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The existing X31 hash propagates bits fairly slowly, resulting in a poor distribution of keys if most of the differences in strings are at the end. Fix by using FNV1a instead, which is a similar speed to calculate but distributes keys much more effectively. Includes kh_stats() function in khash which produces a histogram of probe chain lengths and a khash test framework. The test program can also be used to benchmark insertion and lookup times.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| /* The MIT License | ||
| Copyright (c) 2008, 2009, 2011 by Attractive Chaos <[email protected]> | ||
| Copyright (C) 2014-2015, 2018 Genome Research Ltd. | ||
| Copyright (C) 2014-2015, 2018, 2024 Genome Research Ltd. | ||
| Permission is hereby granted, free of charge, to any person obtaining | ||
| a copy of this software and associated documentation files (the | ||
|
|
@@ -356,7 +356,39 @@ static const double __ac_HASH_UPPER = 0.77; | |
| __ac_set_isdel_true(h->flags, x); \ | ||
| --h->size; \ | ||
| } \ | ||
| } | ||
| } \ | ||
| SCOPE int kh_stats_##name(kh_##name##_t *h, khint_t *empty, \ | ||
| khint_t *deleted, khint_t *hist_size, \ | ||
| khint_t **hist_out) \ | ||
| { \ | ||
| khint_t i, *hist = NULL, dist_max = 0, k, dist, step; \ | ||
| khint_t mask = h->n_buckets - 1; \ | ||
| *empty = *deleted = *hist_size = 0; \ | ||
| hist = (khint_t *) calloc(1, sizeof(*hist)); \ | ||
| if (!hist) { return -1; } \ | ||
| for (i = kh_begin(h); i < kh_end(h); ++i) { \ | ||
| if (__ac_isempty(h->flags, i)) { (*empty)++; continue; } \ | ||
| if (__ac_isdel(h->flags, i)) { (*deleted)++; continue; } \ | ||
| k = __hash_func(h->keys[i]) & (h->n_buckets - 1); \ | ||
| dist = 0; \ | ||
| step = 0; \ | ||
| while (k != i) { \ | ||
| dist++; \ | ||
| k = (k + (++step)) & mask; \ | ||
| } \ | ||
| if (dist_max <= dist) { \ | ||
| khint_t *new_hist = (khint_t *) realloc(hist, sizeof(*new_hist) * (dist + 1)); \ | ||
| if (!new_hist) { free(hist); return -1; } \ | ||
| for (k = dist_max + 1; k <= dist; k++) new_hist[k] = 0; \ | ||
| hist = new_hist; \ | ||
| dist_max = dist; \ | ||
| } \ | ||
| hist[dist]++; \ | ||
| } \ | ||
| *hist_out = hist; \ | ||
| *hist_size = dist_max + 1; \ | ||
| return 0; \ | ||
| } | ||
|
|
||
| #define KHASH_DECLARE(name, khkey_t, khval_t) \ | ||
| __KHASH_TYPE(name, khkey_t, khval_t) \ | ||
|
|
@@ -391,6 +423,7 @@ static const double __ac_HASH_UPPER = 0.77; | |
| @abstract 64-bit integer comparison function | ||
| */ | ||
| #define kh_int64_hash_equal(a, b) ((a) == (b)) | ||
|
|
||
| /*! @function | ||
| @abstract const char* hash function | ||
| @param s Pointer to a null terminated string | ||
|
|
@@ -402,12 +435,28 @@ static kh_inline khint_t __ac_X31_hash_string(const char *s) | |
| if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s; | ||
| return h; | ||
| } | ||
|
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||
| /*! @function | ||
| @abstract const char* FNV1a hash function | ||
| @param s Pointer to a null terminated string | ||
| @return The hash value | ||
| */ | ||
| static kh_inline khint_t __ac_FNV1a_hash_string(const char *s) | ||
| { | ||
| const khint_t offset_basis = 2166136261; | ||
| const khint_t FNV_prime = 16777619; | ||
| khint_t h = offset_basis; | ||
| for (; *s; ++s) h = (h ^ (uint8_t) *s) * FNV_prime; | ||
| return h; | ||
| } | ||
|
|
||
| /*! @function | ||
| @abstract Another interface to const char* hash function | ||
| @param key Pointer to a nul terminated string [const char*] | ||
| @return The hash value [khint_t] | ||
| */ | ||
| #define kh_str_hash_func(key) __ac_X31_hash_string(key) | ||
| #define kh_str_hash_func(key) __ac_FNV1a_hash_string(key) | ||
|
|
||
| /*! @function | ||
| @abstract Const char* comparison function | ||
| */ | ||
|
|
@@ -426,12 +475,29 @@ static kh_inline khint_t __ac_X31_hash_kstring(const kstring_t ks) | |
| h = (h << 5) - h + (khint_t)ks.s[i]; | ||
| return h; | ||
| } | ||
|
|
||
| /*! @function | ||
| @abstract Kstring hash function | ||
| @param s Pointer to a kstring | ||
| @return The hash value | ||
| */ | ||
| static kh_inline khint_t __ac_FNV1a_hash_kstring(const kstring_t ks) | ||
| { | ||
| const khint_t offset_basis = 2166136261; | ||
| const khint_t FNV_prime = 16777619; | ||
| khint_t h = offset_basis; | ||
| size_t i; | ||
| for (i = 0; i < ks.l; i++) | ||
| h = (h ^ (uint8_t) ks.s[i]) * FNV_prime; | ||
| return h; | ||
| } | ||
|
|
||
| /*! @function | ||
| @abstract Interface to kstring hash function. | ||
| @param key Pointer to a khash; permits hashing on non-nul terminated strings. | ||
| @return The hash value [khint_t] | ||
| */ | ||
| #define kh_kstr_hash_func(key) __ac_X31_hash_kstring(key) | ||
| #define kh_kstr_hash_func(key) __ac_FNV1a_hash_kstring(key) | ||
| /*! @function | ||
| @abstract kstring comparison function | ||
| */ | ||
|
|
@@ -604,6 +670,19 @@ static kh_inline khint_t __ac_Wang_hash(khint_t key) | |
| code; \ | ||
| } } | ||
|
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||
| /*! @function | ||
| @abstract Gather hash table statistics | ||
| @param name Name of the hash table [symbol] | ||
| @param h Pointer to the hash table [khash_t(name)*] | ||
| @param empty[out] Number of empty hash bins | ||
| @param deleted[out] Number of hash bins with the deleted flag | ||
| @param hist_size[out] Size of @p hist array | ||
| @param hist[out] Probe count histogram | ||
| @return 0 on success; -1 on failure | ||
| */ | ||
| #define kh_stats(name, h, empty, deleted, hist_size, hist) \ | ||
| kh_stats_##name(h, empty, deleted, hist_size, hist) | ||
|
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| /* More convenient interfaces */ | ||
|
|
||
| /*! @function | ||
|
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