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Merge pull request #1348 from facebook/donotdelete

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Fix #1082
This commit is contained in:
Yann Collet
2018-10-02 16:37:58 -07:00
committed by GitHub
parent 8514bd8eb9 3ca6261223
commit c9843ec232
3 changed files with 523 additions and 415 deletions
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lib/dictBuilder/fastcover.c
+138 -111
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@@ -245,39 +245,41 @@ static int FASTCOVER_checkParameters(ZDICT_cover_params_t parameters,
/**
* Clean up a context initialized with `FASTCOVER_ctx_init()`.
*/
static void FASTCOVER_ctx_destroy(FASTCOVER_ctx_t *ctx) {
if (!ctx) {
return;
}
static void
FASTCOVER_ctx_destroy(FASTCOVER_ctx_t* ctx)
{
if (!ctx) return;
free(ctx->freqs);
ctx->freqs = NULL;
free(ctx->freqs);
ctx->freqs = NULL;
free(ctx->offsets);
ctx->offsets = NULL;
free(ctx->offsets);
ctx->offsets = NULL;
}
/**
* Calculate for frequency of hash value of each dmer in ctx->samples
*/
static void FASTCOVER_computeFrequency(U32 *freqs, FASTCOVER_ctx_t *ctx){
const unsigned f = ctx->f;
const unsigned d = ctx->d;
const unsigned skip = ctx->accelParams.skip;
const unsigned readLength = MAX(d, 8);
size_t start; /* start of current dmer */
size_t i;
for (i = 0; i < ctx->nbTrainSamples; i++) {
size_t currSampleStart = ctx->offsets[i];
size_t currSampleEnd = ctx->offsets[i+1];
start = currSampleStart;
while (start + readLength <= currSampleEnd) {
const size_t dmerIndex = FASTCOVER_hashPtrToIndex(ctx->samples + start, f, d);
freqs[dmerIndex]++;
start = start + skip + 1;
static void
FASTCOVER_computeFrequency(U32* freqs, const FASTCOVER_ctx_t* ctx)
{
const unsigned f = ctx->f;
const unsigned d = ctx->d;
const unsigned skip = ctx->accelParams.skip;
const unsigned readLength = MAX(d, 8);
size_t i;
assert(ctx->nbTrainSamples >= 5);
assert(ctx->nbTrainSamples <= ctx->nbSamples);
for (i = 0; i < ctx->nbTrainSamples; i++) {
size_t start = ctx->offsets[i]; /* start of current dmer */
size_t const currSampleEnd = ctx->offsets[i+1];
while (start + readLength <= currSampleEnd) {
const size_t dmerIndex = FASTCOVER_hashPtrToIndex(ctx->samples + start, f, d);
freqs[dmerIndex]++;
start = start + skip + 1;
}
}
}
}
@@ -288,84 +290,100 @@ static void FASTCOVER_computeFrequency(U32 *freqs, FASTCOVER_ctx_t *ctx){
* Returns 1 on success or zero on error.
* The context must be destroyed with `FASTCOVER_ctx_destroy()`.
