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-rw-r--r--src/diffraction-gpu.c3
-rw-r--r--src/diffraction-gpu.h6
-rw-r--r--src/diffraction.c8
-rw-r--r--src/diffraction.h5
-rw-r--r--src/indexamajig.c202
-rw-r--r--src/list_tmp.h2
6 files changed, 187 insertions, 39 deletions
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index 91d6334f..83445405 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -342,7 +342,8 @@ void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
/* Setup the OpenCL stuff, create buffers, load the structure factor table */
struct gpu_context *setup_gpu(int no_sfac, struct image *image,
- double *intensities, unsigned int *counts)
+ const double *intensities,
+ const unsigned int *counts)
{
struct gpu_context *gctx;
cl_uint nplat;
diff --git a/src/diffraction-gpu.h b/src/diffraction-gpu.h
index 9d74dec4..003c4c3a 100644
--- a/src/diffraction-gpu.h
+++ b/src/diffraction-gpu.h
@@ -26,7 +26,8 @@ struct gpu_context;
extern void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
int na, int nb, int nc, UnitCell *ucell);
extern struct gpu_context *setup_gpu(int no_sfac, struct image *image,
- double *intensities, unsigned int *counts);
+ const double *intensities,
+ const unsigned int *counts);
extern void cleanup_gpu(struct gpu_context *gctx);
#else
@@ -39,7 +40,8 @@ static void get_diffraction_gpu(struct gpu_context *gctx, struct image *image,
}
static struct gpu_context *setup_gpu(int no_sfac, struct image *image,
- double *intensities, unsigned int *counts)
+ const double *intensities,
+ const unsigned int *counts)
{
return NULL;
}
diff --git a/src/diffraction.c b/src/diffraction.c
index 675aa148..ad69c7a3 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -70,8 +70,8 @@ static double lattice_factor(struct rvec q, double ax, double ay, double az,
/* Look up the structure factor for the nearest Bragg condition */
-static double molecule_factor(double *intensities, unsigned int *counts,
- struct rvec q,
+static double molecule_factor(const double *intensities,
+ const unsigned int *counts, struct rvec q,
double ax, double ay, double az,
double bx, double by, double bz,
double cx, double cy, double cz)
@@ -177,8 +177,8 @@ struct rvec get_q(struct image *image, unsigned int xs, unsigned int ys,
void get_diffraction(struct image *image, int na, int nb, int nc,
- double *intensities, unsigned int *counts, UnitCell *cell,
- int do_water)
+ const double *intensities, const unsigned int *counts,
+ UnitCell *cell, int do_water)
{
unsigned int xs, ys;
double ax, ay, az;
diff --git a/src/diffraction.h b/src/diffraction.h
index c317060f..f3608a4b 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -20,8 +20,9 @@
#include "cell.h"
extern void get_diffraction(struct image *image, int na, int nb, int nc,
- double *intensities, unsigned int *counts,
- UnitCell *cell, int do_water);
+ const double *intensities,
+ const unsigned int *counts, UnitCell *cell,
+ int do_water);
extern struct rvec get_q(struct image *image, unsigned int xs, unsigned int ys,
unsigned int sampling, float *ttp, float k);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index c32657d9..71fdf26d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -14,6 +14,7 @@
#include <config.h>
#endif
+#define _GNU_SOURCE 1
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
@@ -22,6 +23,7 @@
#include <getopt.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
+#include <pthread.h>
#include "utils.h"
#include "hdf5-file.h"
@@ -35,6 +37,35 @@
#include "reflections.h"
+#define MAX_THREADS (96)
+
+struct process_args
+{
+ char *filename;
+ UnitCell *cell;
+ int config_cmfilter;
+ int config_noisefilter;
+ int config_writedrx;
+ int config_dumpfound;
+ int config_verbose;
+ int config_alternate;
+ int config_nearbragg;
+ int config_gpu;
+ int config_simulate;
