diff options
| -rwxr-xr-x | configure | 4 | ||||
| -rw-r--r-- | configure.ac | 4 | ||||
| -rw-r--r-- | src/diffraction-gpu.c | 3 | ||||
| -rw-r--r-- | src/diffraction-gpu.h | 6 | ||||
| -rw-r--r-- | src/diffraction.c | 8 | ||||
| -rw-r--r-- | src/diffraction.h | 5 | ||||
| -rw-r--r-- | src/indexamajig.c | 202 | ||||
| -rw-r--r-- | src/list_tmp.h | 2 |
8 files changed, 191 insertions, 43 deletions
@@ -5700,8 +5700,8 @@ done -CFLAGS="$CFLAGS $HDF5_CFLAGS $GTK_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS" -LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS" +CFLAGS="$CFLAGS $HDF5_CFLAGS $GTK_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread" +LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread" ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile" diff --git a/configure.ac b/configure.ac index 0634d89c..ab8b4790 100644 --- a/configure.ac +++ b/configure.ac @@ -91,7 +91,7 @@ AC_CHECK_FUNCS(forkpty, ) -CFLAGS="$CFLAGS $HDF5_CFLAGS $GTK_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS" -LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS" +CFLAGS="$CFLAGS $HDF5_CFLAGS $GTK_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread" +LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread" AC_OUTPUT(Makefile src/Makefile data/Makefile) 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; |