/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5diff.h" #include "ph5diff.h" #include "H5private.h" #include "h5tools.h" /*------------------------------------------------------------------------- * Function: print_size * * Purpose: print dimensions * *------------------------------------------------------------------------- */ static void print_size (int rank, hsize_t *dims) { int i; parallel_print("[" ); for ( i = 0; i < rank-1; i++) { parallel_print("%"H5_PRINTF_LL_WIDTH"u", (unsigned long_long)dims[i]); parallel_print("x"); } parallel_print("%"H5_PRINTF_LL_WIDTH"u", (unsigned long_long)dims[rank-1]); parallel_print("]\n" ); } /*------------------------------------------------------------------------- * Function: diff_dataset * * Purpose: check for comparable datasets and read into a compatible * memory type * * Return: Number of differences found * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: May 9, 2003 * *------------------------------------------------------------------------- */ hsize_t diff_dataset( hid_t file1_id, hid_t file2_id, const char *obj1_name, const char *obj2_name, diff_opt_t *options) { hid_t did1=-1; hid_t did2=-1; hid_t dcpl1=-1; hid_t dcpl2=-1; hsize_t nfound=0; /*------------------------------------------------------------------------- * open the handles *------------------------------------------------------------------------- */ /* disable error reporting */ H5E_BEGIN_TRY { /* Open the datasets */ if ( (did1 = H5Dopen(file1_id,obj1_name)) < 0 ) { printf("Cannot open dataset <%s>\n", obj1_name ); goto error; } if ( (did2 = H5Dopen(file2_id,obj2_name)) < 0 ) { printf("Cannot open dataset <%s>\n", obj2_name ); goto error; } /* enable error reporting */ } H5E_END_TRY; if ((dcpl1=H5Dget_create_plist(did1))<0) goto error; if ((dcpl2=H5Dget_create_plist(did2))<0) goto error; /*------------------------------------------------------------------------- * check if the dataset creation property list has filters that * are not registered in the current configuration * 1) the external filters GZIP and SZIP might not be available * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ if ((h5tools_canreadf((options->m_verbose?obj1_name:NULL),dcpl1)==1) && (h5tools_canreadf((options->m_verbose?obj2_name:NULL),dcpl2)==1)) { nfound=diff_datasetid(did1, did2, obj1_name, obj2_name, options); } /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ /* disable error reporting */ H5E_BEGIN_TRY { H5Pclose(dcpl1); H5Pclose(dcpl2); H5Dclose(did1); H5Dclose(did2); /* enable error reporting */ } H5E_END_TRY; return nfound; error: options->err_stat=1; /* disable error reporting */ H5E_BEGIN_TRY { H5Pclose(dcpl1); H5Pclose(dcpl2); H5Dclose(did1); H5Dclose(did2); /* enable error reporting */ } H5E_END_TRY; return nfound; } /*------------------------------------------------------------------------- * Function: diff_datasetid * * Purpose: check for comparable datasets and read into a compatible * memory type * * Return: Number of differences found * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: May 9, 2003 * * Modifications: * * * October 2006: Read by hyperslabs for big datasets. * * A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done * i.e., if the memory needed to read a dataset is greater than this limit, * then hyperslab I/O is done instead of one operation I/O * For each dataset, the memory needed is calculated according to * * memory needed = number of elements * size of each element * * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations * are done * * H5Dread( input_dataset1 ) * H5Dread( input_dataset2 ) * * with all elements in the datasets selected. If the memory needed is greater than * H5TOOLS_MALLOCSIZE, then the following operations are done instead: * * a strip mine is defined for each dimension k (a strip mine is defined as a * hyperslab whose size is memory manageable) according to the formula * * (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type) * * where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures * that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip * mine size k is simply defined as its dimension k, but for larger datasets the * hyperslab size is still memory manageable. * a cycle is done until the number of elements in the dataset is reached. In each * iteration, two parameters are defined for the function H5Sselect_hyperslab, * the start and size of each hyperslab, according to * * (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k]) * * where hyperslab_offset [k] is initially set to zero, and later incremented in * hyperslab_size[k] offsets. The reason for the operation * * dimension[k] - hyperslab_offset[k] * * in (2) is that, when using the strip mine size, it assures that the "remaining" part * of the dataset that does not fill an entire strip mine is processed. * *------------------------------------------------------------------------- */ hsize_t diff_datasetid( hid_t did1, hid_t did2, const char *obj1_name, const char *obj2_name, diff_opt_t *options) { hid_t sid1=-1; hid_t sid2=-1; hid_t f_tid1=-1; hid_t f_tid2=-1; hid_t m_tid1=-1; hid_t m_tid2=-1; size_t m_size1; size_t m_size2; H5T_sign_t sign1; H5T_sign_t sign2; int rank1; int rank2; hsize_t nelmts1; hsize_t nelmts2; hsize_t dims1[H5S_MAX_RANK]; hsize_t dims2[H5S_MAX_RANK]; hsize_t maxdim1[H5S_MAX_RANK]; hsize_t maxdim2[H5S_MAX_RANK]; const char *name1=NULL; /* relative names */ const char *name2=NULL; hsize_t storage_size1; hsize_t storage_size2; hsize_t nfound=0; /* number of differences found */ int cmp=1; /* do diff or not */ void *buf1=NULL; void *buf2=NULL; void *sm_buf1=NULL; void *sm_buf2=NULL; size_t need; /* bytes needed for malloc */ int i; /* Get the dataspace handle */ if ( (sid1 = H5Dget_space(did1)) < 0 ) goto error; /* Get rank */ if ( (rank1 = H5Sget_simple_extent_ndims(sid1)) < 0 ) goto error; /* Get the dataspace handle */ if ( (sid2 = H5Dget_space(did2)) < 0 ) goto error; /* Get rank */ if ( (rank2 = H5Sget_simple_extent_ndims(sid2)) < 0 ) goto error; /* Get dimensions */ if ( H5Sget_simple_extent_dims(sid1,dims1,maxdim1) < 0 ) goto error; /* Get dimensions */ if ( H5Sget_simple_extent_dims(sid2,dims2,maxdim2) < 0 ) goto error; /*------------------------------------------------------------------------- * Get the file data type *------------------------------------------------------------------------- */ /* Get the data type */ if ( (f_tid1 = H5Dget_type(did1)) < 0 ) goto error; /* Get the data type */ if ( (f_tid2 = H5Dget_type(did2)) < 0 ) goto error; /*------------------------------------------------------------------------- * check for empty datasets *------------------------------------------------------------------------- */ storage_size1=H5Dget_storage_size(did1); storage_size2=H5Dget_storage_size(did2); if (storage_size1<0 || storage_size2<0) goto error; if (storage_size1==0 || storage_size2==0) { if (options->m_verbose && obj1_name && obj2_name) parallel_print("<%s> or <%s> are empty datasets\n", obj1_name, obj2_name); cmp=0; options->not_cmp=1; } /*------------------------------------------------------------------------- * check for comparable TYPE and SPACE *------------------------------------------------------------------------- */ if (diff_can_type(f_tid1, f_tid2, rank1, rank2, dims1, dims2, maxdim1, maxdim2, obj1_name, obj2_name, options)!