[netcdfgroup] Netcdf-4.1.1 fault

• To: <netcdfgroup@xxxxxxxxxxxxxxxx>
• Subject: [netcdfgroup] Netcdf-4.1.1 fault
• From: "Shibaev, Sergei" <Sergei.Shibaev@xxxxxxxxxx>
• Date: Wed, 27 Oct 2010 14:31:43 +0100

Hi,

I have installed netcdf-4.1.1 with recommended hdf5-1.8.4patch1 and got
an interesting effect. My program writes a complex netcdf4 file which
combines data from many sources including hdf5 files, so both netcdf4
and hdf5 APIs are used simultaneously. The program can write only first
780 data items produced as copies from 4 hdf5 files and fails on
nc_put_vara_short() with error -101: "Error at HDF5 layer"; the hdf
error printout is attached.
And this error is not "at HDF5 layer". When I downgrade netcdf back to
version 4.0.1 (only netcdf, hdf5 is the same 1.8.4patch1) the problem
disappears; the program successfully writes 6200 items, copies 26 hdf
files.
It seems that netcdf4.1.1 interferes with hdf5 library not only at file
closing(netcdf file is opened before hdf5 files and closed closed last).

Regards,
Sergei

HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 3086386896:
  #000: H5D.c line 171 in H5Dcreate2(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #001: H5Dint.c line 428 in H5D_create_named(): unable to create and link to 
dataset
    major: Dataset
    minor: Unable to initialize object
  #002: H5L.c line 1639 in H5L_link_object(): unable to create new link to 
object
    major: Links
    minor: Unable to initialize object
  #003: H5L.c line 1862 in H5L_create_real(): can't insert link
    major: Symbol table
    minor: Unable to insert object
  #004: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #005: H5Gtraverse.c line 703 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #006: H5L.c line 1685 in H5L_link_cb(): unable to create object
    major: Object header
    minor: Unable to initialize object
  #007: H5O.c line 2677 in H5O_obj_create(): unable to open object
    major: Object header
    minor: Can't open object
  #008: H5Doh.c line 296 in H5O_dset_create(): unable to create dataset
    major: Dataset
    minor: Unable to initialize object
  #009: H5Dint.c line 1034 in H5D_create(): can't update the metadata cache
    major: Dataset
    minor: Unable to initialize object
  #010: H5Dint.c line 826 in H5D_update_oh_info(): unable to update 
layout/pline/efl header message
    major: Dataset
    minor: Unable to initialize object
  #011: H5Dlayout.c line 223 in H5D_layout_oh_create(): unable to initialize 
layout information
    major: Dataset
    minor: Unable to initialize object
  #012: H5Dchunk.c line 496 in H5D_chunk_init(): memory allocation failed
    major: Resource unavailable
    minor: No space available for allocation
  #013: H5FL.c line 956 in H5FL_blk_calloc(): memory allocation failed
    major: Resource unavailable
    minor: No space available for allocation
  #014: H5FL.c line 888 in H5FL_blk_malloc(): memory allocation failed for chunk
    major: Resource unavailable
    minor: No space available for allocation
  #015: H5FL.c line 208 in H5FL_malloc(): memory allocation failed for chunk
    major: Resource unavailable
    minor: No space available for allocation

• Follow-Ups:
  • [netcdfgroup] FW: Netcdf-4.1.1 fault
    • From: Shibaev, Sergei

• References:
  • [netcdfgroup] how to tell if a hdf5 is netcdf
    • From: Upendra Dadi