[petsc-users] HDF5 (fwd)

[Satish Balay]

Please fix your 'contacts' to use 'petsc-users' and not 'petsc-users-bounces'

Satish


---------- Forwarded message ----------
Date: Wed, 14 Aug 2024 07:09:31 +0000
From: Yang Yehua <yc37416 at connect.um.edu.mo>
To: "petsc-users-bounces at mcs.anl.gov" <petsc-users-bounces at mcs.anl.gov>
Subject: HDF5 

Dear all,
I am trying to use HDF5 to save a DM object, but it is very slow. Here is the code I am using:
PetscViewer viewer;
PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, "mesh.h5", FILE_MODE_WRITE, &viewer));
PetscCall(PetscObjectSetName((PetscObject)dm, "plexA"));
PetscCall(DMView(dm, viewer));
PetscCall(PetscViewerDestroy(&viewer));
The DM object is a parallel mesh with 2 MPI processes. Here are the details:

  *   Type: plex
  *   Parallel Mesh in 3 dimensions:
     *   Number of 0-cells per rank: 1954, 1948
     *   Number of 1-cells per rank: 11794, 11749
     *   Number of 2-cells per rank: 18851, 18773
     *   Number of 3-cells per rank: 9010, 8971
Labels:

  *   Depth: 4 strata with value/size (0 (1954), 1 (11794), 2 (18851), 3 (9010))
  *   Celltype: 4 strata with value/size (0 (1954), 1 (11794), 3 (18851), 6 (9010))
  *   Cell Sets: 1 strata with value/size (2 (9010))
  *   av_section: 1 strata with value/size (0 (9010))
Field phi_grad:

  *   Adjacency FEM
Despite the small mesh size, using 16 ranks takes several minutes, while using 2 ranks takes 21 seconds.
Any suggestions on how to improve the performance would be greatly appreciated.
Best regards, Yehua
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