diff --git a/Projet/CODE/apm/$ b/Projet/CODE/apm/$
deleted file mode 100644
index f2ff57bca5727ab4bcbc529bc656405b7cd5670e..0000000000000000000000000000000000000000
--- a/Projet/CODE/apm/$
+++ /dev/null
@@ -1,318 +0,0 @@
-/**
- * APPROXIMATE PATTERN MATCHING
- *
- * INF560 X2016
- */
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <fcntl.h>
-#include <unistd.h>
-#include <sys/time.h>
-
-#define APM_DEBUG 0
-
-char * read_input_file(char * filename, int * size)
-{
- char * buf;
- off_t fsize;
- int fd = 0;
- int n_bytes = 1;
-
- /* Open the text file */
- fd = open(filename, O_RDONLY);
- if (fd == -1)
- {
- fprintf(stderr, "Unable to open the text file <%s>\n", filename);
- return NULL;
- }
-
- /* Get the number of characters in the textfile */
- fsize = lseek(fd, 0, SEEK_END);
- lseek(fd, 0, SEEK_SET);
- /* TODO check return of lseek */
-
-#if APM_DEBUG
- printf("File length: %lld\n", fsize);
-#endif
-
- /* Allocate data to copy the target text */
- buf = (char *)malloc(fsize * sizeof (char));
- if (buf == NULL)
- {
- fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
- fsize);
- return NULL;
- }
-
- n_bytes = read(fd, buf, fsize);
- if (n_bytes != fsize)
- {
- fprintf(stderr,
- "Unable to copy %ld byte(s) from text file (%d byte(s) copied)\n",
- fsize, n_bytes);
- return NULL;
- }
-
-#if APM_DEBUG
- printf("Number of read bytes: %d\n", n_bytes);
-#endif
-
- *size = n_bytes;
- close(fd);
- return buf;
-}
-
-#define MIN3(a, b, c) ((a)<(b) ? ((a)<(c) ? (a) : (c)) : ((b)<(c) ? (b) : (c)))
-
-int levenshtein(char *s1, char *s2, int len, int * column, int approx_factor)
-{
- int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (s1[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
- return (column[len] <= approx_factor) ? 1 : 0;
-}
-
-__global__ void levenshtein_cu(char *find, char *buf, int len, int n_bytes
- ,int approx_factor, int* g_column, int* result_vec)
-{
- int tId = blockIdx.x * blockDim.x + threadIdx.x;//global thread id
- if (tId > n_bytes)
- {return;}//we are past the buffer length - do not process
-
- //position s2 and column to the right position in the pre-allocated
- //arrays
- char* s2 = buf+tId;
- int* column = g_column+tId*(len+1);
-
- //i do not understand this algorithm and god do i not want to.
- int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (find[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
-
- if (column[len] <= approx_factor)
- {result_vec[tId] = 1;}//its a match
-}
-
-int main(int argc, char ** argv)
-{
- char ** pattern;
- char * filename;
- int approx_factor = 0;
- int nb_patterns = 0;
-
- char * buf;
- struct timeval t1, t2;
- double duration;
- int n_bytes;
- int * n_matches;
-
- //cuda-related vars
- char *buf_dev;
- int NTBB = 1024; //Number of threads by blocks
- int NB;//Number of blocks
- cudaError_t cu_err;
-
- /* Check number of arguments */
- if (argc < 4)
- {
- printf("Usage: %s approximation_factor "
- "dna_database pattern1 pattern2 ...\n",
- argv[0]);
- return 1;
- }
-
- approx_factor = atoi(argv[1]);/* Get the distance factor */
- filename = argv[2];/* Grab the filename containing the target text */
- nb_patterns = argc - 3;/* Get the number of patterns to search for */
-
- pattern = (char **)malloc(nb_patterns * sizeof(char*));
- if (pattern == NULL)/*Fill the pattern*/
- {
- fprintf(stderr,
- "Unable to allocate array of pattern of size %d\n",
- nb_patterns);
- return 1;
- }
-
- for (int i=0; i < nb_patterns; i++) /* Grab the patterns */
- {
- int l;
- l = strlen(argv[i+3]);
-
- if (l <= 0)
- {
- fprintf(stderr, "Error while parsing argument %d\n", i+3);
- return 1;
- }
-
- pattern[i] = (char *)malloc((l+1) * sizeof(char));
- if (pattern[i] == NULL)
- {
- fprintf(stderr, "Unable to allocate string of size %d\n", l);
- return 1;
- }
-
- strncpy(pattern[i], argv[i+3], (l+1));
- }
-
-
- printf("Approximate Pattern Mathing: "
- "looking for %d pattern(s) in file %s w/ distance of %d\n",
- nb_patterns, filename, approx_factor);
-
- buf = read_input_file(filename, &n_bytes);
- if (buf == NULL)
- {
- fprintf(stderr, "Error: NULL pointer from reading input file.");
- return 1;
- }
-
- cudaMalloc((void**)&buf_dev, n_bytes * sizeof(char));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to allocate buffer on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return ;
- }
-
- cudaMemcpy(NULL, buf, n_bytes, cudaMemcpyHostToDevice);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to copy buffer onto device: %s.\n"
- , cudaGetErrorString(cu_err));
- return ;
- }
-
-
- n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
- if (n_matches == NULL)
- {
- fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
- nb_patterns * sizeof(int));
- return 1;
- }
-
- /*****
- * BEGIN MAIN LOOP
- ******/
-
- /* Timer start */
- gettimeofday(&t1, NULL);
-
- for (int i = 0; i < nb_patterns; i++)
- {
- n_matches[i] = 0;
-
- //TODO err check
- int size_pattern = strlen(pattern[i]);
- char* pattern_dev;
- cudaMalloc((void**)&pattern_dev, size_pattern);
-
- cudaMemcpy(pattern_dev, pattern[i]
- , size_pattern, cudaMemcpyHostToDevice);
-
- NB = (n_bytes / NTBB) + (((n_bytes % NTBB) > 0) ? 1 : 0);
- //printf("n_bytes : %i, NB : %i ; nb_threads : %i\n"
- // , n_bytes, NB, NB*NTBB);
-
- //TODO err check
- int * column_dev;
- cudaMalloc((void**)&column_dev, (size_pattern+1)*NTBB*NB*sizeof(int));
-
-
-
- //TODO err check
- int * result_vec_dev; //result vectors.
- cudaMalloc((void**)&result_vec_dev, NTBB*NB*sizeof(int));
-
- int * result_vec =(int*) malloc(NTBB*NB*sizeof(int));
- memset(result_vec, 0, NTBB*NB*sizeof(int));
-
- cudaMemcpy(result_vec_dev, result_vec
- , NTBB*NB, cudaMemcpyHostToDevice);
-
-
-
- levenshtein_cu<<<NB,NTBB>>>(pattern_dev, buf_dev, size_pattern
- , n_bytes, approx_factor, column_dev, result_vec_dev);
-
- //get result
- cudaMemcpy(result_vec, result_vec_dev
- , NTBB*NB*sizeof(int), cudaMemcpyDeviceToHost);
-
- for (int j = 0 ; j<n_bytes ; j++)
- {
- /* Highly advanced debbugging (printfs)
- int column[size_pattern+1];
- int d =
- levenshtein(pattern[i], buf+j, size_pattern, column, approx_factor);
- //printf("%d",d);
- if (d != result_vec[j])
- {
- printf("MISMATCH FOUND %s should have match at %i :"
- ,pattern[i], j);
- printf("%.*s\n",size_pattern,&buf[j]);
- }
- */
- n_matches[i] += result_vec[j];
- }
-
- //free memory - and then get onto the next pattern.