+ int config_nomatch;
+ IndexingMethod indm;
+ const double *intensities;
+ const unsigned int *counts;
+ struct gpu_context *gctx;
+};
+
+struct process_result
+{
+ int hit;
+ struct process_args *pargs;
+};
+
+
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
@@ -51,6 +82,7 @@ static void show_help(const char *s)
"\n"
" --verbose Be verbose about indexing.\n"
" --gpu Use the GPU to speed up the simulation.\n"
+" -j <n> Run <n> analyses in parallel.\n"
"\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
" The intensities in this list are the sum of\n"
@@ -149,8 +181,8 @@ static struct image *get_simage(struct image *template, int alternate)
static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
- double *intensities, unsigned int *counts,
- UnitCell *cell)
+ const double *intensities,
+ const unsigned int *counts, UnitCell *cell)
{
/* Set up GPU if necessary */
if ( (gctx != NULL) && (*gctx == NULL) ) {
@@ -170,37 +202,54 @@ static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
}
-static int process_pattern(const char *filename, UnitCell *cell,
- int config_cmfilter, int config_noisefilter,
- int config_writedrx, int config_dumpfound,
- int config_verbose, int config_alternate,
- int config_nearbragg, int config_gpu,
- int config_simulate, int config_nomatch,
- IndexingMethod indm, double *intensities,
- unsigned int *counts, struct gpu_context *gctx)
+static void *process_image(void *pargsv)
{
+ struct process_args *pargs = pargsv;
struct hdfile *hdfile;
struct image image;
struct image *simage;
float *data_for_measurement;
size_t data_size;
+ const char *filename = pargs->filename;
+ UnitCell *cell = pargs->cell;
+ int config_cmfilter = pargs->config_cmfilter;
+ int config_noisefilter = pargs->config_noisefilter;
+ int config_writedrx = pargs->config_writedrx;
+ int config_dumpfound = pargs->config_dumpfound;
+ int config_verbose = pargs->config_verbose;
+ int config_alternate = pargs->config_alternate;
+ int config_nearbragg = pargs->config_nearbragg;
+ int config_gpu = pargs->config_gpu;
+ int config_simulate = pargs->config_simulate;
+ int config_nomatch = pargs->config_nomatch;
+ IndexingMethod indm = pargs->indm;
+ const double *intensities = pargs->intensities;
+ const unsigned int *counts = pargs->counts;
+ struct gpu_context *gctx = pargs->gctx;
+ struct process_result *result;
image.features = NULL;
image.data = NULL;
image.indexed_cell = NULL;
- #include "geometry-lcls.tmp"
-
STATUS("Processing '%s'\n", filename);
+ result = malloc(sizeof(*result));
+ if ( result == NULL ) return NULL;
+ result->pargs = pargs;
+
hdfile = hdfile_open(filename);
if ( hdfile == NULL ) {
- return 0;
+ result->hit = 0;
+ return result;
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
- return 0;
+ result->hit = 0;
+ return result;
}
+ #include "geometry-lcls.tmp"
+
hdf5_read(hdfile, &image);
if ( config_cmfilter ) {
@@ -278,16 +327,22 @@ static int process_pattern(const char *filename, UnitCell *cell,
/* Only free cell if found */
free(image.indexed_cell);
+ /* Free detector panel records */
+ free(image.det.panels);
+
done:
free(image.data);
free(image.det.panels);
image_feature_list_free(image.features);
free(data_for_measurement);
hdfile_close(hdfile);
- H5close();
- if ( image.indexed_cell == NULL ) return 0;
- return 1;
+ if ( image.indexed_cell == NULL ) {
+ result->hit = 0;
+ } else {
+ result->hit = 1;
+ }
+ return result;
}
@@ -297,7 +352,7 @@ int main(int argc, char *argv[])
struct gpu_context *gctx = NULL;
char *filename = NULL;
FILE *fh;
- char *rval;
+ char *rval = NULL;
int n_images;
int n_hits;
int config_noindex = 0;
@@ -319,6 +374,10 @@ int main(int argc, char *argv[])
unsigned int *counts = NULL;
char *pdb = NULL;
char *prefix = NULL;
+ int nthreads = 1;
+ pthread_t workers[MAX_THREADS];