*/
static int FASTCOVER_ctx_init(FASTCOVER_ctx_t *ctx, const void *samplesBuffer,
const size_t *samplesSizes, unsigned nbSamples,
unsigned d, double splitPoint, unsigned f,
FASTCOVER_accel_t accelParams) {
const BYTE *const samples = (const BYTE *)samplesBuffer;
const size_t totalSamplesSize = COVER_sum(samplesSizes, nbSamples);
/* Split samples into testing and training sets */
const unsigned nbTrainSamples = splitPoint < 1.0 ? (unsigned)((double)nbSamples * splitPoint) : nbSamples;
const unsigned nbTestSamples = splitPoint < 1.0 ? nbSamples - nbTrainSamples : nbSamples;
const size_t trainingSamplesSize = splitPoint < 1.0 ? COVER_sum(samplesSizes, nbTrainSamples) : totalSamplesSize;
const size_t testSamplesSize = splitPoint < 1.0 ? COVER_sum(samplesSizes + nbTrainSamples, nbTestSamples) : totalSamplesSize;
/* Checks */
if (totalSamplesSize < MAX(d, sizeof(U64)) ||
totalSamplesSize >= (size_t)FASTCOVER_MAX_SAMPLES_SIZE) {
DISPLAYLEVEL(1, "Total samples size is too large (%u MB), maximum size is %u MB\n",
(U32)(totalSamplesSize >> 20), (FASTCOVER_MAX_SAMPLES_SIZE >> 20));
return 0;
}
/* Check if there are at least 5 training samples */
if (nbTrainSamples < 5) {
DISPLAYLEVEL(1, "Total number of training samples is %u and is invalid\n", nbTrainSamples);
return 0;
}
/* Check if there's testing sample */
if (nbTestSamples < 1) {
DISPLAYLEVEL(1, "Total number of testing samples is %u and is invalid.\n", nbTestSamples);
return 0;
}
/* Zero the context */
memset(ctx, 0, sizeof(*ctx));
DISPLAYLEVEL(2, "Training on %u samples of total size %u\n", nbTrainSamples,
(U32)trainingSamplesSize);
DISPLAYLEVEL(2, "Testing on %u samples of total size %u\n", nbTestSamples,
(U32)testSamplesSize);
static int
FASTCOVER_ctx_init(FASTCOVER_ctx_t* ctx,
const void* samplesBuffer,
const size_t* samplesSizes, unsigned nbSamples,
unsigned d, double splitPoint, unsigned f,
FASTCOVER_accel_t accelParams)
{
const BYTE* const samples = (const BYTE*)samplesBuffer;
const size_t totalSamplesSize = COVER_sum(samplesSizes, nbSamples);
/* Split samples into testing and training sets */
const unsigned nbTrainSamples = splitPoint < 1.0 ? (unsigned)((double)nbSamples * splitPoint) : nbSamples;
const unsigned nbTestSamples = splitPoint < 1.0 ? nbSamples - nbTrainSamples : nbSamples;
const size_t trainingSamplesSize = splitPoint < 1.0 ? COVER_sum(samplesSizes, nbTrainSamples) : totalSamplesSize;
const size_t testSamplesSize = splitPoint < 1.0 ? COVER_sum(samplesSizes + nbTrainSamples, nbTestSamples) : totalSamplesSize;
ctx->samples = samples;
ctx->samplesSizes = samplesSizes;
ctx->nbSamples = nbSamples;
ctx->nbTrainSamples = nbTrainSamples;
ctx->nbTestSamples = nbTestSamples;
ctx->nbDmers = trainingSamplesSize - MAX(d, sizeof(U64)) + 1;
ctx->d = d;
ctx->f = f;
ctx->accelParams = accelParams;
/* The offsets of each file */
ctx->offsets = (size_t *)malloc((nbSamples + 1) * sizeof(size_t));
if (!ctx->offsets) {
DISPLAYLEVEL(1, "Failed to allocate scratch buffers\n");
FASTCOVER_ctx_destroy(ctx);
return 0;
}
/* Fill offsets from the samplesSizes */
{
U32 i;
ctx->offsets[0] = 0;
for (i = 1; i <= nbSamples; ++i) {
ctx->offsets[i] = ctx->offsets[i - 1] + samplesSizes[i - 1];
/* Checks */
if (totalSamplesSize < MAX(d, sizeof(U64)) ||
