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-rw-r--r--libcrystfel/src/index.c38
-rw-r--r--libcrystfel/src/index.h3
-rw-r--r--src/im-sandbox.c16
-rw-r--r--src/im-sandbox.h7
-rw-r--r--src/process_image.c20
-rw-r--r--src/process_image.h3
6 files changed, 80 insertions, 7 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 1476304d..06d57e52 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -81,6 +81,20 @@ static const char *onoff(int a)
return "off";
}
+/* Definition and function definition duplicated here (from im-sandbox.{c,h})
+ * because libcrystfel code cannot depend on core CrystFEL programs.
+ *
+ * Must match the value and definition in im-sandbox.h
+ */
+#define MAX_TASK_LEN (32)
+
+static void set_last_task(char *lt, const char *task)
+{
+ if ( lt == NULL ) return;
+ assert(strlen(task) < MAX_TASK_LEN-1);
+ strcpy(lt, task);
+}
+
static void show_indexing_flags(IndexingFlags flags)
{
@@ -556,7 +570,7 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
/* Return non-zero for "success" */
static int try_indexer(struct image *image, IndexingMethod indm,
- IndexingPrivate *ipriv, void *mpriv)
+ IndexingPrivate *ipriv, void *mpriv, char *last_task)
{
int i, r;
int n_bad = 0;
@@ -568,34 +582,42 @@ static int try_indexer(struct image *image, IndexingMethod indm,
return 0;
case INDEXING_DIRAX :
+ set_last_task(last_task, "indexing:dirax");
r = run_dirax(image, mpriv);
break;
case INDEXING_ASDF :
+ set_last_task(last_task, "indexing:asdf");
r = run_asdf(image, mpriv);
break;
case INDEXING_MOSFLM :
+ set_last_task(last_task, "indexing:mosflm");
r = run_mosflm(image, mpriv);
break;
case INDEXING_XDS :
+ set_last_task(last_task, "indexing:xds");
r = run_xds(image, mpriv);
break;
case INDEXING_DEBUG :
+ set_last_task(last_task, "indexing:debug");
r = debug_index(image);
break;
case INDEXING_FELIX :
+ set_last_task(last_task, "indexing:felix");
r = felix_index(image, mpriv);
break;
case INDEXING_TAKETWO :
+ set_last_task(last_task, "indexing:taketwo");
r = taketwo_index(image, ipriv->ttopts, mpriv);
break;
case INDEXING_XGANDALF :
+ set_last_task(last_task, "indexing:xgandalf");
r = run_xgandalf(image, mpriv);
break;
@@ -605,6 +627,8 @@ static int try_indexer(struct image *image, IndexingMethod indm,
}
+ set_last_task(last_task, "indexing:finalisation");
+
/* Stop a really difficult to debug situation in its tracks */
if ( image->n_crystals - n_before != r ) {
ERROR("Whoops, indexer didn't return the right number "
@@ -812,12 +836,19 @@ static int finished_retry(IndexingMethod indm, IndexingFlags flags,
void index_pattern(struct image *image, IndexingPrivate *ipriv)
{
- index_pattern_2(image, ipriv, NULL);
+ index_pattern_3(image, ipriv, NULL, NULL);
}
void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
{
+ index_pattern_3(image, ipriv, ping, NULL);
+}
+
+
+void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
+ char *last_task)
+{
int n = 0;
ImageFeatureList *orig;
@@ -841,7 +872,8 @@ void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
do {
r = try_indexer(image, ipriv->methods[n],
- ipriv, ipriv->engine_private[n]);
+ ipriv, ipriv->engine_private[n],
+ last_task);
success += r;
ntry++;
done = finished_retry(ipriv->methods[n], ipriv->flags,
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 2099b4d7..eaf6f912 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -158,6 +158,9 @@ extern void index_pattern(struct image *image, IndexingPrivate *ipriv);
extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv,
int *ping);
+extern void index_pattern_3(struct image *image, IndexingPrivate *ipriv,
+ int *ping, char *last_task);
+
extern void cleanup_indexing(IndexingPrivate *ipriv);
#ifdef __cplusplus