+ struct process_args *worker_args[MAX_THREADS];
+ int i;
/* Long options */
const struct option longopts[] = {
@@ -343,7 +402,7 @@ int main(int argc, char *argv[])
};
/* Short options */
- while ((c = getopt_long(argc, argv, "hi:wp:", longopts, NULL)) != -1) {
+ while ((c = getopt_long(argc, argv, "hi:wp:j:", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
@@ -376,6 +435,11 @@ int main(int argc, char *argv[])
break;
}
+ case 'j' : {
+ nthreads = atoi(optarg);
+ break;
+ }
+
case 0 : {
break;
}
@@ -416,6 +480,11 @@ int main(int argc, char *argv[])
prefix = "";
}
+ if ( nthreads == 0 ) {
+ ERROR("Invalid number of threads.\n");
+ return 1;
+ }
+
if ( indm_str == NULL ) {
STATUS("You didn't specify an indexing method, so I won't"
" try to index anything.\n"
@@ -440,31 +509,106 @@ int main(int argc, char *argv[])
}
gsl_set_error_handler_off();
-
n_images = 0;
n_hits = 0;
- do {
+
+ /* Initially, fire off the full number of threads */
+ for ( i=0; i<nthreads; i++ ) {
char line[1024];
- char prefixed[1024];
+ char *prefixed;
+ struct process_args *pargs;
+ int r;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
+ prefixed = malloc(1024);
snprintf(prefixed, 1023, "%s%s", prefix, line);
n_images++;
- n_hits += process_pattern(line, cell, config_cmfilter,
- config_noisefilter,
- config_writedrx, config_dumpfound,
- config_verbose, config_alternate,
- config_nearbragg, config_gpu,
- config_simulate, config_nomatch, indm,
- intensities, counts, gctx);
+ pargs = malloc(sizeof(*pargs));
+ pargs->filename = prefixed;
+ pargs->config_cmfilter = config_cmfilter;
+ pargs->config_noisefilter = config_noisefilter;
+ pargs->config_writedrx = config_writedrx;
+ pargs->config_dumpfound = config_dumpfound;
+ pargs->config_verbose = config_verbose;
+ pargs->config_alternate = config_alternate;
+ pargs->config_nearbragg = config_nearbragg;
+ pargs->config_gpu = config_gpu;
+ pargs->config_simulate = config_simulate;
+ pargs->config_nomatch = config_nomatch;
+ pargs->cell = cell;
+ pargs->indm = indm;
+ pargs->intensities = intensities;
+ pargs->counts = counts;
+ pargs->gctx = gctx;
+ worker_args[i] = pargs;
+
+ r = pthread_create(&workers[i], NULL, process_image, pargs);
+ if ( r != 0 ) {
+ ERROR("Couldn't start thread %i\n", i);
+ }
+
+ }
+
+ /* Start new threads as old ones finish */
+ do {
+
+ int i;
+
+ for ( i=0; i<nthreads; i++ ) {
+
+ char line[1024];
+ char *prefixed;
+ int r;
+ struct process_result *result = NULL;
+ struct timespec t;
+ struct process_args *pargs;
+
+ t.tv_sec = 0;
+ t.tv_nsec = 20000; /* 20 ms */
+
+ r = pthread_timedjoin_np(workers[i], (void *)&result,
+ &t);
+ if ( r != 0 ) continue; /* Not ready yet */
+
+ if ( result != NULL ) {
+ n_hits += result->hit;
+ free(result);
+ }
+
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) break;
+ chomp(line);
+ prefixed = malloc(1024);
+ snprintf(prefixed, 1023, "%s%s", prefix, line);
+
+ pargs = worker_args[i];
+ free(pargs->filename);
+ pargs->filename = prefixed;
+ /* Other arguments unchanged */
+
+ r = pthread_create(&workers[i], NULL, process_image,
+ pargs);
+ if ( r != 0 ) {
+ ERROR("Couldn't start thread %i\n", i);
+ }
+
+ n_images++;
+ }
} while ( rval != NULL );
+ for ( i=0; i<nthreads; i++ ) {
+ free(worker_args[i]->filename);
+ free(worker_args[i]);
+ }
+
+ free(prefix);
+ free(cell);
fclose(fh);
STATUS("There were %i images.\n", n_images);
diff --git a/src/list_tmp.h b/src/list_tmp.h
index f95b7af9..7b2c9d0c 100644
--- a/src/list_tmp.h
+++ b/src/list_tmp.h
@@ -64,7 +64,7 @@ static inline void LABEL(set)(TYPE *ref, signed int h,
}
-static inline TYPE LABEL(lookup)(TYPE *ref, signed int h,
+static inline TYPE LABEL(lookup)(const TYPE *ref, signed int h,
signed int k, signed int l)
{
int idx;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 10:07:40 +0000