- cudaFree(pattern_dev);
- cudaFree(column_dev);
- cudaFree(result_vec_dev);
- free(result_vec);
- }
-
- /* Timer stop */
- gettimeofday(&t2, NULL);
-
- duration = (t2.tv_sec -t1.tv_sec)+((t2.tv_usec-t1.tv_usec)/1e6);
-
- printf("APM done in %lf s\n", duration);
-
- /*****
- * END MAIN LOOP
- ******/
-
- for (int i=0; i < nb_patterns; i++)
- {
- printf("Number of matches for pattern <%s>: %d\n",
- pattern[i], n_matches[i]);
- }
-
- return 0;
-}
diff --git a/Projet/CODE/apm/Makefile b/Projet/CODE/apm/Makefile
index 41bb027c1298c037c9fc7130565ee1a0a6c953de..0273c75e8474e7922774a646c4267572b796d2a2 100644
--- a/Projet/CODE/apm/Makefile
+++ b/Projet/CODE/apm/Makefile
@@ -1,34 +1,64 @@
INCLUDED=include
CC=gcc
+NVCC=nvcc
CFLAGS=-O3 -I $(INCLUDED) -pg -g -Wall
CFLAGS_OMP= -fopenmp -DUSE_OMP $(CFLAGS)
CFLAGS_CU=-O3 -Xcompiler "$(CFLAGS)"
LDFLAGS=
-OBJ=obj/apm.o
-
.PHONY: all
-all: dir apm apm_omp apm_gpu
-
-dir:
- mkdir -p obj
-
-obj/apm_omp.o : src/apm_omp.c
- $(CC) $(CFLAGS_OMP) -c -o $@ $^
+all:
+ $(MAKE) apm
+ $(MAKE) apm_omp
+ $(MAKE) apm_gpu
-obj/%.o: src/%.c
- $(CC) $(CFLAGS) -c -o $@ $^
-
-apm: obj/apm.o
+apm: src/apm.c
$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^
-apm_omp: obj/apm_omp.o
+apm_omp: src/apm_omp.c
$(CC) $(CFLAGS_OMP) $(LDFLAGS) -o $@ $^
apm_gpu: src/apm_gpu.cu
- nvcc $(CFLAGS_CU) $(LDFLAGS) -o $@ $^
+ $(NVCC) $(CFLAGS_CU) $(LDFLAGS) -o $@ $^
.PHONY: clean
clean:
- rm -rf apm apm_omp apm_gpu obj/ *.out
+ rm -rf apm apm_omp apm_gpu
+
+.PHONY: style
+style:
+ astyle src/*.c src/*.cu \
+ --style=allman \
+ --indent=tab=4 \
+ --indent-switches \
+ --indent-cases \
+ --indent-after-parens \
+ --indent-continuation=2 \
+ --indent-labels \
+ --indent-preproc-block \
+ --indent-preproc-define \
+ --min-conditional-indent=1 \
+ --max-continuation-indent=80 \
+ --break-blocks \
+ --pad-oper \
+ --pad-comma \
+ --pad-header \
+ --unpad-paren \
+ --unpad-brackets \
+ --delete-empty-lines \
+ --squeeze-lines=4 \
+ --squeeze-ws \
+ --align-pointer=name \
+ --align-reference=name \
+ --break-one-line-headers \
+ --add-braces \
+ --break-return-type \
+ --max-code-length=80 \
+ --suffix=none
+# --style=kr / google / mozilla / webkit
+#
+
+
+
+
diff --git a/Projet/CODE/apm/src/apm.c b/Projet/CODE/apm/src/apm.c
index f1bde78a2ff79483d7738581e9a20a48b4ec7317..ff45f737e32b6c6ecfd819d51370f76fa8794d19 100644
--- a/Projet/CODE/apm/src/apm.c
+++ b/Projet/CODE/apm/src/apm.c
@@ -12,230 +12,234 @@
#define APM_DEBUG 0
-char * read_input_file(char * filename, int * size)
+char *
+read_input_file(char *filename, int *size)
{
- char * buf;
- off_t fsize;
- int fd = 0;
- int n_bytes = 1;
-
- /* Open the text file */
- fd = open(filename, O_RDONLY);
- if (fd == -1)
- {
- fprintf(stderr, "Unable to open the text file <%s>\n", filename);
- return NULL;
- }
-
- /* Get the number of characters in the textfile */
- fsize = lseek(fd, 0, SEEK_END);
- lseek(fd, 0, SEEK_SET);
- /* TODO check return of lseek */
-
+ char *buf;
+ off_t fsize;
+ int fd = 0;
+ int n_bytes = 1;
+ /* Open the text file */
+ fd = open(filename, O_RDONLY);
+
+ if (fd == -1)
+ {
+ fprintf(stderr, "Unable to open the text file <%s>\n", filename);
+ return NULL;
+ }
+
+ /* Get the number of characters in the textfile */
+ fsize = lseek(fd, 0, SEEK_END);
+ lseek(fd, 0, SEEK_SET);
+ /* TODO check return of lseek */
#if APM_DEBUG
- printf("File length: %lld\n", fsize);
+ printf("File length: %lld\n", fsize);
#endif
-
- /* Allocate data to copy the target text */
- buf = (char *)malloc(fsize * sizeof (char));
- if (buf == NULL)
- {
- fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
- fsize);
- return NULL;
- }
-
- n_bytes = read(fd, buf, fsize);
- if (n_bytes != fsize)
- {
- fprintf(stderr,
- "Unable to copy %ld byte(s) from text file (%d byte(s) copied)\n",
- fsize, n_bytes);
- return NULL;
- }
+ /* Allocate data to copy the target text */
+ buf = (char *)malloc(fsize * sizeof(char));
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
+ fsize);
+ return NULL;
+ }
+
+ n_bytes = read(fd, buf, fsize);
+
+ if (n_bytes != fsize)
+ {
+ fprintf(stderr,
+ "Unable to copy %ld byte(s) from text file "
+ "(%d byte(s) copied)\n",
+ fsize, n_bytes);
+ return NULL;
+ }
#if APM_DEBUG
- printf("Number of read bytes: %d\n", n_bytes);
+ printf("Number of read bytes: %d\n", n_bytes);
#endif
-
- *size = n_bytes;
- close(fd);
- return buf;
+ *size = n_bytes;
+ close(fd);
+ return buf;
}
#define MIN3(a, b, c) ((a)<(b) ? ((a)<(c) ? (a) : (c)) : ((b)<(c) ? (b) : (c)))
-int levenshtein(char *s1, char *s2, int len, int * column)
+int
+levenshtein(char *s1, char *s2, int len, int *column)
{
- unsigned int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (s1[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
- return(column[len]);
+ unsigned int x, y, lastdiag, olddiag;
+
+ for (y = 1; y <= len; y++)
+ {
+ column[y] = y;
+ }
+
+ for (x = 1; x <= len; x++)
+ {
+ column[0] = x;
+ lastdiag = x - 1;
+
+ for (y = 1; y <= len; y++)
+ {
+ olddiag = column[y];
+ column[y] = MIN3(column[y] + 1,
+ column[y - 1] + 1,
+ lastdiag + (s1[y - 1] == s2[x - 1] ? 0 : 1));
+ lastdiag = olddiag;
+ }
+ }
+
+ return (column[len]);
}
-int main(int argc, char ** argv)
+int
+main(int argc, char **argv)
{
- char ** pattern;
- char * filename;
- int approx_factor = 0;
- int nb_patterns = 0;
- int i, j;
- char * buf;
- struct timeval t1, t2;
- double duration;
- int n_bytes;
- int * n_matches;
-
- /* Check number of arguments */
- if (argc < 4)
- {
- printf("Usage: %s approximation_factor "
- "dna_database pattern1 pattern2 ...\n",
- argv[0]);
- return 1;
- }
-
- approx_factor = atoi(argv[1]);/* Get the distance factor */
- filename = argv[2];/* Grab the filename containing the target text */