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 80ac4166..ad2bc5fc 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -153,6 +153,8 @@ static void check_hung_workers(struct sandbox *sb)
"frame for more than 10 minutes.\n", i);
STATUS("Event ID is: %s\n",
sb->shared->last_ev[i]);
+ STATUS("Task ID is: %s\n",
+ sb->shared->last_task[i]);
sb->shared->warned_long_running[i] = 1;
}
}
@@ -321,6 +323,14 @@ static void shuffle_events(struct sb_shm *sb_shared)
}
+void set_last_task(char *lt, const char *task)
+{
+ if ( lt == NULL ) return;
+ assert(strlen(task) < MAX_TASK_LEN-1);
+ strcpy(lt, task);
+}
+
+
static void run_work(const struct index_args *iargs, Stream *st,
int cookie, const char *tmpdir, struct sandbox *sb)
{
@@ -338,12 +348,14 @@ static void run_work(const struct index_args *iargs, Stream *st,
/* Wait until an event is ready */
time_accounts_set(taccs, TACC_EVENTWAIT);
+ set_last_task(sb->shared->last_task[cookie], "wait_event");
if ( sem_wait(sb->queue_sem) != 0 ) {
ERROR("Failed to wait on queue semaphore: %s\n",
strerror(errno));
}
/* Get the event from the queue */
+ set_last_task(sb->shared->last_task[cookie], "read_queue");
pthread_mutex_lock(&sb->shared->queue_lock);
if ( sb->shared->no_more ) {
pthread_mutex_unlock(&sb->shared->queue_lock);
@@ -390,7 +402,7 @@ static void run_work(const struct index_args *iargs, Stream *st,
sb->shared->time_last_start[cookie] = get_monotonic_seconds();
process_image(iargs, &pargs, st, cookie, tmpdir, ser,
- sb->shared, taccs);
+ sb->shared, taccs, sb->shared->last_task[cookie]);
free_filename_plus_event(pargs.filename_p_e);
@@ -705,6 +717,8 @@ static void handle_zombie(struct sandbox *sb, int respawn)
i, WTERMSIG(status));
STATUS("Event ID was: %s\n",
sb->shared->last_ev[i]);
+ STATUS("Task ID was: %s\n",
+ sb->shared->last_task[i]);
if ( respawn ) start_worker_process(sb, i);
}
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 1412d199..e5f3422b 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -49,6 +49,10 @@ struct sb_shm;
/* Maximum length of an event ID including serial number */
#define MAX_EV_LEN (1024)
+/* Maximum length of a task ID, e.g. indexing:xgandalf.
+ * NB If changing this, also update the value in index.c */
+#define MAX_TASK_LEN (32)
+
/* Maximum number of workers */
#define MAX_NUM_WORKERS (1024)
@@ -61,6 +65,7 @@ struct sb_shm
char queue[QUEUE_SIZE][MAX_EV_LEN];
int no_more;
char last_ev[MAX_NUM_WORKERS][MAX_EV_LEN];
+ char last_task[MAX_NUM_WORKERS][MAX_TASK_LEN];
int pings[MAX_NUM_WORKERS];
time_t time_last_start[MAX_NUM_WORKERS];
int warned_long_running[MAX_NUM_WORKERS];
@@ -73,6 +78,8 @@ struct sb_shm
extern char *create_tempdir(const char *temp_location);
+extern void set_last_task(char *lt, const char *task);
+
extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh, Stream *stream,
const char *tempdir, int serial_start);
diff --git a/src/process_image.c b/src/process_image.c
index 10863fd3..2fbf0e4a 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -99,7 +99,8 @@ static void restore_image_data(float **dp, struct detector *det, float **bu)
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie, const char *tmpdir,
- int serial, struct sb_shm *sb_shared, TimeAccounts *taccs)
+ int serial, struct sb_shm *sb_shared, TimeAccounts *taccs,
+ char *last_task)
{
int check;
struct imagefile *imfile;
@@ -124,6 +125,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
image.indexed_by = INDEXING_NONE;
time_accounts_set(taccs, TACC_HDF5OPEN);
+ set_last_task(last_task, "open file");
sb_shared->pings[cookie]++;
imfile = imagefile_open(image.filename);
if ( imfile == NULL ) {
@@ -132,6 +134,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
}
time_accounts_set(taccs, TACC_HDF5READ);
+ set_last_task(last_task, "read file");
sb_shared->pings[cookie]++;
check = imagefile_read(imfile, &image, image.event);