totalSamplesSize >= (size_t)FASTCOVER_MAX_SAMPLES_SIZE) {
DISPLAYLEVEL(1, "Total samples size is too large (%u MB), maximum size is %u MB\n",
(U32)(totalSamplesSize >> 20), (FASTCOVER_MAX_SAMPLES_SIZE >> 20));
return 0;
}
}
/* Initialize frequency array of size 2^f */
ctx->freqs = (U32 *)calloc(((U64)1 << f), sizeof(U32));
/* Check if there are at least 5 training samples */
if (nbTrainSamples < 5) {
DISPLAYLEVEL(1, "Total number of training samples is %u and is invalid\n", nbTrainSamples);
return 0;
}
DISPLAYLEVEL(2, "Computing frequencies\n");
FASTCOVER_computeFrequency(ctx->freqs, ctx);
/* Check if there's testing sample */
if (nbTestSamples < 1) {
DISPLAYLEVEL(1, "Total number of testing samples is %u and is invalid.\n", nbTestSamples);
return 0;
}
return 1;
/* Zero the context */
memset(ctx, 0, sizeof(*ctx));
DISPLAYLEVEL(2, "Training on %u samples of total size %u\n", nbTrainSamples,
(U32)trainingSamplesSize);
DISPLAYLEVEL(2, "Testing on %u samples of total size %u\n", nbTestSamples,
(U32)testSamplesSize);
ctx->samples = samples;
ctx->samplesSizes = samplesSizes;
ctx->nbSamples = nbSamples;
ctx->nbTrainSamples = nbTrainSamples;
ctx->nbTestSamples = nbTestSamples;
ctx->nbDmers = trainingSamplesSize - MAX(d, sizeof(U64)) + 1;
ctx->d = d;
ctx->f = f;
ctx->accelParams = accelParams;
/* The offsets of each file */
ctx->offsets = (size_t*)calloc((nbSamples + 1), sizeof(size_t));
if (ctx->offsets == NULL) {
DISPLAYLEVEL(1, "Failed to allocate scratch buffers \n");
FASTCOVER_ctx_destroy(ctx);
return 0;
}
/* Fill offsets from the samplesSizes */
{ U32 i;
ctx->offsets[0] = 0;
assert(nbSamples >= 5);
for (i = 1; i <= nbSamples; ++i) {
ctx->offsets[i] = ctx->offsets[i - 1] + samplesSizes[i - 1];
}
}
/* Initialize frequency array of size 2^f */
ctx->freqs = (U32*)calloc(((U64)1 << f), sizeof(U32));
if (ctx->freqs == NULL) {
DISPLAYLEVEL(1, "Failed to allocate frequency table \n");
FASTCOVER_ctx_destroy(ctx);
return 0;
}
DISPLAYLEVEL(2, "Computing frequencies\n");
FASTCOVER_computeFrequency(ctx->freqs, ctx);
return 1;
}
/**
* Given the prepared context build the dictionary.
*/
static size_t FASTCOVER_buildDictionary(const FASTCOVER_ctx_t *ctx, U32 *freqs,
void *dictBuffer, size_t dictBufferCapacity,
ZDICT_cover_params_t parameters, U16* segmentFreqs){
static size_t
FASTCOVER_buildDictionary(const FASTCOVER_ctx_t* ctx,
U32* freqs,
void* dictBuffer, size_t dictBufferCapacity,
ZDICT_cover_params_t parameters,
U16* segmentFreqs)
{
BYTE *const dict = (BYTE *)dictBuffer;
size_t tail = dictBufferCapacity;
/* Divide the data up into epochs of equal size.
@@ -416,10 +434,10 @@ static size_t FASTCOVER_buildDictionary(const FASTCOVER_ctx_t *ctx, U32 *freqs,
* Parameters for FASTCOVER_tryParameters().
*/
typedef struct FASTCOVER_tryParameters_data_s {
const FASTCOVER_ctx_t *ctx;
COVER_best_t *best;
size_t dictBufferCapacity;
ZDICT_cover_params_t parameters;
const FASTCOVER_ctx_t* ctx;
COVER_best_t* best;
size_t dictBufferCapacity;
ZDICT_cover_params_t parameters;
} FASTCOVER_tryParameters_data_t;
@@ -428,7 +446,8 @@ typedef struct FASTCOVER_tryParameters_data_s {
* This function is thread safe if zstd is compiled with multithreaded support.
* It takes its parameters as an *OWNING* opaque pointer to support threading.