- nb_patterns = argc - 3;/* Get the number of patterns to search for */
-
- pattern = (char **)malloc(nb_patterns * sizeof(char*));
- if (pattern == NULL)/*Fill the pattern*/
- {
- fprintf(stderr,
- "Unable to allocate array of pattern of size %d\n",
- nb_patterns);
- return 1;
- }
-
- for (i=0; i < nb_patterns; i++) /* Grab the patterns */
- {
- int l;
- l = strlen(argv[i+3]);
-
- if (l <= 0)
- {
- fprintf(stderr, "Error while parsing argument %d\n", i+3);
- return 1;
- }
-
- pattern[i] = (char *)malloc((l+1) * sizeof(char));
- if (pattern[i] == NULL)
- {
- fprintf(stderr, "Unable to allocate string of size %d\n", l);
- return 1;
- }
-
- strncpy(pattern[i], argv[i+3], (l+1));
- }
-
-
- printf("Approximate Pattern Mathing: "
- "looking for %d pattern(s) in file %s w/ distance of %d\n",
- nb_patterns, filename, approx_factor);
-
- buf = read_input_file(filename, &n_bytes);
- if (buf == NULL)
- {
- fprintf(stderr, "Error: NULL pointer from reading input file.");
- return 1;
- }
-
- n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
- if (n_matches == NULL)
- {
- fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
- nb_patterns * sizeof(int));
- return 1;
- }
-
- /*****
- * BEGIN MAIN LOOP
- ******/
-
- /* Timer start */
- gettimeofday(&t1, NULL);
-
- for (i = 0; i < nb_patterns; i++)
- {
- int size_pattern = strlen(pattern[i]);
- int * column;
-
- n_matches[i] = 0;
-
- column = (int *)malloc((size_pattern+1) * sizeof(int));
- if (column == NULL)
- {
- fprintf(stderr,
- "Error: unable to allocate memory for column (%ldB)\n",
- (size_pattern+1) * sizeof(int));
- return 1;
- }
-
- for (j = 0; j < n_bytes; j++)
- {
- int distance = 0;
- int size;
-
+ char **pattern;
+ char *filename;
+ int approx_factor = 0;
+ int nb_patterns = 0;
+ int i, j;
+ char *buf;
+ struct timeval t1, t2;
+ double duration;
+ int n_bytes;
+ int *n_matches;
+
+ /* Check number of arguments */
+ if (argc < 4)
+ {
+ printf("Usage: %s approximation_factor "
+ "dna_database pattern1 pattern2 ...\n",
+ argv[0]);
+ return 1;
+ }
+
+ approx_factor = atoi(argv[1]);/* Get the distance factor */
+ filename = argv[2];/* Grab the filename containing the target text */
+ nb_patterns = argc - 3;/* Get the number of patterns to search for */
+ pattern = (char **)malloc(nb_patterns * sizeof(char *));
+
+ if (pattern == NULL)/*Fill the pattern*/
+ {
+ fprintf(stderr,
+ "Unable to allocate array of pattern of size %d\n",
+ nb_patterns);
+ return 1;
+ }
+
+ for (i = 0; i < nb_patterns; i++) /* Grab the patterns */
+ {
+ int l;
+ l = strlen(argv[i + 3]);
+
+ if (l <= 0)
+ {
+ fprintf(stderr, "Error while parsing argument %d\n", i + 3);
+ return 1;
+ }
+
+ pattern[i] = (char *)malloc((l + 1) * sizeof(char));
+
+ if (pattern[i] == NULL)
+ {
+ fprintf(stderr, "Unable to allocate string of size %d\n", l);
+ return 1;
+ }
+
+ strncpy(pattern[i], argv[i + 3], (l + 1));
+ }
+
+ printf("Approximate Pattern Mathing: "
+ "looking for %d pattern(s) in file %s w/ distance of %d\n",
+ nb_patterns, filename, approx_factor);
+ buf = read_input_file(filename, &n_bytes);
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Error: NULL pointer from reading input file.");
+ return 1;
+ }
+
+ n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
+
+ if (n_matches == NULL)
+ {
+ fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
+ nb_patterns * sizeof(int));
+ return 1;
+ }
+
+ /*****
+ * BEGIN MAIN LOOP
+ ******/
+ /* Timer start */
+ gettimeofday(&t1, NULL);
+
+ for (i = 0; i < nb_patterns; i++)
+ {
+ int size_pattern = strlen(pattern[i]);
+ int *column;
+ n_matches[i] = 0;
+ column = (int *)malloc((size_pattern + 1) * sizeof(int));
+
+ if (column == NULL)
+ {
+ fprintf(stderr,
+ "Error: unable to allocate memory for column (%ldB)\n",
+ (size_pattern + 1) * sizeof(int));
+ return 1;
+ }
+
+ for (j = 0; j < n_bytes; j++)
+ {
+ int distance = 0;
+ int size;
#if APM_DEBUG
- if (j % 100 == 0)
- {
- printf("Procesing byte %d (out of %d)\n", j, n_bytes);
- }
-#endif
-
- size = size_pattern;
- if (n_bytes - j < size_pattern)
- {
- //size = n_bytes - j;
- //NO ! we do not want to match substring of our input, wth
- break;
- }
-
- distance = levenshtein(pattern[i], &buf[j], size, column);
- if (distance <= approx_factor)
- {
- n_matches[i]++;
- }
- }
+ if (j % 100 == 0)
+ {
+ printf("Procesing byte %d (out of %d)\n", j, n_bytes);
+ }
- free(column);
- }
-
- /* Timer stop */
- gettimeofday(&t2, NULL);
-
- duration = (t2.tv_sec -t1.tv_sec)+((t2.tv_usec-t1.tv_usec)/1e6);
-
- printf("APM done in %lf s\n", duration);
-
- /*****
- * END MAIN LOOP
- ******/
-
- for (i = 0; i < nb_patterns; i++)
- {
- printf("Number of matches for pattern <%s>: %d\n",
- pattern[i], n_matches[i]);
- }
-
- return 0;
+#endif
+ size = size_pattern;
+
+ if (n_bytes - j < size_pattern)
+ {
+ //size = n_bytes - j;
+ //NO ! we do not want to match substring of our input, wth
+ break;
+ }
+
+ distance = levenshtein(pattern[i], &buf[j], size, column);
+
+ if (distance <= approx_factor)
+ {
+ n_matches[i]++;
+ }
+ }
+
+ free(column);
+ }
+
+ /* Timer stop */
+ gettimeofday(&t2, NULL);
+ duration = (t2.tv_sec - t1.tv_sec) + ((t2.tv_usec - t1.tv_usec) / 1e6);
+ printf("APM done in %lf s\n", duration);
+
+ /*****
+ * END MAIN LOOP
+ ******/
+
+ for (i = 0; i < nb_patterns; i++)
+ {
+ printf("Number of matches for pattern <%s>: %d\n",
+ pattern[i], n_matches[i]);
+ }
+
+ return 0;
}
diff --git a/Projet/CODE/apm/src/apm_gpu.cu b/Projet/CODE/apm/src/apm_gpu.cu
index ab42d361d11f2345c3ddac9e9c9219590e39ec31..efbdb48eb79ab70db5e8e35bd0a431b4921139c1 100644
--- a/Projet/CODE/apm/src/apm_gpu.cu
+++ b/Projet/CODE/apm/src/apm_gpu.cu
@@ -18,491 +18,511 @@
//the amount of RAM used by the programm is approx~Â 30*MAX_BUFFER_SIZE.
