Resolved strict aliasing violation resulted in invalid code generatio…

…n by Intel compiler.

CHANGES

@@ -1,3 +1,7 @@
+Changes in 2.7.4 (February 23, 2024)
+- Improved performance of suffix array and burrows wheeler transform construction on degenerate inputs.
+- Resolved strict aliasing violation resulted in invalid code generation by Intel compiler.
+
 Changes in 2.7.3 (April 21, 2023)
 - CMake script for library build and integration with other projects.
 

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.10)
 
-project(libsais VERSION 2.7.3 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
+project(libsais VERSION 2.7.4 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
 
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_C_STANDARD_REQUIRED ON)

README.md

@@ -6,7 +6,7 @@ The libsais is a library for fast (see [Benchmarks](#benchmarks) below) linear t
 * Nataliya Timoshevskaya, Wu-chun Feng *SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction*, 2014
 * Jing Yi Xie, Ge Nong, Bin Lao, Wentao Xu *Scalable Suffix Sorting on a Multicore Machine*, 2020
 
-Copyright (c) 2021-2022 Ilya Grebnov <[email protected]>
+Copyright (c) 2021-2024 Ilya Grebnov <[email protected]>
 
 >The libsais is inspired by [libdivsufsort](https://github.com/y-256/libdivsufsort), [sais](https://sites.google.com/site/yuta256/sais) libraries by Yuta Mori and [msufsort](https://github.com/michaelmaniscalco/msufsort) by Michael Maniscalco.
 
@@ -23,6 +23,9 @@ The libsais provides simple C99 API to construct suffix array and Burrows-Wheele
 The libsais is released under the [Apache License Version 2.0](LICENSE "Apache license")
 
 ## Changes
+* February 23, 2024 (2.7.4)
+  * Improved performance of suffix array and burrows wheeler transform construction on degenerate inputs.
+  * Resolved strict aliasing violation resulted in invalid code generation by Intel compiler.
 * April 21, 2023 (2.7.3)
   * CMake script for library build and integration with other projects.
 * April 18, 2023 (2.7.2)

VERSION

@@ -1 +1 @@
-2.7.3
+2.7.4

include/libsais.h

@@ -3,7 +3,7 @@
 This file is a part of libsais, a library for linear time suffix array,
 longest common prefix array and burrows wheeler transform construction.
 
-   Copyright (c) 2021-2022 Ilya Grebnov <[email protected]>
+   Copyright (c) 2021-2024 Ilya Grebnov <[email protected]>
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS_VERSION_MAJOR   2
 #define LIBSAIS_VERSION_MINOR   7
-#define LIBSAIS_VERSION_PATCH   3
-#define LIBSAIS_VERSION_STRING  "2.7.3"
+#define LIBSAIS_VERSION_PATCH   4
+#define LIBSAIS_VERSION_STRING  "2.7.4"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED

include/libsais16.h

@@ -3,7 +3,7 @@
 This file is a part of libsais, a library for linear time suffix array,
 longest common prefix array and burrows wheeler transform construction.
 
-   Copyright (c) 2021-2022 Ilya Grebnov <[email protected]>
+   Copyright (c) 2021-2024 Ilya Grebnov <[email protected]>
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
@@ -26,21 +26,21 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS16_VERSION_MAJOR   2
 #define LIBSAIS16_VERSION_MINOR   7
-#define LIBSAIS16_VERSION_PATCH   3
-#define LIBSAIS16_VERSION_STRING  "2.7.3"
+#define LIBSAIS16_VERSION_PATCH   4
+#define LIBSAIS16_VERSION_STRING  "2.7.4"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED
         #ifdef LIBSAIS_EXPORTS
-            #define LIBSAIS_API __declspec(dllexport)
+            #define LIBSAIS16_API __declspec(dllexport)
         #else
-            #define LIBSAIS_API __declspec(dllimport)
+            #define LIBSAIS16_API __declspec(dllimport)
         #endif
     #else
-        #define LIBSAIS_API
+        #define LIBSAIS16_API
     #endif
 #else
-    #define LIBSAIS_API
+    #define LIBSAIS16_API
 #endif
 