*/
static void FASTCOVER_tryParameters(void *opaque) {
static void FASTCOVER_tryParameters(void *opaque)
{
/* Save parameters as local variables */
FASTCOVER_tryParameters_data_t *const data = (FASTCOVER_tryParameters_data_t *)opaque;
const FASTCOVER_ctx_t *const ctx = data->ctx;
@@ -447,8 +466,7 @@ static void FASTCOVER_tryParameters(void *opaque) {
/* Copy the frequencies because we need to modify them */
memcpy(freqs, ctx->freqs, ((U64)1 << ctx->f) * sizeof(U32));
/* Build the dictionary */
{
const size_t tail = FASTCOVER_buildDictionary(ctx, freqs, dict, dictBufferCapacity,
{ const size_t tail = FASTCOVER_buildDictionary(ctx, freqs, dict, dictBufferCapacity,
parameters, segmentFreqs);
const unsigned nbFinalizeSamples = (unsigned)(ctx->nbTrainSamples * ctx->accelParams.finalize / 100);
dictBufferCapacity = ZDICT_finalizeDictionary(
@@ -474,9 +492,10 @@ _cleanup:
}
static void FASTCOVER_convertToCoverParams(ZDICT_fastCover_params_t fastCoverParams,
ZDICT_cover_params_t *coverParams) {
static void
FASTCOVER_convertToCoverParams(ZDICT_fastCover_params_t fastCoverParams,
ZDICT_cover_params_t* coverParams)
{
coverParams->k = fastCoverParams.k;
coverParams->d = fastCoverParams.d;
coverParams->steps = fastCoverParams.steps;
@@ -486,9 +505,11 @@ static void FASTCOVER_convertToCoverParams(ZDICT_fastCover_params_t fastCoverPar
}
static void FASTCOVER_convertToFastCoverParams(ZDICT_cover_params_t coverParams,
ZDICT_fastCover_params_t *fastCoverParams,
unsigned f, unsigned accel) {
static void
FASTCOVER_convertToFastCoverParams(ZDICT_cover_params_t coverParams,
ZDICT_fastCover_params_t* fastCoverParams,
unsigned f, unsigned accel)
{
fastCoverParams->k = coverParams.k;
fastCoverParams->d = coverParams.d;
fastCoverParams->steps = coverParams.steps;
@@ -500,9 +521,12 @@ static void FASTCOVER_convertToFastCoverParams(ZDICT_cover_params_t coverParams,
}
ZDICTLIB_API size_t ZDICT_trainFromBuffer_fastCover(
void *dictBuffer, size_t dictBufferCapacity, const void *samplesBuffer,
const size_t *samplesSizes, unsigned nbSamples, ZDICT_fastCover_params_t parameters) {
ZDICTLIB_API size_t
ZDICT_trainFromBuffer_fastCover(void* dictBuffer, size_t dictBufferCapacity,
const void* samplesBuffer,
const size_t* samplesSizes, unsigned nbSamples,
ZDICT_fastCover_params_t parameters)
{
BYTE* const dict = (BYTE*)dictBuffer;
FASTCOVER_ctx_t ctx;
ZDICT_cover_params_t coverParams;
@@ -562,10 +586,13 @@ ZDICTLIB_API size_t ZDICT_trainFromBuffer_fastCover(
}
ZDICTLIB_API size_t ZDICT_optimizeTrainFromBuffer_fastCover(
void *dictBuffer, size_t dictBufferCapacity, const void *samplesBuffer,
const size_t *samplesSizes, unsigned nbSamples,
ZDICT_fastCover_params_t *parameters) {
ZDICTLIB_API size_t
ZDICT_optimizeTrainFromBuffer_fastCover(
void* dictBuffer, size_t dictBufferCapacity,
const void* samplesBuffer,
const size_t* samplesSizes, unsigned nbSamples,
ZDICT_fastCover_params_t* parameters)
{
ZDICT_cover_params_t coverParams;
FASTCOVER_accel_t accelParams;
/* constants */