aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--src/gui_backend_local.c2
-rw-r--r--src/gui_backend_slurm.c219
-rw-r--r--src/gui_index.c6
-rw-r--r--src/gui_index.h2
4 files changed, 179 insertions, 50 deletions
diff --git a/src/gui_backend_local.c b/src/gui_backend_local.c
index 7411c9a2..a43e3632 100644
--- a/src/gui_backend_local.c
+++ b/src/gui_backend_local.c
@@ -218,6 +218,8 @@ static void *run_indexing(const char *job_title,
snprintf(n_thread_str, 63, "%i", opts->n_processes);
args = indexamajig_command_line(geom_filename,
n_thread_str,
+ "files.lst",
+ "crystfel.stream",
peak_search_params,
indexing_params);
diff --git a/src/gui_backend_slurm.c b/src/gui_backend_slurm.c
index 036cf4ef..38ead6b1 100644
--- a/src/gui_backend_slurm.c
+++ b/src/gui_backend_slurm.c
@@ -52,7 +52,8 @@ struct slurm_indexing_opts
struct slurm_job
{
double frac_complete;
- /* FIXME: List of SLURM job numbers to track */
+ int n_blocks;
+ uint32_t *job_ids;
};
@@ -73,7 +74,7 @@ static void cancel_task(void *job_priv)
}
-static char **create_env(uint32_t *psize, char *path_add)
+static char **create_env(int *psize, char *path_add)
{
char **env;
const char *base_path = "PATH=/bin:/usr/bin";
@@ -115,6 +116,117 @@ static char **create_env(uint32_t *psize, char *path_add)
}
+static uint32_t submit_batch_job(const char *geom_filename,
+ const char *file_list,
+ const char *stream_filename,
+ const char *email_address,
+ const char *partition,
+ char **env,
+ int n_env,
+ const char *job_name,
+ const char *workdir,
+ struct peak_params *peak_search_params,
+ struct index_params *indexing_params)
+
+{
+ job_desc_msg_t job_desc_msg;
+ submit_response_msg_t *resp;
+ char **cmdline;
+ char *cmdline_all;
+ char *script;
+ int job_id;
+ int r;
+
+ cmdline = indexamajig_command_line(geom_filename,
+ "`nproc`",
+ file_list,
+ stream_filename,
+ peak_search_params,
+ indexing_params);
+
+ cmdline_all = g_strjoinv(" ", cmdline);
+
+ script = malloc(strlen(cmdline_all)+16);
+ if ( script == NULL ) return 0;
+
+ strcpy(script, "#!/bin/sh\n");
+ strcat(script, cmdline_all);
+ g_free(cmdline_all);
+
+ slurm_init_job_desc_msg(&job_desc_msg);
+ job_desc_msg.user_id = getuid();
+ job_desc_msg.group_id = getgid();
+ job_desc_msg.mail_user = strdup(email_address);
+ job_desc_msg.mail_type = MAIL_JOB_FAIL;
+ job_desc_msg.comment = "Submitted via CrystFEL GUI";
+ job_desc_msg.shared = 0;
+ job_desc_msg.time_limit = 60;
+ job_desc_msg.partition = strdup(partition);
+ job_desc_msg.min_nodes = 1;
+ job_desc_msg.max_nodes = 1;
+ job_desc_msg.name = strdup(job_name);
+ job_desc_msg.std_err = strdup("job.err");
+ job_desc_msg.std_out = strdup("job.out");
+ job_desc_msg.work_dir = strdup(workdir);
+ job_desc_msg.script = script;
+ job_desc_msg.environment = env;
+ job_desc_msg.env_size = n_env;
+
+ r = slurm_submit_batch_job(&job_desc_msg, &resp);
+ if ( r ) {
+ ERROR("Couldn't submit job: %i\n", errno);
+ return 0;
+ }
+
+ free(job_desc_msg.mail_user);
+ free(job_desc_msg.partition);
+ free(job_desc_msg.name);
+ free(job_desc_msg.work_dir);
+ free(job_desc_msg.std_err);
+ free(job_desc_msg.std_out);
+
+ job_id = resp->job_id;
+ slurm_free_submit_response_response_msg(resp);
+
+ return job_id;
+}
+
+
+static void write_partial_file_list(GFile *workdir,
+ const char *list_filename,
+ int j,
+ int block_size,
+ char **filenames,
+ char **events,
+ int n_frames)