 #ifdef __cplusplus
@@ -54,7 +54,7 @@ extern "C" {
     * In multi-threaded environments, use one context per thread for parallel executions.
     * @return the libsais16 context, NULL otherwise.
     */
-    LIBSAIS_API void * libsais16_create_ctx(void);
+    LIBSAIS16_API void * libsais16_create_ctx(void);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -63,14 +63,14 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return the libsais16 context, NULL otherwise.
     */
-    LIBSAIS_API void * libsais16_create_ctx_omp(int32_t threads);
+    LIBSAIS16_API void * libsais16_create_ctx_omp(int32_t threads);
 #endif
 
     /**
     * Destroys the libsass context and free previusly allocated memory.
     * @param ctx The libsais16 context (can be NULL).
     */
-    LIBSAIS_API void libsais16_free_ctx(void * ctx);
+    LIBSAIS16_API void libsais16_free_ctx(void * ctx);
 
     /**
     * Constructs the suffix array of a given 16-bit string.
@@ -81,7 +81,7 @@ extern "C" {
     * @param freq [0..65535] The output 16-bit symbol frequency table (can be NULL).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
+    LIBSAIS16_API int32_t libsais16(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
 
     /**
     * Constructs the suffix array of a given 16-bit string using libsais16 context.
@@ -93,7 +93,7 @@ extern "C" {
     * @param freq [0..65535] The output 16-bit symbol frequency table (can be NULL).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_ctx(const void * ctx, const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
+    LIBSAIS16_API int32_t libsais16_ctx(const void * ctx, const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -106,7 +106,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_omp(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_omp(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
 #endif
 
     /**
@@ -119,7 +119,7 @@ extern "C" {
     * @param freq [0..65535] The output 16-bit symbol frequency table (can be NULL).
     * @return The primary index if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq);
+    LIBSAIS16_API int32_t libsais16_bwt(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq);
 
     /**
     * Constructs the burrows-wheeler transformed 16-bit string (BWT) of a given 16-bit string with auxiliary indexes.
@@ -133,7 +133,7 @@ extern "C" {
     * @param I [0..(n-1)/r] The output auxiliary indexes.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt_aux(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I);
+    LIBSAIS16_API int32_t libsais16_bwt_aux(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I);
 
     /**
     * Constructs the burrows-wheeler transformed 16-bit string (BWT) of a given 16-bit string using libsais16 context.
@@ -146,7 +146,7 @@ extern "C" {
     * @param freq [0..65535] The output 16-bit symbol frequency table (can be NULL).
     * @return The primary index if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq);
+    LIBSAIS16_API int32_t libsais16_bwt_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq);
 
     /**
     * Constructs the burrows-wheeler transformed 16-bit string (BWT) of a given 16-bit string with auxiliary indexes using libsais16 context.
@@ -161,7 +161,7 @@ extern "C" {
     * @param I [0..(n-1)/r] The output auxiliary indexes.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt_aux_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I);
+    LIBSAIS16_API int32_t libsais16_bwt_aux_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -175,7 +175,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return The primary index if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_bwt_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
 
     /**
     * Constructs the burrows-wheeler transformed 16-bit string (BWT) of a given 16-bit string with auxiliary indexes in parallel using OpenMP.
@@ -190,15 +190,15 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_bwt_aux_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_bwt_aux_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq, int32_t r, int32_t * I, int32_t threads);
 #endif
 
     /**
     * Creates the libsais16 reverse BWT context that allows reusing allocated memory with each libsais16_unbwt_* operation. 
     * In multi-threaded environments, use one context per thread for parallel executions.
     * @return the libsais16 context, NULL otherwise.
     */
-    LIBSAIS_API void * libsais16_unbwt_create_ctx(void);
+    LIBSAIS16_API void * libsais16_unbwt_create_ctx(void);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -207,14 +207,14 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return the libsais16 context, NULL otherwise.
     */
-    LIBSAIS_API void * libsais16_unbwt_create_ctx_omp(int32_t threads);
+    LIBSAIS16_API void * libsais16_unbwt_create_ctx_omp(int32_t threads);
 #endif
 