=1) { cmp=0; options->not_cmp=1; } /*------------------------------------------------------------------------- * memory type and sizes *------------------------------------------------------------------------- */ if ((m_tid1=h5tools_get_native_type(f_tid1))<0) goto error; if ((m_tid2=h5tools_get_native_type(f_tid2))<0) goto error; m_size1 = H5Tget_size( m_tid1 ); m_size2 = H5Tget_size( m_tid2 ); /*------------------------------------------------------------------------- * check for different signed/unsigned types *------------------------------------------------------------------------- */ sign1=H5Tget_sign(m_tid1); sign2=H5Tget_sign(m_tid2); if ( sign1 != sign2 ) { if (options->m_verbose && obj1_name) { parallel_print("Comparison not supported: <%s> has sign %s ", obj1_name, get_sign(sign1)); parallel_print("and <%s> has sign %s\n", obj2_name, get_sign(sign2)); } cmp=0; options->not_cmp=1; } /*------------------------------------------------------------------------- * only attempt to compare if possible *------------------------------------------------------------------------- */ if (cmp) { /*------------------------------------------------------------------------- * get number of elements *------------------------------------------------------------------------- */ nelmts1 = 1; for (i = 0; i < rank1; i++) { nelmts1 *= dims1[i]; } nelmts2 = 1; for (i = 0; i < rank2; i++) { nelmts2 *= dims2[i]; } assert(nelmts1==nelmts2); /*------------------------------------------------------------------------- * "upgrade" the smaller memory size *------------------------------------------------------------------------- */ if ( m_size1 != m_size2 ) { if ( m_size1 < m_size2 ) { H5Tclose(m_tid1); if ((m_tid1=h5tools_get_native_type(f_tid2))<0) goto error; m_size1 = H5Tget_size( m_tid1 ); } else { H5Tclose(m_tid2); if ((m_tid2=h5tools_get_native_type(f_tid1))<0) goto error; m_size2 = H5Tget_size( m_tid2 ); } } assert(m_size1==m_size2); /* print names */ if (obj1_name) { name1=diff_basename(obj1_name); } if (obj2_name) { name2=diff_basename(obj2_name); } /*------------------------------------------------------------------------- * read/compare *------------------------------------------------------------------------- */ need = (size_t)(nelmts1*m_size1); /* bytes needed */ if ( need < H5TOOLS_MALLOCSIZE) { buf1 = HDmalloc(need); buf2 = HDmalloc(need); } if ( buf1!=NULL && buf2!=NULL) { if ( H5Dread(did1,m_tid1,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf1) < 0 ) goto error; if ( H5Dread(did2,m_tid2,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf2) < 0 ) goto error; /* array diff */ nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1, options, name1, name2, m_tid1, did1, did2); } else /* possibly not enough memory, read/compare by hyperslabs */ { size_t p_type_nbytes = m_size1; /*size of memory type */ hsize_t p_nelmts = nelmts1; /*total selected elmts */ hsize_t elmtno; /*counter */ int carry; /*counter carry value */ unsigned int vl_data = 0; /*contains VL datatypes */ /* stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ hsize_t sm_nbytes; /*bytes per stripmine */ hsize_t sm_nelmts; /*elements per stripmine*/ hid_t sm_space; /*stripmine data space */ /* hyperslab info */ hsize_t hs_offset[H5S_MAX_RANK]; /*starting offset */ hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */ hsize_t hs_nelmts; /*elements in request */ hsize_t zero[8]; /*vector of zeros */ /* check if we have VL data in the dataset's datatype */ if (H5Tdetect_class(m_tid1, H5T_VLEN) == TRUE) vl_data = TRUE; /* * determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ sm_nbytes = p_type_nbytes; for (i = rank1; i > 0; --i) { sm_size[i - 1] = MIN(dims1[i - 1], H5TOOLS_BUFSIZE / sm_nbytes); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } sm_buf1 = malloc((size_t)sm_nbytes); sm_buf2 = malloc((size_t)sm_nbytes); sm_nelmts = sm_nbytes / p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); /* the stripmine loop */ memset(hs_offset, 0, sizeof hs_offset); memset(zero, 0, sizeof zero); for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { /* calculate the hyperslab size */ if (rank1 > 0) { for (i = 0, hs_nelmts = 1; i < rank1; i++) { hs_size[i] = MIN(dims1[i] - hs_offset[i], sm_size[i]); hs_nelmts *= hs_size[i]; } if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0) goto error; if (H5Sselect_hyperslab(sid2, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0) goto