//If you get out of memory errors, you should reduce this value
-char * read_input_file(char * filename, int * size)
+char *
+read_input_file(char *filename, int *size)
{
- char * buf;
- off_t fsize;
- int fd = 0;
- int n_bytes = 1;
-
- /* Open the text file */
- fd = open(filename, O_RDONLY);
- if (fd == -1)
- {
- fprintf(stderr, "Unable to open the text file <%s>\n", filename);
- return NULL;
- }
-
- /* Get the number of characters in the textfile */
- fsize = lseek(fd, 0, SEEK_END);
- lseek(fd, 0, SEEK_SET);
- /* TODO check return of lseek */
-
- #if APM_DEBUG
- printf("File length: %lld\n", fsize);
- #endif
-
- /* Allocate data to copy the target text */
- buf = (char *)malloc(fsize * sizeof (char));
- if (buf == NULL)
- {
- fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
- fsize);
- return NULL;
- }
-
- n_bytes = read(fd, buf, fsize);
- if (n_bytes != fsize)
- {
- fprintf(stderr,
- "Unable to copy %ld byte(s) from text file (%d byte(s) copied)\n",
- fsize, n_bytes);
- return NULL;
- }
-
- #if APM_DEBUG
- printf("Number of read bytes: %d\n", n_bytes);
- #endif
-
- *size = n_bytes;
- close(fd);
- return buf;
+ char *buf;
+ off_t fsize;
+ int fd = 0;
+ int n_bytes = 1;
+ /* Open the text file */
+ fd = open(filename, O_RDONLY);
+
+ if (fd == -1)
+ {
+ fprintf(stderr, "Unable to open the text file <%s>\n", filename);
+ return NULL;
+ }
+
+ /* Get the number of characters in the textfile */
+ fsize = lseek(fd, 0, SEEK_END);
+ lseek(fd, 0, SEEK_SET);
+ /* TODO check return of lseek */
+#if APM_DEBUG
+ printf("File length: %lld\n", fsize);
+#endif
+ /* Allocate data to copy the target text */
+ buf = (char *)malloc(fsize * sizeof(char));
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
+ fsize);
+ return NULL;
+ }
+
+ n_bytes = read(fd, buf, fsize);
+
+ if (n_bytes != fsize)
+ {
+ fprintf(stderr,
+ "Unable to copy %ld byte(s) from text file "
+ "(%d byte(s) copied)\n",
+ fsize, n_bytes);
+ return NULL;
+ }
+
+#if APM_DEBUG
+ printf("Number of read bytes: %d\n", n_bytes);
+#endif
+ *size = n_bytes;
+ close(fd);
+ return buf;
}
-off_t get_file_size(int fd)
+off_t
+get_file_size(int fd)
{
off_t size;
size = lseek(fd, 0, SEEK_END);
lseek(fd, 0, SEEK_SET);
return size;
-}
-char * read_input_file_max(int fd, int * size
- , int pattern_len, off_t offset)
+}
+char *
+read_input_file_max(int fd, int *size
+ , int pattern_len, off_t offset)
{
- char * buf;
- off_t fsize;
- int n_bytes = 1;
- int to_read;
-
- fsize = lseek(fd, 0, SEEK_END);
- to_read =
- ((fsize - offset) > MAX_BUFFER_SIZE) ? MAX_BUFFER_SIZE : (fsize-offset);
- lseek(fd, offset, SEEK_SET);
-
- #if APM_DEBUG
- printf("File length: %lld\n", fsize);
- printf("diff: %i\n", to_read);
- #endif
-
- /* Allocate data to copy the target text */
- buf = (char *)malloc(fsize * sizeof (char));
- if (buf == NULL)
- {
- fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
- fsize);
- return NULL;
- }
-
- n_bytes = read(fd, buf, to_read);
- if (n_bytes != to_read)
- {
- fprintf(stderr,
- "Unable to copy %ld byte(s) from text file (%d byte(s) copied)\n",
- fsize, n_bytes);
- return NULL;
- }
-
- #if APM_DEBUG
- printf("Number of read bytes: %d\n", n_bytes);
- #endif
-
- *size = n_bytes;
- return buf;
+ char *buf;
+ off_t fsize;
+ int n_bytes = 1;
+ int to_read;
+ fsize = lseek(fd, 0, SEEK_END);
+ to_read =
+ ((fsize - offset) > MAX_BUFFER_SIZE)
+ ? MAX_BUFFER_SIZE : (fsize - offset);
+ lseek(fd, offset, SEEK_SET);
+#if APM_DEBUG
+ printf("File length: %lld\n", fsize);
+ printf("diff: %i\n", to_read);
+#endif
+ /* Allocate data to copy the target text */
+ buf = (char *)malloc(fsize * sizeof(char));
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
+ fsize);
+ return NULL;
+ }
+
+ n_bytes = read(fd, buf, to_read);
+
+ if (n_bytes != to_read)
+ {
+ fprintf(stderr,
+ "Unable to copy %ld byte(s) from text file "
+ "(%d byte(s) copied)\n",
+ fsize, n_bytes);
+ return NULL;
+ }
+
+#if APM_DEBUG
+ printf("Number of read bytes: %d\n", n_bytes);
+#endif
+ *size = n_bytes;
+ return buf;
}
#define MIN3(a, b, c) ((a)<(b) ? ((a)<(c) ? (a) : (c)) : ((b)<(c) ? (b) : (c)))
-int levenshtein(char *s1, char *s2, int len, int * column, int approx_factor)
+int
+levenshtein(char *s1, char *s2, int len, int *column, int approx_factor)
{
- int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (s1[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
- return (column[len] <= approx_factor) ? 1 : 0;
+ int x, y, lastdiag, olddiag;
+
+ for (y = 1; y <= len; y++)
+ {
+ column[y] = y;
+ }
+
+ for (x = 1; x <= len; x++)
+ {
+ column[0] = x;
+ lastdiag = x - 1;
+
+ for (y = 1; y <= len; y++)
+ {
+ olddiag = column[y];
+ column[y] = MIN3(column[y] + 1,
+ column[y - 1] + 1,
+ lastdiag + (s1[y - 1] == s2[x - 1] ? 0 : 1));
+ lastdiag = olddiag;
+ }
+ }
+
+ return (column[len] <= approx_factor) ? 1 : 0;
}
-__global__ void levenshtein_cu(char *find, char *buf, int len, int n_bytes
- ,int approx_factor, int* g_column, int* result)
-{
- int tId = blockIdx.x * blockDim.x + threadIdx.x;//global thread id
- if (tId > n_bytes)
- {return;}//we are past the buffer length - do not process
-
- //position s2 and column to the right position in the pre-allocated
- //arrays
- char* s2 = buf+tId;
- int* column = g_column+tId*(len+1);
-
- //i do not understand this algorithm and god do i not want to.