if ( check ) {
@@ -140,6 +143,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Take snapshot of image before applying horrible noise filters */
time_accounts_set(taccs, TACC_FILTER);
+ set_last_task(last_task, "image filter");
sb_shared->pings[cookie]++;
prefilter = backup_image_data(image.dp, image.det);
@@ -152,6 +156,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
}
time_accounts_set(taccs, TACC_RESRANGE);
+ set_last_task(last_task, "resolution range");
sb_shared->pings[cookie]++;
mark_resolution_range_as_bad(&image, iargs->highres, +INFINITY);
@@ -162,6 +167,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
struct hdfile *hdfile;
case PEAK_HDF5:
+ set_last_task(last_task, "peaksearch:hdf5");
hdfile = imagefile_get_hdfile(imfile);
if ( (hdfile == NULL)
|| (get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
@@ -178,6 +184,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_CXI:
+ set_last_task(last_task, "peaksearch:cxi");
hdfile = imagefile_get_hdfile(imfile);
if ( (hdfile == NULL)
|| (get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
@@ -195,6 +202,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_ZAEF:
+ set_last_task(last_task, "peaksearch:zaef");
search_peaks(&image, iargs->threshold,
iargs->min_gradient, iargs->min_snr,
iargs->pk_inn, iargs->pk_mid, iargs->pk_out,
@@ -202,6 +210,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_PEAKFINDER8:
+ set_last_task(last_task, "peaksearch:pf8");
if ( search_peaks_peakfinder8(&image, 2048,
iargs->threshold,
iargs->min_snr,
@@ -224,6 +233,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_PEAKFINDER9:
+ set_last_task(last_task, "peaksearch:pf9");
if ( search_peaks_peakfinder9(&image,
iargs->min_snr_biggest_pix,
iargs->min_snr_peak_pix,
@@ -297,7 +307,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Index the pattern */
time_accounts_set(taccs, TACC_INDEXING);
- index_pattern_2(&image, iargs->ipriv, &sb_shared->pings[cookie]);
+ set_last_task(last_task, "indexing");
+ index_pattern_3(&image, iargs->ipriv, &sb_shared->pings[cookie],
+ last_task);
r = chdir(rn);
if ( r ) {
@@ -309,6 +321,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Set beam/crystal parameters */
time_accounts_set(taccs, TACC_PREDPARAMS);
+ set_last_task(last_task, "prediction params");
if ( iargs->fix_profile_r >= 0.0 ) {
for ( i=0; i<image.n_crystals; i++ ) {
crystal_set_profile_radius(image.crystals[i],
@@ -332,6 +345,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Integrate! */
time_accounts_set(taccs, TACC_INTEGRATION);
+ set_last_task(last_task, "integration");
sb_shared->pings[cookie]++;
integrate_all_5(&image, iargs->int_meth, PMODEL_XSPHERE,
iargs->push_res,
@@ -342,6 +356,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
streamwrite:
time_accounts_set(taccs, TACC_WRITESTREAM);
+ set_last_task(last_task, "stream write");
sb_shared->pings[cookie]++;
ret = write_chunk(st, &image, imfile,
iargs->stream_peaks, iargs->stream_refls,
@@ -363,6 +378,7 @@ streamwrite:
out:
/* Count crystals which are still good */
time_accounts_set(taccs, TACC_TOTALS);
+ set_last_task(last_task, "process_image finalisation");
sb_shared->pings[cookie]++;
pthread_mutex_lock(&sb_shared->totals_lock);
any_crystals = 0;
diff --git a/src/process_image.h b/src/process_image.h
index d4dcbf04..d4b1ce59 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -127,7 +127,8 @@ struct pattern_args
extern void process_image(const struct index_args *iargs,
struct pattern_args *pargs, Stream *st,
int cookie, const char *tmpdir, int serial,
- struct sb_shm *sb_shared, TimeAccounts *taccs);
+ struct sb_shm *sb_shared, TimeAccounts *taccs,
+ char *last_task);
#endif /* PROCESS_IMAGE_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-03 07:00:40 +0000