aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--libcrystfel/src/integration.c31
-rw-r--r--libcrystfel/src/integration.h7
-rw-r--r--src/im-sandbox.c85
-rw-r--r--src/indexamajig.c5
-rw-r--r--src/process_image.c4
-rw-r--r--src/process_image.h2
6 files changed, 76 insertions, 58 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 825531a5..336e99ed 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -38,6 +38,7 @@
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_eigen.h>
+#include <semaphore.h>
#ifdef HAVE_CURSES_COLOR
#include <ncurses.h>
@@ -252,14 +253,14 @@ static void show_reference_profile(struct intcontext *ic, int i)
static void show_peak_box(struct intcontext *ic, struct peak_box *bx,
- int results_pipe)
+ sem_t *term_sem)
{
#ifdef HAVE_CURSES_COLOR
int q;
signed int h, k, l;
double fs, ss;
- if ( results_pipe != 0 ) write(results_pipe, "SUSPEND\n", 8);
+ if ( term_sem != NULL ) sem_wait(term_sem);
initscr();
clear();
@@ -323,7 +324,7 @@ static void show_peak_box(struct intcontext *ic, struct peak_box *bx,
getch();
endwin();
- if ( results_pipe != 0 ) write(results_pipe, "RELEASE\n", 8);
+ if ( term_sem != NULL ) sem_post(term_sem);
#else
STATUS("Not showing peak box because CrystFEL was compiled without "
"ncurses.\n");
@@ -1170,7 +1171,7 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl)
static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx,
- int results_pipe)
+ sem_t *sem)
{
bx->intensity = fit_intensity(ic, bx);
bx->sigma = calc_sigma(ic, bx);
@@ -1200,8 +1201,7 @@ static void integrate_prof2d_once(struct intcontext *ic, struct peak_box *bx,
set_redundancy(bx->refl, 0);
}
- if ( get_int_diag(ic, bx->refl) ) show_peak_box(ic, bx,
- results_pipe);
+ if ( get_int_diag(ic, bx->refl) ) show_peak_box(ic, bx, sem);
} else {
@@ -1294,7 +1294,7 @@ static void integrate_prof2d(IntegrationMethod meth,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
- int results_pipe, int **masks)
+ sem_t *term_sem, int **masks)
{
RefList *list;
UnitCell *cell;
@@ -1338,7 +1338,7 @@ static void integrate_prof2d(IntegrationMethod meth,
for ( i=0; i<ic.n_boxes; i++ ) {
struct peak_box *bx;
bx = &ic.boxes[i];
- integrate_prof2d_once(&ic, bx, results_pipe);
+ integrate_prof2d_once(&ic, bx, term_sem);
}
//refine_rigid_groups(&ic);
@@ -1351,7 +1351,7 @@ static void integrate_prof2d(IntegrationMethod meth,
static void integrate_rings_once(Reflection *refl, struct image *image,
struct intcontext *ic, UnitCell *cell,
- int results_pipe)
+ sem_t *term_sem)
{
double pfs, pss;
struct peak_box *bx;
@@ -1450,7 +1450,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image,
pss += bx->offs_ss;
set_detector_pos(refl, pfs, pss);
- if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx, results_pipe);
+ if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx, term_sem);
if ( intensity < -5.0*sigma ) {
ic->n_implausible++;
@@ -1550,7 +1550,7 @@ static void integrate_rings(IntegrationMethod meth,
Crystal *cr, struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
- int results_pipe, int **masks)
+ sem_t *term_sem, int **masks)
{
RefList *list;
Reflection *refl;
@@ -1586,7 +1586,7 @@ static void integrate_rings(IntegrationMethod meth,
refl != NULL;
refl = next_refl(refl, iter) )
{
- integrate_rings_once(refl, image, &ic, cell, results_pipe);
+ integrate_rings_once(refl, image, &ic, cell, term_sem);
}
//refine_rigid_groups(&ic);
@@ -1602,8 +1602,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
- signed int idh, signed int idk, signed int idl,
- int results_pipe)
+ signed int idh, signed int idk, signed int idl, sem_t *sem)
