JLD.load triggers libhdf5 error when reading in 0-row dataset

[jiahao]

The MIMIC II dataset contains a data table with 0 rows. JLD.save appears to write this out properly but it fails to load using JLD.load.

jldopen(filename) do f
        read(f, "d_chartitems_detail")
end

HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 140159754770304:
  #000: ../../../src/H5Tcset.c line 90 in H5Tget_cset(): operation not defined for data type class
    major: Datatype
    minor: Feature is unsupported
ERROR: Error getting character set encoding
 in read at /home/jiahao/.julia/v0.3/HDF5/src/plain.jl:1165
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:387
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:286
 in getrefs at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:476
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:411
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:286
 in getrefs at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:476
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:440
 in read at /home/jiahao/.julia/v0.3/HDF5/src/jld.jl:286

$ h5dump d_chartitems_detail-save.jld
HDF5 "d_chartitems_detail-save.jld" {
GROUP "/" {
   GROUP "_refs" {
      GROUP "d_chartitems_detail" {
         DATASET "1" {
            DATATYPE  H5T_REFERENCE { H5T_STD_REF_OBJECT }
            DATASPACE  NULL
            DATA {
            }
            ATTRIBUTE "julia type" {
               DATATYPE  H5T_STRING {
                  STRSIZE 22;
                  STRPAD H5T_STR_NULLTERM;
                  CSET H5T_CSET_ASCII;
                  CTYPE H5T_C_S1;
               }
               DATASPACE  SCALAR
               DATA {
               (0): "Core.Array{Core.Any,1}"
               }
            }
         }
         GROUP "1g" {
         }
         DATASET "2" {
            DATATYPE  H5T_REFERENCE { H5T_STD_REF_OBJECT }
            DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
            DATA {
            (0): DATASET 16312 /_refs/d_chartitems_detail/2g/1 ,
            (1): DATASET 17288 /_refs/d_chartitems_detail/2g/2 
            }
            ATTRIBUTE "CompositeKind" {
               DATATYPE  H5T_STRING {
                  STRSIZE 5;
                  STRPAD H5T_STR_NULLTERM;
                  CSET H5T_CSET_ASCII;
                  CTYPE H5T_C_S1;
               }
               DATASPACE  SCALAR
               DATA {
               (0): "Index"
               }
            }
            ATTRIBUTE "TypeParameters" {
               DATATYPE  H5T_STRING {
                  STRSIZE 1;
                  STRPAD H5T_STR_NULLTERM;
                  CSET H5T_CSET_ASCII;
                  CTYPE H5T_C_S1;
               }
               DATASPACE  NULL
               DATA {
               }
            }
            ATTRIBUTE "julia type" {
               DATATYPE  H5T_STRING {
                  STRSIZE 13;
                  STRPAD H5T_STR_NULLTERM;
                  CSET H5T_CSET_ASCII;
                  CTYPE H5T_C_S1;
               }
               DATASPACE  SCALAR
               DATA {
               (0): "CompositeKind"
               }
            }
         }
         GROUP "2g" {
            DATASET "1" {
               DATATYPE  H5T_REFERENCE { H5T_STD_REF_OBJECT }
               DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
               DATA {
               (0): DATASET 15064 /_refs/d_chartitems_detail/2g/1g/1 ,
               (1): DATASET 16040 /_refs/d_chartitems_detail/2g/1g/2 
               }
               ATTRIBUTE "julia type" {
                  DATATYPE  H5T_STRING {
                     STRSIZE 71;
                     STRPAD H5T_STR_NULLTERM;
                     CSET H5T_CSET_ASCII;
                     CTYPE H5T_C_S1;
                  }
                  DATASPACE  SCALAR
                  DATA {
      }
      ATTRIBUTE "julia type" {
         DATATYPE  H5T_STRING {
            STRSIZE 53;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SCALAR
         DATA {
         (0): "Core.Array{Union(Core.UTF8String,Core.ASCIIString),1}"
         }
      }
   }
   GROUP "_types" {
      DATASET "DataFrame" {
         DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_UTF8;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SIMPLE { ( 2, 2 ) / ( 2, 2 ) }
         DATA {
         (0,0): "columns", "Array{Any,1}",
         (1,0): "colindex", "Index"
         }
         ATTRIBUTE "Module" {
            DATATYPE  H5T_STRING {
               STRSIZE H5T_VARIABLE;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
            DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
            DATA {
            (0): "DataFrames"
            }
         }
      }
      DATASET "Index" {
         DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_UTF8;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SIMPLE { ( 2, 2 ) / ( 2, 2 ) }
         DATA {
         (0,0): "lookup", "Dict{Symbol,Union(AbstractArray{Real,1},Real)}",
         (1,0): "names", "Array{Symbol,1}"
         }
         ATTRIBUTE "Module" {
            DATATYPE  H5T_STRING {
               STRSIZE H5T_VARIABLE;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
            DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
            DATA {
            (0): "DataFrames"
            }
         }
      }
   }
   DATASET "d_chartitems_detail" {
      DATATYPE  H5T_REFERENCE { H5T_STD_REF_OBJECT }
      DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
      DATA {
      (0): DATASET 9704 /_refs/d_chartitems_detail/1 ,
      (1): DATASET 17560 /_refs/d_chartitems_detail/2 
      }
      ATTRIBUTE "CompositeKind" {
         DATATYPE  H5T_STRING {
            STRSIZE 9;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SCALAR
         DATA {
         (0): "DataFrame"
         }
      }
      ATTRIBUTE "TypeParameters" {
         DATATYPE  H5T_STRING {
            STRSIZE 1;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
         DATASPACE  NULL
         DATA {
         }
      }
      ATTRIBUTE "julia type" {
         DATATYPE  H5T_STRING {
            STRSIZE 13;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
         DATASPACE  SCALAR
         DATA {
         (0): "CompositeKind"
         }
      }
   }
}
}

[timholy]

Thanks for kicking the tires so hard! Will try to tackle this over the weekend.

[timholy]

I see I let this languish. If this is still a problem, how do I get my hands on that dataset?

[kleinhenz]

@musm should we close these old JLD issues from before it got split into its own package?

[musm]

yes thanks for asking