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Save segmentFreqs in ctx instead of malloc and memset in SelectSegment

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This commit is contained in:
Jennifer Liu
2018-07-27 16:51:38 -07:00
parent 49b398e93f
commit 61262f6c0d
4 changed files with 141 additions and 16 deletions
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contrib/experimental_dict_builders/fastCover/Makefile
+3 -3
View File
@@ -1,7 +1,7 @@
ARG :=
CC ?= gcc
CFLAGS ?= -O3
CFLAGS ?= -O3 -g
INCLUDES := -I ../../../programs -I ../randomDictBuilder -I ../../../lib/common -I ../../../lib -I ../../../lib/dictBuilder
IO_FILE := ../randomDictBuilder/io.c
@@ -9,7 +9,7 @@ IO_FILE := ../randomDictBuilder/io.c
TEST_INPUT := ../../../lib
TEST_OUTPUT := fastCoverDict
all: main run clean
all: main run
.PHONY: test
test: main testrun testshell clean
@@ -32,7 +32,7 @@ io.o: $(IO_FILE)
$(CC) $(CFLAGS) $(INCLUDES) -c $(IO_FILE)
libzstd.a:
$(MAKE) -C ../../../lib libzstd.a
$(MAKE) MOREFLAGS=-g -C ../../../lib libzstd.a
mv ../../../lib/libzstd.a .
.PHONY: testrun
contrib/experimental_dict_builders/fastCover/fastCover.c
+17 -11
View File
@@ -82,6 +82,7 @@ typedef struct {
size_t nbTestSamples;
size_t nbDmers;
U32 *freqs;
U16 *segmentFreqs;
unsigned d;
} FASTCOVER_ctx_t;
@@ -142,9 +143,6 @@ static FASTCOVER_segment_t FASTCOVER_selectSegment(const FASTCOVER_ctx_t *ctx,
activeSegment.end = begin;
activeSegment.score = 0;
{
/* Keep track of number of times an index has been seen in current segment */
U16* currfreqs =(U16 *)malloc((1 << parameters.f) * sizeof(U16));
memset(currfreqs, 0, (1 << parameters.f) * sizeof(*currfreqs));
/* Slide the activeSegment through the whole epoch.
* Save the best segment in bestSegment.
*/
@@ -152,19 +150,19 @@ static FASTCOVER_segment_t FASTCOVER_selectSegment(const FASTCOVER_ctx_t *ctx,
/* Get hash value of current dmer */
const size_t index = FASTCOVER_hashPtrToIndex(ctx->samples + activeSegment.end, parameters.f, ctx->d);
/* Add frequency of this index to score if this is the first occurence of index in active segment */
if (currfreqs[index] == 0) {
if (ctx->segmentFreqs[index] == 0) {
activeSegment.score += freqs[index];
}
currfreqs[index] += 1;
ctx->segmentFreqs[index] += 1;
/* Increment end of segment */
activeSegment.end += 1;
/* If the window is now too large, drop the first position */
if (activeSegment.end - activeSegment.begin == dmersInK + 1) {
/* Get hash value of the dmer to be eliminated from active segment */
const size_t delIndex = FASTCOVER_hashPtrToIndex(ctx->samples + activeSegment.begin, parameters.f, ctx->d);
currfreqs[delIndex] -= 1;
ctx->segmentFreqs[delIndex] -= 1;
/* Subtract frequency of this index from score if this is the last occurrence of this index in active segment */
if (currfreqs[delIndex] == 0) {
if (ctx->segmentFreqs[delIndex] == 0) {
activeSegment.score -= freqs[delIndex];
}
/* Increment start of segment */
@@ -175,7 +173,12 @@ static FASTCOVER_segment_t FASTCOVER_selectSegment(const FASTCOVER_ctx_t *ctx,
bestSegment = activeSegment;
}
}
free(currfreqs);
/* Zero out rest of segmentFreqs array */
while (activeSegment.begin < end) {
const size_t delIndex = FASTCOVER_hashPtrToIndex(ctx->samples + activeSegment.begin, parameters.f, ctx->d);
ctx->segmentFreqs[delIndex] -= 1;
activeSegment.begin += 1;
}
}
{
/* Trim off the zero frequency head and tail from the segment. */
@@ -245,6 +248,10 @@ static void FASTCOVER_ctx_destroy(FASTCOVER_ctx_t *ctx) {
if (!ctx) {
return;
}
if (ctx->segmentFreqs) {
free(ctx->segmentFreqs);
ctx->segmentFreqs = NULL;
}
if (ctx->freqs) {
free(ctx->freqs);
ctx->freqs = NULL;
@@ -347,9 +354,8 @@ static int FASTCOVER_ctx_init(FASTCOVER_ctx_t *ctx, const void *samplesBuffer,
}
/* Initialize frequency array of size 2^f */
ctx->freqs =(U32 *)malloc((1 << f) * sizeof(U32));
memset(ctx->freqs, 0, (1 << f) * sizeof(U32));
ctx->freqs = (U32 *)calloc((1 << f), sizeof(U32));
ctx->segmentFreqs = (U16 *)calloc((1 << f), sizeof(U16));
DISPLAYLEVEL(2, "Computing frequencies\n");
FASTCOVER_computeFrequency(ctx->freqs, f, ctx);