{
int i;
int *masks[image->det->n_panels];
@@ -1643,14 +1642,14 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
integrate_rings(meth, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
- results_pipe, masks);
+ sem, masks);
break;
case INTEGRATION_PROF2D :
integrate_prof2d(meth, cr, image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
- results_pipe, masks);
+ sem, masks);
break;
default :
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index ca04157a..7414f818 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -3,11 +3,11 @@
*
* Integration of intensities
*
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2014 Thomas White <taw@physics.org>
+ * 2010-2015 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -33,6 +33,7 @@
#include <config.h>
#endif
+#include <semaphore.h>
#include "geometry.h"
@@ -127,7 +128,7 @@ extern void integrate_all_4(struct image *image, IntegrationMethod meth,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
- int results_pipe);
+ sem_t *term_sem);
#ifdef __cplusplus
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index ba709f6f..b800f5b4 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -48,6 +48,8 @@
#include <signal.h>
#include <sys/stat.h>
#include <assert.h>
+#include <sys/mman.h>
+#include <semaphore.h>
#ifdef HAVE_CLOCK_GETTIME
#include <time.h>
@@ -85,6 +87,12 @@ struct sb_reader
};
+struct sb_shm
+{
+ sem_t term_sem;
+};
+
+
struct sandbox
{
pthread_mutex_t lock;
@@ -96,7 +104,6 @@ struct sandbox
int n_hadcrystals_last_stats;
int n_crystals_last_stats;
int t_last_stats;
- int suspend_stats;
struct index_args *iargs;
@@ -110,6 +117,8 @@ struct sandbox
struct filename_plus_event **last_filename;
int serial;
+ struct sb_shm *shared;
+
char *tmpdir;
struct sb_reader *reader;
@@ -359,7 +368,7 @@ static int read_fpe_data(struct buffer_data *bd)
static void run_work(const struct index_args *iargs,
int filename_pipe, int results_pipe, Stream *st,
- int cookie, const char *tmpdir)
+ int cookie, const char *tmpdir, sem_t *term_sem)
{
FILE *fh;
int allDone = 0;
@@ -494,7 +503,7 @@ static void run_work(const struct index_args *iargs,
pargs.n_crystals = 0;
process_image(iargs, &pargs, st, cookie, tmpdir,
- results_pipe, ser);
+ results_pipe, ser, term_sem);
/* Request another image */
c = sprintf(buf, "%i\n", pargs.n_crystals);
@@ -815,11 +824,12 @@ static void start_worker_process(struct sandbox *sb, int slot)
st = open_stream_fd_for_write(stream_pipe[1]);
run_work(sb->iargs, filename_pipe[0], result_pipe[1],
- st, slot, tmp);
+ st, slot, tmp, &sb->shared->term_sem);
close_stream(st);
//close(filename_pipe[0]);
close(result_pipe[1]);
+ munmap(sb->shared, sizeof(struct sb_shm));
free(sb);
@@ -894,6 +904,25 @@ static void handle_zombie(struct sandbox *sb)
}
+static int setup_shm(struct sandbox *sb)
+{
+ sb->shared = mmap(NULL, sizeof(struct sb_shm), PROT_READ | PROT_WRITE,
+ MAP_SHARED | MAP_ANONYMOUS, -1, 0);
+
+ if ( sb->shared == MAP_FAILED ) {
+ ERROR("SHM setup failed: %s\n", strerror(errno));
+ return 1;
+ }
+
+ if ( sem_init(&sb->shared->term_sem, 1, 1) ) {
+ ERROR("Terminal semaphore setup failed: %s\n", strerror(errno));
+ return 1;
+ }
+
+ return 0;
+}
+
+
void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh,
Stream *stream, const char *tempdir)
@@ -930,7 +959,6 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
sb->n_hadcrystals_last_stats = 0;
sb->n_crystals_last_stats = 0;
sb->t_last_stats = get_monotonic_seconds();
- sb->suspend_stats = 0;
sb->n_proc = n_proc;
sb->iargs = iargs;
sb->serial = 1;
@@ -939,6 +967,12 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
