1. My problem
I get the next error when trying to read my HDF5 file using Dask and I don't know why
>>> dd.read_hdf("test.h5", key="/RECORDS/STATES")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/dask/dataframe/io/hdf.py", line 514, in read_hdf
for path in paths
File "/usr/local/lib/python3.7/site-packages/dask/dataframe/io/hdf.py", line 514, in <listcomp>
for path in paths
File "/usr/local/lib/python3.7/site-packages/dask/dataframe/io/hdf.py", line 382, in _read_single_hdf
for k, s, d in zip(keys, stops, divisions)
File "/usr/local/lib/python3.7/site-packages/dask/dataframe/multi.py", line 1071, in concat
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
2. The HDF5 file
The file I'm tryig to read with Dask was generated by me using the C API of HDF5. If you ask, I generate the HDF5 using C, not Python (numpy, pandas), for the sake of performance because I need to parse many GB of unformatted data in ASCII. The data is stored in the file as a HDF5 Table (https://portal.hdfgroup.org/display/HDF5/Tables). The header of my files looks like this:
HDF5 "rhoPimpleExtrae10TimeSteps.00.1iter.h5" {
GROUP "/" {
ATTRIBUTE "hdf5_metadata_apps" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "hdf5_metadata_date" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "hdf5_metadata_hwcpu" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 48 ) / ( 48 ) }
}
ATTRIBUTE "hdf5_metadata_hwnodes" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
}
ATTRIBUTE "hdf5_metadata_name" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "hdf5_metadata_nodes" {
DATATYPE H5T_STD_I64LE
DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
}
ATTRIBUTE "hdf5_metadata_path" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "hdf5_metadata_threads" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 48 ) / ( 48 ) }
}
ATTRIBUTE "hdf5_metadata_time" {
DATATYPE H5T_STD_I64LE
DATASPACE SCALAR
}
ATTRIBUTE "hdf5_metadata_type" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
GROUP "RECORDS" {
DATASET "COMMUNICATIONS" {
DATATYPE H5T_COMPOUND {
H5T_STD_U32LE "CPU Send ID";
H5T_STD_U32LE "Phy. Task Send ID";
H5T_STD_U32LE "Log. Task Send ID";
H5T_STD_U32LE "Thread Send ID";
H5T_STD_U64LE "Log. Send Time";
H5T_STD_U64LE "Phy. Send Time";
H5T_STD_U32LE "CPU Receive ID";
H5T_STD_U32LE "Phy. Task Receive ID";
H5T_STD_U32LE "Log. Task Receive ID";
H5T_STD_U32LE "Thread Receive ID";
H5T_STD_U64LE "Log. Receive Time";
H5T_STD_U64LE "Phy. Receive Time";
H5T_STD_U64LE "Size";
H5T_STD_U64LE "Tag";
}
DATASPACE SIMPLE { ( 67574 ) / ( H5S_UNLIMITED ) }
ATTRIBUTE "CLASS" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_0_NAME" {
DATATYPE H5T_STRING {
STRSIZE 12;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_10_NAME" {
DATATYPE H5T_STRING {
STRSIZE 18;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_11_NAME" {
DATATYPE H5T_STRING {
STRSIZE 18;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_12_NAME" {
DATATYPE H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_13_NAME" {
DATATYPE H5T_STRING {
STRSIZE 4;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_1_NAME" {
DATATYPE H5T_STRING {
STRSIZE 18;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_2_NAME" {
DATATYPE H5T_STRING {
STRSIZE 18;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_3_NAME" {
DATATYPE H5T_STRING {
STRSIZE 15;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_4_NAME" {
DATATYPE H5T_STRING {
STRSIZE 15;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_5_NAME" {
DATATYPE H5T_STRING {
STRSIZE 15;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_6_NAME" {
DATATYPE H5T_STRING {
STRSIZE 15;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_7_NAME" {
DATATYPE H5T_STRING {
STRSIZE 21;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_8_NAME" {
DATATYPE H5T_STRING {
STRSIZE 21;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_9_NAME" {
DATATYPE H5T_STRING {
STRSIZE 18;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "TITLE" {
DATATYPE H5T_STRING {
STRSIZE 22;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "VERSION" {
DATATYPE H5T_STRING {
STRSIZE 4;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
}
DATASET "EVENTS" {
DATATYPE H5T_COMPOUND {
H5T_STD_U32LE "CPU ID";
H5T_STD_U16LE "APP ID";
H5T_STD_U32LE "Task ID";
H5T_STD_U32LE "Thread ID";
H5T_STD_U64LE "Time";
H5T_STD_U64LE "Event Type";
H5T_STD_U64LE "Event Value";
}
DATASPACE SIMPLE { ( 3643006 ) / ( H5S_UNLIMITED ) }
ATTRIBUTE "CLASS" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_0_NAME" {
DATATYPE H5T_STRING {
STRSIZE 7;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_1_NAME" {
DATATYPE H5T_STRING {
STRSIZE 7;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_2_NAME" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_3_NAME" {
DATATYPE H5T_STRING {
STRSIZE 10;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_4_NAME" {
DATATYPE H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_5_NAME" {
DATATYPE H5T_STRING {
STRSIZE 11;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_6_NAME" {
DATATYPE H5T_STRING {
STRSIZE 12;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "TITLE" {
DATATYPE H5T_STRING {
STRSIZE 14;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "VERSION" {
DATATYPE H5T_STRING {
STRSIZE 4;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
}
DATASET "STATES" {
DATATYPE H5T_COMPOUND {
H5T_STD_U32LE "CPU ID";
H5T_STD_U16LE "APP ID";
H5T_STD_U32LE "Task ID";
H5T_STD_U32LE "Thread ID";
H5T_STD_U64LE "Time ini";
H5T_STD_U64LE "Time fi";
H5T_STD_U16LE "State";
}
DATASPACE SIMPLE { ( 301496 ) / ( H5S_UNLIMITED ) }
ATTRIBUTE "CLASS" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_0_NAME" {
DATATYPE H5T_STRING {
STRSIZE 7;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_1_NAME" {
DATATYPE H5T_STRING {
STRSIZE 7;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_2_NAME" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_3_NAME" {
DATATYPE H5T_STRING {
STRSIZE 10;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_4_NAME" {
DATATYPE H5T_STRING {
STRSIZE 9;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_5_NAME" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "FIELD_6_NAME" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "TITLE" {
DATATYPE H5T_STRING {
STRSIZE 14;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "VERSION" {
DATATYPE H5T_STRING {
STRSIZE 4;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
}
}
}
}
Where I basically have 3 datasets under /RECORDS (STATES, EVENTS and COMMUNICATIONS). I think my HDF5 doesn't have anything weird. I've tried to load these datasets using Pandas and Dask arrays and it works.
3. What I would like to know
What is wrong with my HDF5 file making Dask unable to read it as a dataframe?
I've tried to find in the Dask documentation what requirements HDF5 files must satisfy, but there is nothing covering this topic. If at least I knew what problem my file has, I would be able to fix it.
PR https://github.com/dask/dask/pull/6204 was merged recently into dask master that, with luck, solved this issue for you.