[petsc-users] VecView to hdf5 broken for large (complex) vectors

[Sajid Ali]

Hi PETSc developers,

I’m trying to write a large vector created with VecCreateMPI (size
32768x32768) concurrently from 4 nodes (+32 tasks per node, total 128
mpi-ranks) and I see the following (indicative) error : [Full error log is
here : https://file.io/CdjUfe]

HDF5-DIAG: Error detected in HDF5 (1.10.5) MPI-process 52:
  #000: H5D.c line 145 in H5Dcreate2(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #001: H5Dint.c line 329 in H5D__create_named(): unable to create and
link to dataset
    major: Dataset
    minor: Unable to initialize object
  #002: H5L.c line 1557 in H5L_link_object(): unable to create new
link to object
    major: Links
    minor: Unable to initialize object
  #003: H5L.c line 1798 in H5L__create_real(): can't insert link
    major: Links
    minor: Unable to insert object
  #004: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed
    major: Symbol table
HDF5-DIAG: Error detected in HDF5 (1.10.5) MPI-process 59:
  #000: H5D.c line 145 in H5Dcreate2(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #001: H5Dint.c line 329 in H5D__create_named(): unable to create and
link to dataset
    major: Dataset
    minor: Unable to initialize object
  #002: H5L.c line 1557 in H5L_link_object(): unable to create new
link to object
    major: Links
    minor: Unable to initialize object
  #003: H5L.c line 1798 in H5L__create_real(): can't insert link
    major: Links
    minor: Unable to insert object
  #004: H5Gtraverse.c line 851 in H5G_traverse(): internal path
traversal failed
    major: Symbol table
    minor: Object not found
  #005: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal
operator failed
    major: Symbol table
    minor: Callback failed
  #006: H5L.c line 1604 in H5L__link_cb(): unable to create object
    major: Links
    minor: Unable to initialize object
  #007: H5Oint.c line 2453 in H5O_obj_create(): unable to open object
    major: Object header
    minor: Can't open object
  #008: H5Doh.c line 300 in H5O__dset_create(): unable to create
dataset
    minor: Object not found
  #005: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal
operator failed
    major: Symbol table
    minor: Callback failed
  #006: H5L.c line 1604 in H5L__link_cb(): unable to create object
    major: Links
    minor: Unable to initialize object
  #007: H5Oint.c line 2453 in H5O_obj_create(): unable to open object
    major: Object header
    minor: Can't open object
  #008: H5Doh.c line 300 in H5O__dset_create(): unable to create
dataset
    major: Dataset
    minor: Unable to initialize object
  #009: H5Dint.c line 1274 in H5D__create(): unable to construct
layout information
    major: Dataset
    minor: Unable to initialize object
  #010: H5Dchunk.c line 872 in H5D__chunk_construct(): unable to set chunk sizes
    major: Dataset
    minor: Bad value
  #011: H5Dchunk.c line 831 in H5D__chunk_set_sizes(): chunk size must be < 4GB
    major: Dataset
    minor: Unable to initialize object
    major: Dataset
    minor: Unable to initialize object
  #009: H5Dint.c line 1274 in H5D__create(): unable to construct
layout information
    major: Dataset
    minor: Unable to initialize object
  #010: H5Dchunk.c line 872 in H5D__chunk_construct(): unable to set chunk sizes
    major: Dataset
    minor: Bad value
  #011: H5Dchunk.c line 831 in H5D__chunk_set_sizes(): chunk size must be < 4GB
    major: Dataset
    minor: Unable to initialize object
.......

I spoke to Barry last evening who said that this is a known error that was
fixed for DMDA vecs but is broken for non-dmda vecs.

Could this be fixed ?

Thank You,
Sajid Ali
Applied Physics
Northwestern University
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