     /**
     * Destroys the libsass reverse BWT context and free previusly allocated memory.
     * @param ctx The libsais16 context (can be NULL).
     */
-    LIBSAIS_API void libsais16_unbwt_free_ctx(void * ctx);
+    LIBSAIS16_API void libsais16_unbwt_free_ctx(void * ctx);
 
     /**
     * Constructs the original 16-bit string from a given burrows-wheeler transformed 16-bit string (BWT) with primary index.
@@ -226,7 +226,7 @@ extern "C" {
     * @param i The primary index.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i);
+    LIBSAIS16_API int32_t libsais16_unbwt(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i);
 
     /**
     * Constructs the original 16-bit string from a given burrows-wheeler transformed 16-bit string (BWT) with primary index using libsais16 reverse BWT context.
@@ -239,7 +239,7 @@ extern "C" {
     * @param i The primary index.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i);
+    LIBSAIS16_API int32_t libsais16_unbwt_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i);
 
     /**
     * Constructs the original 16-bit string from a given burrows-wheeler transformed 16-bit string (BWT) with auxiliary indexes.
@@ -252,7 +252,7 @@ extern "C" {
     * @param I [0..(n-1)/r] The input auxiliary indexes.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt_aux(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I);
+    LIBSAIS16_API int32_t libsais16_unbwt_aux(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I);
 
     /**
     * Constructs the original 16-bit string from a given burrows-wheeler transformed 16-bit string (BWT) with auxiliary indexes using libsais16 reverse BWT context.
@@ -266,7 +266,7 @@ extern "C" {
     * @param I [0..(n-1)/r] The input auxiliary indexes.
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt_aux_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I);
+    LIBSAIS16_API int32_t libsais16_unbwt_aux_ctx(const void * ctx, const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -280,7 +280,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_unbwt_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i, int32_t threads);
 
     /**
     * Constructs the original 16-bit string from a given burrows-wheeler transformed 16-bit string (BWT) with auxiliary indexes in parallel using OpenMP.
@@ -294,7 +294,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_unbwt_aux_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_unbwt_aux_omp(const uint16_t * T, uint16_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t r, const int32_t * I, int32_t threads);
 #endif
 
     /**
@@ -305,7 +305,7 @@ extern "C" {
     * @param n The length of the 16-bit string and the suffix array.
     * @return 0 if no error occurred, -1 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_plcp(const uint16_t * T, const int32_t * SA, int32_t * PLCP, int32_t n);
+    LIBSAIS16_API int32_t libsais16_plcp(const uint16_t * T, const int32_t * SA, int32_t * PLCP, int32_t n);
 
     /**
     * Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array.
@@ -315,7 +315,7 @@ extern "C" {
     * @param n The length of the permuted longest common prefix array and the suffix array.
     * @return 0 if no error occurred, -1 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_lcp(const int32_t * PLCP, const int32_t * SA, int32_t * LCP, int32_t n);
+    LIBSAIS16_API int32_t libsais16_lcp(const int32_t * PLCP, const int32_t * SA, int32_t * LCP, int32_t n);
 
 #if defined(LIBSAIS_OPENMP)
     /**
@@ -327,7 +327,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_plcp_omp(const uint16_t * T, const int32_t * SA, int32_t * PLCP, int32_t n, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_plcp_omp(const uint16_t * T, const int32_t * SA, int32_t * PLCP, int32_t n, int32_t threads);
 
     /**
     * Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array in parallel using OpenMP.
@@ -338,7 +338,7 @@ extern "C" {
     * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
     * @return 0 if no error occurred, -1 otherwise.
     */
-    LIBSAIS_API int32_t libsais16_lcp_omp(const int32_t * PLCP, const int32_t * SA, int32_t * LCP, int32_t n, int32_t threads);
+    LIBSAIS16_API int32_t libsais16_lcp_omp(const int32_t * PLCP, const int32_t * SA, int32_t * LCP, int32_t n, int32_t threads);
 #endif
 
 #ifdef __cplusplus