Moving 1 file around is much easier than remembering 2. I > just always regenerate the xdmf when needed. > > >> And what about big 3D simulations? PETSc always serialize the output of >> the distributed dmplex? Is there a way to output one .h5 per mesh >> partition? >> > > Given the way I/O is structured on big machines, we believe the multiple > file route is a huge mistake. Also, all our measurements > say that sending some data on the network is not noticeable given the disk > access costs. > I have slightly different things here. We tried the serial output, it looks really slow for large-scale problems, and the first processor often runs out of memory because of gathering all data from other processor cores. The parallel IO runs smoothly and much faster than I excepted. We have done experiments with ten thousands of cores for a problem with 1 billion of unknowns. I did not see any concern so far. Fande, > > Thanks, > > Matt > > >> Best regards, >> Adriano. >> >> >> 2017-09-14 12:00 GMT-03:00 Matthew Knepley <knep...@gmail.com>: >> >>> On Thu, Sep 14, 2017 at 10:30 AM, Adriano Côrtes <adrimacor...@gmail.com >>> > wrote: >>> >>>> Dear all, >>>> >>>> I am running the SNES ex12 and I'm passing the options -dm_view >>>> hdf5:sol.h5 -vec_view hdf5:sol.h5::append to generate an output file. The >>>> .h5 file is generated, but I'm not being able to load it in Paraview >>>> (5.4.0-64bits). Paraview recognizes the file and offers severel options to >>>> read it, here is the complete list >>>> >>>> Chombo Files >>>> GTC Files >>>> M3DC1 Files >>>> Multilevel 3D Plasma Files >>>> PFLOTRAN Files >>>> Pixie Files >>>> Tetrad Files >>>> UNIC Files >>>> VizSchema Files >>>> >>>> The problem is none of the options above work :( >>>> I'm using the configure option '-download-hdf5' and it installs hdf5 >>>> version 1.8.18 >>>> Any hint of how to fix it and have the visualization working? >>>> >>> >>> Yes, Paraview does not directly read HDF5. It needs you to tell it what >>> the data in the HDF5 file means. You do >>> this by creating a *.xdmf file, which is XML. We provide a tool >>> >>> $PETSC_DIR/bin/petsc_gen_xdmf.py <HDF5 file> >>> >>> which should automatically produce this file for you. Let us know if it >>> does not work. >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> >>>> Best regards, >>>> Adriano. >>>> >>>> -- >>>> Adriano Côrtes >>>> ================================================= >>>> *Campus Duque de Caxias and* >>>> *High-performance Computing Center (NACAD/COPPE)* >>>> Federal University of Rio de Janeiro (UFRJ) >>>> >>> >>> >>> >>> -- >>> 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 >>> >>> http://www.caam.rice.edu/~mk51/ >>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&m=4H_Jl8Ex4tyDDtEJRWDYBqSUWZTlt2N0nDQD6_nPQn0&s=v0mwIWnPBNUdE0PYg8qYZ40fhnBA5I5AqDVWOpe2wdU&e=> >>> >> >> >> >> -- >> Adriano Côrtes >> ================================================= >> *Campus Duque de Caxias and* >> *High-performance Computing Center (NACAD/COPPE)* >> Federal University of Rio de Janeiro (UFRJ) >> > > > > -- > 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 > > http://www.caam.rice.edu/~mk51/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&m=4H_Jl8Ex4tyDDtEJRWDYBqSUWZTlt2N0nDQD6_nPQn0&s=v0mwIWnPBNUdE0PYg8qYZ40fhnBA5I5AqDVWOpe2wdU&e=> >