- int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (find[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
-
- int res = 0;
- if (column[len] <= approx_factor)
- res = 1;
- //{result_vec[tId] = 1;}//its a match
-
- atomicAdd(result, res);
-}
-
-int main(int argc, char ** argv)
+__global__ void
+levenshtein_cu(char *find, char *buf, int len, int n_bytes
+ , int approx_factor, int *g_column, int *result)
{
- char ** pattern;
- char * filename;
- int fdesc;
- off_t filesize;
- int approx_factor = 0;
- int nb_patterns = 0;
-
- char * buf;
- struct timeval t1, t2;
- double duration;
- int n_bytes;
- int * n_matches;
-
- //cuda-related vars
- char *buf_dev;
- int NTBB = NUMBER_THREADS_BY_BLOCK; //Number of threads by blocks
- int NB = 0;//Number of blocks
- cudaError_t cu_err;
-
- /* Check number of arguments */
- if (argc < 4)
- {
- printf("Usage: %s approximation_factor "
- "dna_database pattern1 pattern2 ...\n",
- argv[0]);
- return 1;
- }
-
- approx_factor = atoi(argv[1]);/* Get the distance factor */
- filename = argv[2];/* Grab the filename containing the target text */
-
- /* Open the text file */
- fdesc = open(filename, O_RDONLY);
- if (fdesc == -1)
- {
- fprintf(stderr, "Unable to open the text file <%s>\n", filename);
- return 1;
- }
-
- filesize = get_file_size(fdesc);
- if (filesize == 0)
+ int tId = blockIdx.x * blockDim.x + threadIdx.x;//global thread id
+
+ if (tId > n_bytes)
+ {
+ return; //we are past the buffer length - do not process
+ }
+
+ //position s2 and column to the right position in the pre-allocated
+ //arrays
+ char *s2 = buf + tId;
+ int *column = g_column + tId * (len + 1);
+ //i do not understand this algorithm and god do i not want to.
+ int x, y, lastdiag, olddiag;
+
+ for (y = 1; y <= len; y++)
+ {
+ column[y] = y;
+ }
+
+ for (x = 1; x <= len; x++)
+ {
+ column[0] = x;
+ lastdiag = x - 1;
+
+ for (y = 1; y <= len; y++)
{
- fprintf(stderr, "File <%s> is empty !\n", filename);
- return 1;
- }
-
- nb_patterns = argc - 3;/* Get the number of patterns to search for */
-
- pattern = (char **)malloc(nb_patterns * sizeof(char*));
- if (pattern == NULL)/*Fill the pattern*/
- {
- fprintf(stderr,
- "Unable to allocate array of pattern of size %d\n",
- nb_patterns);
- return 1;
- }
-
- for (int i=0; i < nb_patterns; i++) /* Grab the patterns */
- {
- int l;
- l = strlen(argv[i+3]);
-
- if (l <= 0)
- {
- fprintf(stderr, "Error while parsing argument %d\n", i+3);
- return 1;
- }
-
- pattern[i] = (char *)malloc((l+1) * sizeof(char));
- if (pattern[i] == NULL)
- {
- fprintf(stderr, "Unable to allocate string of size %d\n", l);
- return 1;
- }
-
- strncpy(pattern[i], argv[i+3], (l+1));
- }
-
-
- printf("Approximate Pattern Mathing: "
- "looking for %d pattern(s) in file %s w/ distance of %d\n",
- nb_patterns, filename, approx_factor);
-
-
-
- n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
- if (n_matches == NULL)
- {
- fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
- nb_patterns * sizeof(int));
- return 1;
- }
-
- /*****
- * BEGIN MAIN LOOP
- ******/
-
- /* Timer start */
- //TODO MAYBE count time with cudaevents (see older tp)
- gettimeofday(&t1, NULL);
-
- for (int i = 0; i < nb_patterns; i++)
- {
- n_matches[i] = 0;
-
- int size_pattern = strlen(pattern[i]);
- char* pattern_dev;
-
- cudaMalloc((void**)&pattern_dev, size_pattern);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ olddiag = column[y];
+ column[y] = MIN3(column[y] + 1,
+ column[y - 1] + 1,
+ lastdiag + (find[y - 1] == s2[x - 1] ? 0 : 1));
+ lastdiag = olddiag;
+ }
+ }
+
+ int res = 0;
+
+ if (column[len] <= approx_factor)
+ {
+ res = 1;
+ }
+
+ //{result_vec[tId] = 1;}//its a match
+ atomicAdd(result, res);
+}
+
+int
+main(int argc, char **argv)
+{
+ char **pattern;
+ char *filename;
+ int fdesc;
+ off_t filesize;
+ int approx_factor = 0;
+ int nb_patterns = 0;
+ char *buf;
+ struct timeval t1, t2;
+ double duration;
+ int n_bytes;
+ int *n_matches;
+ //cuda-related vars
+ char *buf_dev;
+ int NTBB = NUMBER_THREADS_BY_BLOCK; //Number of threads by blocks
+ int NB = 0;//Number of blocks
+ cudaError_t cu_err;
+
+ /* Check number of arguments */
+ if (argc < 4)
+ {
+ printf("Usage: %s approximation_factor "
+ "dna_database pattern1 pattern2 ...\n",
+ argv[0]);
+ return 1;
+ }
+
+ approx_factor = atoi(argv[1]);/* Get the distance factor */
+ filename = argv[2];/* Grab the filename containing the target text */
+ /* Open the text file */
+ fdesc = open(filename, O_RDONLY);
+
+ if (fdesc == -1)
+ {
+ fprintf(stderr, "Unable to open the text file <%s>\n", filename);
+ return 1;
+ }
+
+ filesize = get_file_size(fdesc);
+
+ if (filesize == 0)
+ {
+ fprintf(stderr, "File <%s> is empty !\n", filename);
+ return 1;
+ }
+
+ nb_patterns = argc - 3;/* Get the number of patterns to search for */
+ pattern = (char **)malloc(nb_patterns * sizeof(char *));
+
+ if (pattern == NULL)/*Fill the pattern*/
+ {
+ fprintf(stderr,
+ "Unable to allocate array of pattern of size %d\n",
+ nb_patterns);
+ return 1;
+ }
+
+ for (int i = 0; i < nb_patterns; i++) /* Grab the patterns */
+ {
+ int l;
+ l = strlen(argv[i + 3]);
+
+ if (l <= 0)
+ {
+ fprintf(stderr, "Error while parsing argument %d\n", i + 3);
+ return 1;
+ }
+
+ pattern[i] = (char *)malloc((l + 1) * sizeof(char));
+
+ if (pattern[i] == NULL)
+ {
+ fprintf(stderr, "Unable to allocate string of size %d\n", l);
+ return 1;
+ }
+
+ strncpy(pattern[i], argv[i + 3], (l + 1));
+ }
+
+ printf("Approximate Pattern Mathing: "
+ "looking for %d pattern(s) in file %s w/ distance of %d\n",
+ nb_patterns, filename, approx_factor);
+ n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
+
+ if (n_matches == NULL)
+ {
+ fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
+ nb_patterns * sizeof(int));
+ return 1;
+ }
+
+ /*****
+ * BEGIN MAIN LOOP
+ ******/
+ /* Timer start */
+ //TODO MAYBE count time with cudaevents (see older tp)
+ gettimeofday(&t1, NULL);
+
+ for (int i = 0; i < nb_patterns; i++)
+ {
+ n_matches[i] = 0;
+ int size_pattern = strlen(pattern[i]);
+ char *pattern_dev;
+ cudaMalloc((void **)&pattern_dev, size_pattern);
+
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to allocate pattern on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
+
+ cudaMemcpy(pattern_dev, pattern[i],
+ size_pattern, cudaMemcpyHostToDevice);
+
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to copy pattern onto device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
+
+ int result = 0;
+ int *result_dev;
+ cudaMalloc((void **)&result_dev, sizeof(int));
+
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to allocate result on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