error; if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0) goto error; } else { H5Sselect_all(sid1); H5Sselect_all(sid2); H5Sselect_all(sm_space); hs_nelmts = 1; } /* rank */ if ( H5Dread(did1,m_tid1,sm_space,sid1,H5P_DEFAULT,sm_buf1) < 0 ) goto error; if ( H5Dread(did2,m_tid2,sm_space,sid2,H5P_DEFAULT,sm_buf2) < 0 ) goto error; /* get array differences. in the case of hyperslab read, increment the number of differences found in each hyperslab and pass the position at the beggining for printing */ nfound += diff_array(sm_buf1, sm_buf2, hs_nelmts, elmtno, rank1, dims1, options, name1, name2, m_tid1, did1, did2); /* reclaim any VL memory, if necessary */ if(vl_data) { H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf1); H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf2); } /* calculate the next hyperslab offset */ for (i = rank1, carry = 1; i > 0 && carry; --i) { hs_offset[i - 1] += hs_size[i - 1]; if (hs_offset[i - 1] == dims1[i - 1]) hs_offset[i - 1] = 0; else carry = 0; } /* i */ } /* elmtno */ H5Sclose(sm_space); /* free */ if (sm_buf1!=NULL) { free(sm_buf1); sm_buf1=NULL; } if (sm_buf2!=NULL) { free(sm_buf2); sm_buf2=NULL; } } /* hyperslab read */ }/*cmp*/ /*------------------------------------------------------------------------- * compare attributes * the if condition refers to cases when the dataset is a referenced object *------------------------------------------------------------------------- */ if (obj1_name) nfound += diff_attr(did1,did2,obj1_name,obj2_name,options); /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ /* free */ if (buf1!=NULL) { free(buf1); buf1=NULL; } if (buf2!=NULL) { free(buf2); buf2=NULL; } if (sm_buf1!=NULL) { free(sm_buf1); sm_buf1=NULL; } if (sm_buf2!=NULL) { free(sm_buf2); sm_buf2=NULL; } H5E_BEGIN_TRY { H5Sclose(sid1); H5Sclose(sid2); H5Tclose(f_tid1); H5Tclose(f_tid2); H5Tclose(m_tid1); H5Tclose(m_tid2); } H5E_END_TRY; return nfound; error: options->err_stat=1; /* free */ if (buf1!=NULL) { free(buf1); buf1=NULL; } if (buf2!=NULL) { free(buf2); buf2=NULL; } if (sm_buf1!=NULL) { free(sm_buf1); sm_buf1=NULL; } if (sm_buf2!=NULL) { free(sm_buf2); sm_buf2=NULL; } /* disable error reporting */ H5E_BEGIN_TRY { H5Sclose(sid1); H5Sclose(sid2); H5Tclose(f_tid1); H5Tclose(f_tid2); H5Tclose(m_tid1); H5Tclose(m_tid2); /* enable error reporting */ } H5E_END_TRY; return nfound; } /*------------------------------------------------------------------------- * Function: diff_can_type * * Purpose: check for comparable TYPE and SPACE * * Return: * 1, can compare * 0, cannot compare * -1, error * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 3, 2003 * *------------------------------------------------------------------------- */ int diff_can_type( hid_t f_tid1, /* file data type */ hid_t f_tid2, /* file data type */ int rank1, int rank2, hsize_t *dims1, hsize_t *dims2, hsize_t *maxdim1, hsize_t *maxdim2, const char *obj1_name, const char *obj2_name, diff_opt_t *options ) { H5T_class_t tclass1; H5T_class_t tclass2; int maxdim_diff=0; /* maximum dimensions are different */ int dim_diff=0; /* current dimensions are different */ int i; /*------------------------------------------------------------------------- * check for the same class *------------------------------------------------------------------------- */ if ((tclass1=H5Tget_class(f_tid1))<0) return -1; if ((tclass2=H5Tget_class(f_tid2))<0) return -1; if ( tclass1 != tclass2 ) { if (options->m_verbose && obj1_name) { printf("Comparison not possible: <%s> is of class %s and <%s> is of class %s\n", obj1_name, get_class(tclass1), obj2_name, get_class(tclass2) ); } return 0; } /*------------------------------------------------------------------------- * check for non supported classes *------------------------------------------------------------------------- */ assert(tclass1==tclass2); switch (tclass1) { case H5T_INTEGER: case H5T_FLOAT: case