bsc 3.3.2

CHANGES

@@ -1,3 +1,6 @@
+Changes in 3.3.2 (March, 24 2023)
+- Reduced memory usage and improved performance of GPU accelerated forward BWT.
+
 Changes in 3.3.1 (February, 15 2023)
 - Added ability to specify block size in bytes as oppose to megabytes.
 

README

@@ -54,7 +54,7 @@ Compression and decompression requirements are the same and in bytes, can
 be estimated as 16Mb + 5 x block size x number of blocks processed in parallel.
 
 GPU memory usage for NVIDIA CUDA technology is different from CPU memory usage
-and can be estimated as 20 x block size for ST and 32 x block size for BWT.
+and can be estimated as 20 x block size for ST and 21 x block size for BWT.
 
 
 NVIDIA GPU acceleration:

VERSION

@@ -1 +1 @@
-3.3.1
+3.3.2

bsc.cpp

@@ -869,7 +869,7 @@ void ProcessCommandline(int argc, char * argv[])
 
 int main(int argc, char * argv[])
 {
-    fprintf(stdout, "This is bsc, Block Sorting Compressor. Version 3.3.1. 15 February 2023.\n");
+    fprintf(stdout, "This is bsc, Block Sorting Compressor. Version 3.3.2. 24 March 2023.\n");
     fprintf(stdout, "Copyright (c) 2009-2023 Ilya Grebnov <Ilya.Grebnov@gmail.com>.\n\n");
 
 #if defined(_OPENMP) && defined(__INTEL_COMPILER)

libbsc/bwt/libcubwt/CHANGES

@@ -1,3 +1,6 @@
+Changes in 1.5.0 (March 24, 2023)
+- Reduced memory usage and improved performance.
+
 Changes in 1.0.0 (February 10, 2023)
 - Initial public release of the libcubwt.
 

libbsc/bwt/libcubwt/VERSION

@@ -1 +1 @@
-1.0.0
+1.5.0

libbsc/bwt/libcubwt/libcubwt.cuh

@@ -1,7 +1,7 @@
 /*--
 
 This file is a part of libcubwt, a library for CUDA accelerated
-suffix array and burrows wheeler transform construction.
+burrows wheeler transform construction.
 
    Copyright (c) 2022-2023 Ilya Grebnov <ilya.grebnov@gmail.com>
 
@@ -25,9 +25,9 @@ Please see the file LICENSE for full copyright and license details.
 #define LIBCUBWT_CUH 1
 
 #define LIBCUBWT_VERSION_MAJOR          1
-#define LIBCUBWT_VERSION_MINOR          0
+#define LIBCUBWT_VERSION_MINOR          5
 #define LIBCUBWT_VERSION_PATCH          0
-#define LIBCUBWT_VERSION_STRING	        "1.0.0"
+#define LIBCUBWT_VERSION_STRING	        "1.5.0"
 
 #define LIBCUBWT_NO_ERROR               0
 #define LIBCUBWT_BAD_PARAMETER          -1
@@ -57,37 +57,6 @@ extern "C" {
     */
     int64_t libcubwt_free_device_storage(void * device_storage);
 
-    /**
-    * Constructs the suffix array (SA) of a given string.
-    * @param device_storage The previously allocated storage on the CUDA device.
-    * @param T [0..n-1] The input string.
-    * @param SA [0..n-1] The output array of suffixes.
-    * @param n The length of the input string.
-    * @return LIBCUBWT_NO_ERROR if no error occurred, libcubwt error code otherwise.
-    */
-    int64_t libcubwt_sa(void * device_storage, const uint8_t * T, uint32_t * SA, int64_t n);
-
-    /**
-    * Constructs the inverse suffix array (ISA) of a given string.
-    * @param device_storage The previously allocated storage on the CUDA device.
-    * @param T [0..n-1] The input string.
-    * @param ISA [0..n-1] The output inverse array of suffixes.
-    * @param n The length of the input string.
-    * @return LIBCUBWT_NO_ERROR if no error occurred, libcubwt error code otherwise.
-    */
-    int64_t libcubwt_isa(void * device_storage, const uint8_t * T, uint32_t * ISA, int64_t n);
-
-    /**
-    * Constructs the suffix array (SA) and inverse suffix array (ISA) of a given string.
-    * @param device_storage The previously allocated storage on the CUDA device.
-    * @param T [0..n-1] The input string.
-    * @param SA [0..n-1] The output array of suffixes.
-    * @param ISA [0..n-1] The output inverse array of suffixes.
-    * @param n The length of the input string.
-    * @return LIBCUBWT_NO_ERROR if no error occurred, libcubwt error code otherwise.
-    */
-    int64_t libcubwt_sa_isa(void * device_storage, const uint8_t * T, uint32_t * SA, uint32_t * ISA, int64_t n);
-
     /**
     * Constructs the Burrows-Wheeler Transform (BWT) of a given string.
     * @param device_storage The previously allocated storage on the CUDA device.
@@ -98,17 +67,6 @@ extern "C" {
     */
     int64_t libcubwt_bwt(void * device_storage, const uint8_t * T, uint8_t * L, int64_t n);
 
-    /**
-    * Constructs the Burrows-Wheeler Transform (BWT) and inverse suffix array (ISA) of a given string.
-    * @param device_storage The previously allocated storage on the CUDA device.
-    * @param T [0..n-1] The input string.
-    * @param L [0..n-1] The output string (can be T).
-    * @param ISA [0..n-1] The output inverse array of suffixes.
-    * @param n The length of the input string.
-    * @return The primary index if no error occurred, libcubwt error code otherwise.
-    */
-    int64_t libcubwt_bwt_isa(void * device_storage, const uint8_t * T, uint8_t * L, uint32_t * ISA, int64_t n);
-
     /**
     * Constructs the Burrows-Wheeler Transform (BWT) of a given string with auxiliary indexes.
     * @param device_storage The previously allocated storage on the CUDA device.

libbsc/libbsc.h

@@ -35,8 +35,8 @@ See also the bsc and libbsc web site:
 
 #define LIBBSC_VERSION_MAJOR           3
 #define LIBBSC_VERSION_MINOR           3
-#define LIBBSC_VERSION_PATCH           1
-#define LIBBSC_VERSION_STRING          "3.3.1"
+#define LIBBSC_VERSION_PATCH           2
+#define LIBBSC_VERSION_STRING          "3.3.2"
 
 #define LIBBSC_NO_ERROR                0
 #define LIBBSC_BAD_PARAMETER          -1