+
+ off_t offset = 0;
+
+ while (offset < filesize)
+ {
+#if APM_DEBUG
+ printf("offset: %i, filesize: %i\n", offset, filesize);
+#endif
+ buf = read_input_file_max(fdesc, &n_bytes, size_pattern, offset);
+
+ if (buf == NULL)
{
- fprintf(stderr, "Unable to allocate pattern on device: %s.\n"
- , cudaGetErrorString(cu_err));
+ fprintf(stderr, "Error: NULL pointer from reading input file.");
return 1;
}
-
- cudaMemcpy(pattern_dev, pattern[i]
- , size_pattern, cudaMemcpyHostToDevice);
+
+ cudaMalloc((void **)&buf_dev, n_bytes * sizeof(char));
+
if ((cu_err = cudaGetLastError()) != cudaSuccess)
{
- fprintf(stderr, "Unable to copy pattern onto device: %s.\n"
- , cudaGetErrorString(cu_err));
+ fprintf(stderr, "Unable to allocate buffer on device: %s.\n",
+ cudaGetErrorString(cu_err));
return 1;
}
-
- int result = 0;
- int* result_dev;
- cudaMalloc((void**)&result_dev, sizeof(int));
+
+ cudaMemcpy(buf_dev, buf, n_bytes, cudaMemcpyHostToDevice);
+
if ((cu_err = cudaGetLastError()) != cudaSuccess)
{
- fprintf(stderr, "Unable to allocate result on device: %s.\n"
- , cudaGetErrorString(cu_err));
+ fprintf(stderr, "Unable to copy buffer onto device: %s.\n",
+ cudaGetErrorString(cu_err));
return 1;
}
+ NB = (n_bytes / NTBB) + (((n_bytes % NTBB) > 0) ? 1 : 0);
+ int *column_dev;
+ cudaMalloc((void **)&column_dev,
+ (size_pattern + 1)*NTBB * NB * sizeof(int));
- off_t offset = 0;
- while (offset < filesize)
- {
- #if APM_DEBUG
- printf("offset: %i, filesize: %i\n",offset,filesize);
- #endif
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr,
+ "Unable to allocate column vector on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
- buf = read_input_file_max(fdesc, &n_bytes, size_pattern, offset);
- if (buf == NULL)
- {
- fprintf(stderr, "Error: NULL pointer from reading input file.");
- return 1;
- }
+ char *result_vec_dev; //result vectors.
+ cudaMalloc((void **)&result_vec_dev, NTBB * NB * sizeof(char));
- cudaMalloc((void**)&buf_dev, n_bytes * sizeof(char));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to allocate buffer on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr,
+ "Unable to allocate result vector on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
- cudaMemcpy(buf_dev, buf, n_bytes, cudaMemcpyHostToDevice);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to copy buffer onto device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
+ char *result_vec = (char *) malloc(NTBB * NB * sizeof(char));
+ if (result_vec == NULL)
+ {
+ fprintf(stderr, "Unable to allocate result vec on host.");
+ return 1;
+ }
- NB = (n_bytes / NTBB) + (((n_bytes % NTBB) > 0) ? 1 : 0);
-
+ /*
+ cudaMemset(result_vec_dev, 0, NTBB*NB*sizeof(char));
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to init result vector to 0 on device: %s.\n"
+ , cudaGetErrorString(cu_err));
+ return 1;
+ }
- int * column_dev;
- cudaMalloc((void**)&column_dev
- , (size_pattern+1)*NTBB*NB*sizeof(int));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to allocate column vector on device: %s.\n"
+ cudaMemset(result_dev, 0, sizeof(int));
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to init result to 0 on device: %s.\n"
, cudaGetErrorString(cu_err));
- return 1;
- }
-
- char * result_vec_dev; //result vectors.
- cudaMalloc((void**)&result_vec_dev, NTBB*NB*sizeof(char));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to allocate result vector on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
-
- char* result_vec =(char*) malloc(NTBB*NB*sizeof(char));
- if (result_vec == NULL)
- {
- fprintf(stderr, "Unable to allocate result vec on host.");
- return 1;
- }
-
- /*
- cudaMemset(result_vec_dev, 0, NTBB*NB*sizeof(char));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to init result vector to 0 on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
-
- cudaMemset(result_dev, 0, sizeof(int));
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to init result to 0 on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
- */
+ return 1;
+ }
+ */
+ levenshtein_cu <<< NB, NTBB>>>(pattern_dev, buf_dev, size_pattern,
+ n_bytes, approx_factor, column_dev, result_dev);
- levenshtein_cu<<<NB,NTBB>>>(pattern_dev, buf_dev, size_pattern
- , n_bytes, approx_factor, column_dev, result_dev);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Kernel execution of levenshtein_cu failed: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
-
- //get result
- cudaMemcpy(&result, result_dev
- , sizeof(int), cudaMemcpyDeviceToHost);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to retrieve result on host: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
-
- n_matches[i] += result;
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr,
+ "Kernel execution of levenshtein_cu failed: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
- /*
- for (int j = 0 ; j<n_bytes ; j++)
- {
- // Highly advanced debbugging (printfs)
- int column[size_pattern+1];
- int d =
- levenshtein(pattern[i], buf+j, size_pattern, column
- , approx_factor);
- //printf("%d",d);
- if (d != result_vec[j])
- {
- printf("MISMATCH FOUND %s should have match at %i :"
- ,pattern[i], j);
- printf("%.*s\n",size_pattern,&buf[j]);
- }
-
- n_matches[i] += result_vec[j];
- }
- */
-
- offset += (MAX_BUFFER_SIZE - size_pattern + 1);
+ //get result
+ cudaMemcpy(&result, result_dev,
+ sizeof(int), cudaMemcpyDeviceToHost);
- cudaFree(buf_dev);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to free memory for dev on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
- free(buf);
-
- cudaFree(column_dev);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
- {
- fprintf(stderr, "Unable to free memory for column on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
- }
-
- /*
- cudaFree(result_vec_dev);
- if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to retrieve result on host: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
+
+ n_matches[i] += result;
+ /*
+ for (int j = 0 ; j<n_bytes ; j++)
+ {
+ // Highly advanced debbugging (printfs)
+ int column[size_pattern+1];
+ int d =
+ levenshtein(pattern[i], buf+j, size_pattern, column
+ , approx_factor);
+ //printf("%d",d);
+ if (d != result_vec[j])
{
- fprintf(stderr, "Unable to free memory for result on device: %s.\n"
- , cudaGetErrorString(cu_err));
- return 1;
+ printf("MISMATCH FOUND %s should have match at %i :"
+ ,pattern[i], j);
+ printf("%.*s\n",size_pattern,&buf[j]);
}
- free(result_vec);
- */
+ n_matches[i] += result_vec[j];
}
+ */
+ offset += (MAX_BUFFER_SIZE - size_pattern + 1);
+ cudaFree(buf_dev);
- //free memory - and then get onto the next pattern.