H5T_COMPOUND: case H5T_STRING: case H5T_ARRAY: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_ENUM: case H5T_VLEN: case H5T_REFERENCE: break; default: /*H5T_TIME */ if (options->m_verbose && obj1_name ) printf("Comparison not supported: <%s> and <%s> are of class %s\n", obj1_name,obj2_name,get_class(tclass2) ); return 0; } /*------------------------------------------------------------------------- * check for equal file datatype; warning only *------------------------------------------------------------------------- */ if ( (H5Tequal(f_tid1, f_tid2)==0) && options->m_verbose && obj1_name) { printf("Warning: different storage datatype\n"); printf("<%s> has file datatype ", obj1_name); print_type(f_tid1); printf("\n"); printf("<%s> has file datatype ", obj2_name); print_type(f_tid2); printf("\n"); } /*------------------------------------------------------------------------- * check for the same rank *------------------------------------------------------------------------- */ if ( rank1 != rank2 ) { if (options->m_verbose && obj1_name) { printf("Comparison not supported: <%s> has rank %d, dimensions ", obj1_name, rank1); print_dimensions(rank1,dims1); printf(", max dimensions "); print_dimensions(rank1,maxdim1); printf("\n" ); printf("<%s> has rank %d, dimensions ", obj2_name, rank2); print_dimensions(rank2,dims2); printf(", max dimensions "); print_dimensions(rank2,maxdim2); } return 0; } /*------------------------------------------------------------------------- * check for different dimensions *------------------------------------------------------------------------- */ assert(rank1==rank2); for ( i=0; im_verbose && obj1_name) { printf("Comparison not supported: <%s> has rank %d, dimensions ", obj1_name, rank1); print_dimensions(rank1,dims1); if (maxdim1 && maxdim2) { printf(", max dimensions "); print_dimensions(rank1,maxdim1); printf("\n" ); printf("<%s> has rank %d, dimensions ", obj2_name, rank2); print_dimensions(rank2,dims2); printf(", max dimensions "); print_dimensions(rank2,maxdim2); } } return 0; } /*------------------------------------------------------------------------- * maximum dimensions; just give a warning *------------------------------------------------------------------------- */ if (maxdim1 && maxdim2 && maxdim_diff==1 && obj1_name ) { if (options->m_verbose) { printf( "Warning: different maximum dimensions\n"); printf("<%s> has max dimensions ", obj1_name); print_dimensions(rank1,maxdim1); printf("\n"); printf("<%s> has max dimensions ", obj2_name); print_dimensions(rank2,maxdim2); printf("\n"); } } return 1; } /*------------------------------------------------------------------------- * Function: print_sizes * * Purpose: Print datatype sizes * *------------------------------------------------------------------------- */ #if defined (H5DIFF_DEBUG) void print_sizes( const char *obj1, const char *obj2, hid_t f_tid1, hid_t f_tid2, hid_t m_tid1, hid_t m_tid2 ) { size_t f_size1, f_size2; /* size of type in file */ size_t m_size1, m_size2; /* size of type in memory */ f_size1 = H5Tget_size( f_tid1 ); f_size2 = H5Tget_size( f_tid2 ); m_size1 = H5Tget_size( m_tid1 ); m_size2 = H5Tget_size( m_tid2 ); printf("\n"); printf("------------------\n"); printf("sizeof(char) %u\n", sizeof(char) ); printf("sizeof(short) %u\n", sizeof(short) ); printf("sizeof(int) %u\n", sizeof(int) ); printf("sizeof(long) %u\n", sizeof(long) ); printf("<%s> ------------------\n", obj1); printf("type on file "); print_type(f_tid1); printf("\n"); printf("size on file %u\n", f_size1 ); printf("type on memory "); print_type(m_tid1); printf("\n"); printf("size on memory %u\n", m_size1 ); printf("<%s> ------------------\n", obj2); printf("type on file "); print_type(f_tid2); printf("\n"); printf("size on file %u\n", f_size2 ); printf("type on memory "); print_type(m_tid2); printf("\n"); printf("size on memory %u\n", m_size2 ); printf("\n"); } #endif /* H5DIFF_DEBUG */