sb->reader->fhs = NULL;
sb->reader->stream = stream;
+ if ( setup_shm(sb) ) {
+ ERROR("Failed to set up SHM.\n");
+ free(sb);
+ return;
+ }
+
sb->stream_pipe_write = calloc(n_proc, sizeof(int));
if ( sb->stream_pipe_write == NULL ) {
ERROR("Couldn't allocate memory for pipes.\n");
@@ -1106,34 +1140,20 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
chomp(results);
- if ( strcmp(results, "SUSPEND") == 0 ) {
- sb->suspend_stats++;
- continue; /* Do not send next filename */
- } else if ( strcmp(results, "RELEASE") == 0 ) {
- if ( sb->suspend_stats > 0 ) {
- sb->suspend_stats--;
- } else {
- ERROR("RELEASE before SUSPEND.\n");
+ strtol(results, &eptr, 10);
+ if ( eptr == results ) {
+ if ( strlen(results) > 0 ) {
+ ERROR("Invalid result '%s'\n",
+ results);
}
- continue; /* Do not send next filename */
} else {
- strtol(results, &eptr, 10);
- if ( eptr == results ) {
- if ( strlen(results) > 0 ) {
- ERROR("Invalid result '%s'\n",
- results);
- }
- } else {
-
- int nc = atoi(results);
- sb->n_crystals += nc;
- if ( nc > 0 ) {
- sb->n_hadcrystals++;
- }
- sb->n_processed++;
-
+ int nc = atoi(results);
+ sb->n_crystals += nc;
+ if ( nc > 0 ) {
+ sb->n_hadcrystals++;
}
+ sb->n_processed++;
}
@@ -1210,8 +1230,8 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
/* Update progress */
lock_sandbox(sb);
tNow = get_monotonic_seconds();
- if ( !sb->suspend_stats
- && (tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS) )
+ r = sem_trywait(&sb->shared->term_sem);
+ if ((r==0) && (tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS))
{
STATUS("%4i indexable out of %4i processed (%4.1f%%), "
@@ -1228,7 +1248,9 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
sb->n_crystals_last_stats = sb->n_crystals;
sb->t_last_stats = tNow;
+
}
+ if ( r == 0 ) sem_post(&sb->shared->term_sem);
unlock_sandbox(sb);
allDone = 1;
@@ -1264,6 +1286,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
free(sb->result_fhs);
free(sb->pids);
free(sb->tmpdir);
+ munmap(sb->shared, sizeof(struct sb_shm));
pthread_mutex_destroy(&sb->lock);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index eb619a87..c7e4a270 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -695,11 +695,6 @@ int main(int argc, char *argv[])
free(int_diag);
- if ( (n_proc > 1) && (iargs.int_diag != INTDIAG_NONE) ) {
- n_proc = 1;
- STATUS("Ignored \"-j\" because you used --int-diag.\n");
- }
-
}
st = open_stream_for_write_2(outfile, geom_filename, argc, argv);
diff --git a/src/process_image.c b/src/process_image.c
index 1a5a3477..5ead2c61 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -78,7 +78,7 @@ static void try_refine_autoR(struct image *image, Crystal *cr)
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie, const char *tmpdir, int results_pipe,
- int serial)
+ int serial, sem_t *term_sem)
{
float *data_for_measurement;
size_t data_size;
@@ -260,7 +260,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->int_diag, iargs->int_diag_h,
iargs->int_diag_k, iargs->int_diag_l,
- results_pipe);
+ term_sem);
ret = write_chunk(st, &image, hdfile,
iargs->stream_peaks, iargs->stream_refls,
diff --git a/src/process_image.h b/src/process_image.h
index de364772..6e44c173 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -104,7 +104,7 @@ struct pattern_args
extern void process_image(const struct index_args *iargs,
struct pattern_args *pargs, Stream *st,
int cookie, const char *tmpdir, int results_pipe,
- int serial);
+ int serial, sem_t *term_sem);
#endif /* PROCESS_IMAGEs_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-23 02:48:17 +0000