- cudaFree(pattern_dev);
if ((cu_err = cudaGetLastError()) != cudaSuccess)
{
- fprintf(stderr, "Unable to free memory for pattern on device: %s.\n"
- , cudaGetErrorString(cu_err));
+ fprintf(stderr,
+ "Unable to free memory for dev on device: %s.\n",
+ cudaGetErrorString(cu_err));
return 1;
}
- }
- /* Timer stop */
- gettimeofday(&t2, NULL);
+ free(buf);
+ cudaFree(column_dev);
- duration = (t2.tv_sec -t1.tv_sec)+((t2.tv_usec-t1.tv_usec)/1e6);
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr,
+ "Unable to free memory for column on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
- printf("APM done in %lf s\n", duration);
+ /*
+ cudaFree(result_vec_dev);
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr, "Unable to free memory for result on device: %s.\n"
+ , cudaGetErrorString(cu_err));
+ return 1;
+ }
- /*****
- * END MAIN LOOP
- ******/
+ free(result_vec);
+ */
+ }
- for (int i=0; i < nb_patterns; i++)
- {
- printf("Number of matches for pattern <%s>: %d\n",
- pattern[i], n_matches[i]);
- }
+ //free memory - and then get onto the next pattern.
+ cudaFree(pattern_dev);
- return 0;
+ if ((cu_err = cudaGetLastError()) != cudaSuccess)
+ {
+ fprintf(stderr,
+ "Unable to free memory for pattern on device: %s.\n",
+ cudaGetErrorString(cu_err));
+ return 1;
+ }
+ }
+
+ /* Timer stop */
+ gettimeofday(&t2, NULL);
+ duration = (t2.tv_sec - t1.tv_sec) + ((t2.tv_usec - t1.tv_usec) / 1e6);
+ printf("APM done in %lf s\n", duration);
+
+ /*****
+ * END MAIN LOOP
+ ******/
+
+ for (int i = 0; i < nb_patterns; i++)
+ {
+ printf("Number of matches for pattern <%s>: %d\n",
+ pattern[i], n_matches[i]);
+ }
+
+ return 0;
}
diff --git a/Projet/CODE/apm/src/apm_omp.c b/Projet/CODE/apm/src/apm_omp.c
index 853c628cb2318bfca1542ebd10f24c931a8487ac..c0d595cc4c39cda787cfa792aeb99c3e0b2ad69f 100644
--- a/Projet/CODE/apm/src/apm_omp.c
+++ b/Projet/CODE/apm/src/apm_omp.c
@@ -14,238 +14,243 @@
#define APM_DEBUG 0
-char * read_input_file(char * filename, int * size)
+char *
+read_input_file(char *filename, int *size)
{
- char * buf;
- off_t fsize;
- int fd = 0;
- int n_bytes = 1;
-
- /* Open the text file */
- fd = open(filename, O_RDONLY);
- if (fd == -1)
- {
- fprintf(stderr, "Unable to open the text file <%s>\n", filename);
- return NULL;
- }
-
- /* Get the number of characters in the textfile */
- fsize = lseek(fd, 0, SEEK_END);
- lseek(fd, 0, SEEK_SET);
- /* TODO check return of lseek */
-
+ char *buf;
+ off_t fsize;
+ int fd = 0;
+ int n_bytes = 1;
+ /* Open the text file */
+ fd = open(filename, O_RDONLY);
+
+ if (fd == -1)
+ {
+ fprintf(stderr, "Unable to open the text file <%s>\n", filename);
+ return NULL;
+ }
+
+ /* Get the number of characters in the textfile */
+ fsize = lseek(fd, 0, SEEK_END);
+ lseek(fd, 0, SEEK_SET);
+ /* TODO check return of lseek */
#if APM_DEBUG
- printf("File length: %lld\n", fsize);
+ printf("File length: %lld\n", fsize);
#endif
-
- /* Allocate data to copy the target text */
- buf = (char *)malloc(fsize * sizeof (char));
- if (buf == NULL)
- {
- fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
- fsize);
- return NULL;
- }
-
- n_bytes = read(fd, buf, fsize);
- if (n_bytes != fsize)
- {
- fprintf(stderr,
- "Unable to copy %ld byte(s) from text file (%d byte(s) copied)\n",
- fsize, n_bytes);
- return NULL;
- }
+ /* Allocate data to copy the target text */
+ buf = (char *)malloc(fsize * sizeof(char));
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Unable to allocate %ld byte(s) for main array\n",
+ fsize);
+ return NULL;
+ }
+
+ n_bytes = read(fd, buf, fsize);
+
+ if (n_bytes != fsize)
+ {
+ fprintf(stderr,
+ "Unable to copy %ld byte(s) from text file "
+ "(%d byte(s) copied)\n",
+ fsize, n_bytes);
+ return NULL;
+ }
#if APM_DEBUG
- printf("Number of read bytes: %d\n", n_bytes);
+ printf("Number of read bytes: %d\n", n_bytes);
#endif
-
- *size = n_bytes;
- close(fd);
- return buf;
+ *size = n_bytes;
+ close(fd);
+ return buf;
}
#define MIN3(a, b, c) ((a)<(b) ? ((a)<(c) ? (a) : (c)) : ((b)<(c) ? (b) : (c)))
-int levenshtein(char *s1, char *s2, int len, int * column)
+int
+levenshtein(char *s1, char *s2, int len, int *column)
{
- unsigned int x, y, lastdiag, olddiag;
-
- for (y = 1; y <= len; y++)
- {
- column[y] = y;
- }
- for (x = 1; x <= len; x++)
- {
- column[0] = x;
- lastdiag = x-1;
- for (y = 1; y <= len; y++)
- {
- olddiag = column[y];
- column[y] = MIN3(column[y] + 1,
- column[y-1] + 1,
- lastdiag + (s1[y-1] == s2[x-1] ? 0 : 1));
- lastdiag = olddiag;
- }
- }
- return(column[len]);
-}
+ unsigned int x, y, lastdiag, olddiag;
+ for (y = 1; y <= len; y++)
+ {
+ column[y] = y;
+ }
-int main(int argc, char ** argv)
-{
- char ** pattern;
- char * filename;
- int approx_factor = 0;
- int nb_patterns = 0;
- int i, j;
- char * buf;
- struct timeval t1, t2;
- double duration;
- int n_bytes;
- int * n_matches;
- int num_threads;
-
- /* Check number of arguments */
- if (argc < 4)
- {
- printf("Usage: %s approximation_factor "
- "dna_database pattern1 pattern2 ...\n",
- argv[0]);
- return 1;
- }
-
- approx_factor = atoi(argv[1]);/* Get the distance factor */
- filename = argv[2];/* Grab the filename containing the target text */
- nb_patterns = argc - 3;/* Get the number of patterns to search for */
-
- pattern = (char **)malloc(nb_patterns * sizeof(char*));
- if (pattern == NULL)/*Fill the pattern*/
- {
- fprintf(stderr,
- "Unable to allocate array of pattern of size %d\n",
- nb_patterns);
- return 1;
- }
-
- for (i=0; i < nb_patterns; i++) /* Grab the patterns */
- {
- int l;
- l = strlen(argv[i+3]);
-
- if (l <= 0)
- {
- fprintf(stderr, "Error while parsing argument %d\n", i+3);
- return 1;
- }
-
- pattern[i] = (char *)malloc((l+1) * sizeof(char));
