Hello, I have reported this in the previous thread: http://hdf-forum.184993.n3.nabble.com/H5SL-insert-common-can-t-insert-duplicate-key-with-HDF5-1-8-13-td4027464.html
Here I modified the example code provided on the official website to show this limitation. (ex_table_02.c in http://www.hdfgroup.org/HDF5/Tutor/h5table.html) I ran into the following error when appending table for the 599169th iteration. HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 140557357188896: #000: H5Tnative.c line 122 in H5Tget_native_type(): unable to register data type major: Datatype minor: Unable to register new atom #001: H5I.c line 895 in H5I_register(): can't insert ID node into skip list major: Object atom minor: Unable to insert object #002: H5SL.c line 995 in H5SL_insert(): can't create new skip list node major: Skip Lists minor: Unable to insert object #003: H5SL.c line 687 in H5SL_insert_common(): can't insert duplicate key major: Skip Lists minor: Unable to insert object iteration: 599169 Best, Ching-Chia Wang
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from [email protected]. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "hdf5.h" #include "hdf5_hl.h" #include <stdlib.h> /*------------------------------------------------------------------------- * Table API example * * H5TBappend_records * *------------------------------------------------------------------------- */ #define NFIELDS (hsize_t) 5 #define NRECORDS (hsize_t) 8 #define NRECORDS_ADD (hsize_t) 2 #define TABLE_NAME "table" int main( void ) { typedef struct Particle { char name[16]; int lati; int longi; float pressure; double temperature; } Particle; Particle dst_buf[NRECORDS+NRECORDS_ADD]; /* Define an array of Particles */ Particle p_data[NRECORDS] = { {"zero",0,0, 0.0f, 0.0}, {"one",10,10, 1.0f, 10.0}, {"two", 20,20, 2.0f, 20.0}, {"three",30,30, 3.0f, 30.0}, {"four", 40,40, 4.0f, 40.0}, {"five", 50,50, 5.0f, 50.0}, {"six", 60,60, 6.0f, 60.0}, {"seven",70,70, 7.0f, 70.0} }; /* Calculate the size and the offsets of our struct members in memory */ size_t dst_size = sizeof( Particle ); size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ), HOFFSET( Particle, lati ), HOFFSET( Particle, longi ), HOFFSET( Particle, pressure ), HOFFSET( Particle, temperature )}; size_t dst_sizes[NFIELDS] = { sizeof( p_data[0].name), sizeof( p_data[0].lati), sizeof( p_data[0].longi), sizeof( p_data[0].pressure), sizeof( p_data[0].temperature)}; /* Define field information */ const char *field_names[NFIELDS] = { "Name","Latitude", "Longitude", "Pressure", "Temperature" }; hid_t field_type[NFIELDS]; hid_t string_type; hid_t file_id; hsize_t chunk_size = 10; int *fill_data = NULL; int compress = 0; herr_t status; int i; /* Append particles */ Particle particle_in[ NRECORDS_ADD ] = {{ "eight",80,80, 8.0f, 80.0}, {"nine",90,90, 9.0f, 90.0} }; /* Initialize the field field_type */ string_type = H5Tcopy( H5T_C_S1 ); H5Tset_size( string_type, 16 ); field_type[0] = string_type; field_type[1] = H5T_NATIVE_INT; field_type[2] = H5T_NATIVE_INT; field_type[3] = H5T_NATIVE_FLOAT; field_type[4] = H5T_NATIVE_DOUBLE; /* Create a new file using default properties. */ file_id = H5Fcreate( "ex_table_02.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT ); /* make a table */ status=H5TBmake_table( "Table Title",file_id,TABLE_NAME,NFIELDS,NRECORDS, dst_size, field_names, dst_offset, field_type, chunk_size, fill_data, compress, p_data ); /* append two records for one billion times*/ unsigned long long j = 0; for(; j < 1000000000; j++){ printf("\riteration: %llu", j); status=H5TBappend_records(file_id, TABLE_NAME,NRECORDS_ADD, dst_size, dst_offset, dst_sizes, &particle_in ); if(status < 0){ printf("\nH5TBappend_records failed.\n"); exit(-1); } } printf("\nwriting done\n"); /* read the table */ status=H5TBread_table( file_id, TABLE_NAME, dst_size, dst_offset, dst_sizes, dst_buf ); /* print it by rows */ for (i=0; i<NRECORDS+NRECORDS_ADD; i++) { printf ("%-5s %-5d %-5d %-5f %-5f", dst_buf[i].name, dst_buf[i].lati, dst_buf[i].longi, dst_buf[i].pressure, dst_buf[i].temperature); printf ("\n"); } /* close type */ H5Tclose( string_type ); /* close the file */ H5Fclose( file_id ); return 0; }
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