- if (pattern[i] == NULL)
- {
- fprintf(stderr, "Unable to allocate string of size %d\n", l);
- return 1;
- }
-
- strncpy(pattern[i], argv[i+3], (l+1));
- }
-
-
- printf("Approximate Pattern Mathing: "
- "looking for %d pattern(s) in file %s w/ distance of %d\n",
- nb_patterns, filename, approx_factor);
-
- buf = read_input_file(filename, &n_bytes);
- if (buf == NULL)
- {
- fprintf(stderr, "Error: NULL pointer from reading input file.");
- return 1;
- }
-
- n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
- if (n_matches == NULL)
- {
- fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
- nb_patterns * sizeof(int));
- return 1;
- }
-
- #pragma omp parallel
- {
- num_threads = omp_get_num_threads();
- }
-
- /*****
- * BEGIN MAIN LOOP
- ******/
-
- /* Timer start */
- gettimeofday(&t1, NULL);
-
- for (i = 0; i < nb_patterns; i++)
- {
- int size_pattern = strlen(pattern[i]);
- int * column;
- int distance = 0;
-
- n_matches[i] = 0;
-
- column = (int *)malloc((size_pattern+1) * num_threads * sizeof(int));
- if (column == NULL)
- {
- fprintf(stderr,
- "Error: unable to allocate memory for column (%ldB)\n",
- (size_pattern+1) * sizeof(int) * n_bytes);
- return 1;
- }
-
- int matches = 0;
- #pragma omp parallel for reduction(+:matches) private(distance)
- for (j = 0; j < n_bytes; j++)
- {
-
-#if APM_DEBUG
- if (j % 100 == 0)
- {
- printf("Procesing byte %d (out of %d)\n", j, n_bytes);
- }
-#endif
+ for (x = 1; x <= len; x++)
+ {
+ column[0] = x;
+ lastdiag = x - 1;
- if (n_bytes - j < size_pattern)
- {
- //size = n_bytes - j;
- //NO ! we do not want to match substring of our input, wth
- continue;
- }
+ for (y = 1; y <= len; y++)
+ {
+ olddiag = column[y];
+ column[y] = MIN3(column[y] + 1,
+ column[y - 1] + 1,
+ lastdiag + (s1[y - 1] == s2[x - 1] ? 0 : 1));
+ lastdiag = olddiag;
+ }
+ }
+
+ return (column[len]);
+}
- distance = levenshtein(pattern[i], &buf[j], size_pattern,
- column+(omp_get_thread_num()*(size_pattern+1)));
- if (distance <= approx_factor)
- {
- matches++;
- }
- }
+int
+main(int argc, char **argv)
+{
+ char **pattern;
+ char *filename;
+ int approx_factor = 0;
+ int nb_patterns = 0;
+ int i, j;
+ char *buf;
+ struct timeval t1, t2;
+ double duration;
+ int n_bytes;
+ int *n_matches;
+ int num_threads;
+
+ /* Check number of arguments */
+ if (argc < 4)
+ {
+ printf("Usage: %s approximation_factor "
+ "dna_database pattern1 pattern2 ...\n",
+ argv[0]);
+ return 1;
+ }
+
+ approx_factor = atoi(argv[1]);/* Get the distance factor */
+ filename = argv[2];/* Grab the filename containing the target text */
+ nb_patterns = argc - 3;/* Get the number of patterns to search for */
+ pattern = (char **)malloc(nb_patterns * sizeof(char *));
+
+ if (pattern == NULL)/*Fill the pattern*/
+ {
+ fprintf(stderr,
+ "Unable to allocate array of pattern of size %d\n",
+ nb_patterns);
+ return 1;
+ }
+
+ for (i = 0; i < nb_patterns; i++) /* Grab the patterns */
+ {
+ int l;
+ l = strlen(argv[i + 3]);
+
+ if (l <= 0)
+ {
+ fprintf(stderr, "Error while parsing argument %d\n", i + 3);
+ return 1;
+ }
- n_matches[i] = matches;
- free(column);
- }
+ pattern[i] = (char *)malloc((l + 1) * sizeof(char));
- /* Timer stop */
- gettimeofday(&t2, NULL);
+ if (pattern[i] == NULL)
+ {
+ fprintf(stderr, "Unable to allocate string of size %d\n", l);
+ return 1;
+ }
+
+ strncpy(pattern[i], argv[i + 3], (l + 1));
+ }
+
+ printf("Approximate Pattern Mathing: "
+ "looking for %d pattern(s) in file %s w/ distance of %d\n",
+ nb_patterns, filename, approx_factor);
+ buf = read_input_file(filename, &n_bytes);
+
+ if (buf == NULL)
+ {
+ fprintf(stderr, "Error: NULL pointer from reading input file.");
+ return 1;
+ }
+
+ n_matches = (int *)malloc(nb_patterns * sizeof(int));/*Alloc the matches*/
+
+ if (n_matches == NULL)
+ {
+ fprintf(stderr, "Error: unable to allocate memory for %ldB\n",
+ nb_patterns * sizeof(int));
+ return 1;
+ }
+
+ #pragma omp parallel
+ {
+ num_threads = omp_get_num_threads();
+ }
+ /*****
+ * BEGIN MAIN LOOP
+ ******/
+ /* Timer start */
+ gettimeofday(&t1, NULL);
+
+ for (i = 0; i < nb_patterns; i++)
+ {
+ int size_pattern = strlen(pattern[i]);
+ int *column;
+ int distance = 0;
+ n_matches[i] = 0;
+ column = (int *)malloc((size_pattern + 1) * num_threads * sizeof(int));
+
+ if (column == NULL)
+ {
+ fprintf(stderr,
+ "Error: unable to allocate memory for column (%ldB)\n",
+ (size_pattern + 1) * sizeof(int) * n_bytes);
+ return 1;
+ }
- duration = (t2.tv_sec -t1.tv_sec)+((t2.tv_usec-t1.tv_usec)/1e6);
+ int matches = 0;
+ #pragma omp parallel for reduction(+:matches) private(distance)
- printf("APM done in %lf s\n", duration);
+ for (j = 0; j < n_bytes; j++)
+ {
+#if APM_DEBUG
- /*****
- * END MAIN LOOP
- ******/
+ if (j % 100 == 0)
+ {
+ printf("Procesing byte %d (out of %d)\n", j, n_bytes);
+ }
- for (i = 0; i < nb_patterns; i++)
- {
- printf("Number of matches for pattern <%s>: %d\n",
- pattern[i], n_matches[i]);
- }
+#endif
- return 0;
+ if (n_bytes - j < size_pattern)
+ {
+ //size = n_bytes - j;
+ //NO ! we do not want to match substring of our input, wth
+ continue;
+ }
+
+ distance = levenshtein(pattern[i], &buf[j], size_pattern,
+ column + (omp_get_thread_num() * (size_pattern + 1))
+ );
+
+ if (distance <= approx_factor)
+ {
+ matches++;
+ }
+ }
+
+ n_matches[i] = matches;
+ free(column);
+ }
+
+ /* Timer stop */
+ gettimeofday(&t2, NULL);
+ duration = (t2.tv_sec - t1.tv_sec) + ((t2.tv_usec - t1.tv_usec) / 1e6);
+ printf("APM done in %lf s\n", duration);
+
+ /*****
+ * END MAIN LOOP
+ ******/
+
+ for (i = 0; i < nb_patterns; i++)
+ {
+ printf("Number of matches for pattern <%s>: %d\n",
+ pattern[i], n_matches[i]);
+ }
+
+ return 0;
}