+{
+ GFile *file;
+ char *file_path;
+ FILE *fh;
+ int i;
+
+ file = g_file_get_child(workdir, list_filename);
+ file_path = g_file_get_path(file);
+
+ fh = fopen(file_path, "w");
+ for ( i=j*block_size;
+ (i<(j+1)*block_size) && (i<n_frames);
+ i++ )
+ {
+ fprintf(fh, "%s", filenames[i]);
+ if ( events[i] != NULL ) {
+ fprintf(fh, " %s\n", events[i]);
+ } else {
+ fprintf(fh, "\n");
+ }
+ }
+
+ fclose(fh);
+ g_free(file_path);
+ g_object_unref(file);
+}
+
+
static void *run_indexing(const char *job_title,
const char *job_notes,
char **filenames,
@@ -127,19 +239,17 @@ static void *run_indexing(const char *job_title,
{
struct slurm_indexing_opts *opts = opts_priv;
struct slurm_job *job;
- job_desc_msg_t job_desc_msg;
- submit_response_msg_t *resp;
- int r;
char *workdir;
struct stat s;
- char **cmdline;
- char *cmdline_all;
- char *script;
- GFile *workdir_file;
GFile *cwd_file;
GFile *notes_file;
+ GFile *workdir_file;
char *notes_path;
FILE *fh;
+ char **env;
+ int n_env;
+ int i;
+ int fail = 0;
workdir = strdup(job_title);
if ( workdir == NULL ) return NULL;
@@ -168,55 +278,68 @@ static void *run_indexing(const char *job_title,
g_free(notes_path);
g_object_unref(notes_file);
- cmdline = indexamajig_command_line(geom_filename,
- "`nproc`",
- peak_search_params,
- indexing_params);
-
- cmdline_all = g_strjoinv(" ", cmdline);
+ workdir = g_file_get_path(workdir_file);
- script = malloc(strlen(cmdline_all)+16);
- if ( script == NULL ) return NULL;
-
- strcpy(script, "#!/bin/sh\n");
- strcat(script, cmdline_all);
- g_free(cmdline_all);
+ env = create_env(&n_env, opts->path_add);
job = malloc(sizeof(struct slurm_job));
- if ( job == NULL ) return NULL;
+ if ( job == NULL ) return 0;
+
+ job->n_blocks = n_frames / opts->block_size;
+ if ( n_frames % opts->block_size ) job->n_blocks++;
+ STATUS("Splitting job into %i blocks of max %i frames\n",
+ job->n_blocks, opts->block_size);
+
+ job->job_ids = malloc(job->n_blocks * sizeof(uint32_t));
+ if ( job->job_ids == NULL ) return NULL;
+
+ for ( i=0; i<job->n_blocks; i++ ) {
+
+ char job_name[128];
+ char file_list[128];
+ char stream_filename[128];
+ int job_id;
+
+ snprintf(job_name, 127, "%s-%i", job_title, i);
+ snprintf(file_list, 127, "files-%i.lst", i);
+ snprintf(stream_filename, 127,
+ "crystfel-%i.stream", i);
+
+ write_partial_file_list(workdir_file, file_list,
+ i, opts->block_size,
+ filenames, events, n_frames);
+
+ job_id = submit_batch_job(geom_filename,
+ file_list,
+ stream_filename,
+ opts->email_address,
+ opts->partition,
+ env,
+ n_env,
+ job_name,
+ workdir,
+ peak_search_params,
+ indexing_params);
+
+ if ( job_id == 0 ) {
+ fail = 1;
+ break;
+ }
- slurm_init_job_desc_msg(&job_desc_msg);
- job_desc_msg.user_id = getuid();
- job_desc_msg.group_id = getgid();
- job_desc_msg.mail_user = strdup(opts->email_address);
- job_desc_msg.mail_type = MAIL_JOB_FAIL;
- job_desc_msg.comment = strdup("Submitted via CrystFEL GUI");
- job_desc_msg.shared = 0;
- job_desc_msg.time_limit = 60;
- job_desc_msg.partition = strdup(opts->partition);
- job_desc_msg.min_nodes = 1;
- job_desc_msg.max_nodes = 1;
- job_desc_msg.name = strdup(job_title);
- job_desc_msg.std_err = strdup("job.err");
- job_desc_msg.std_out = strdup("job.out");
- job_desc_msg.work_dir = g_file_get_path(workdir_file);
- job_desc_msg.script = script;
- job_desc_msg.environment = create_env(&job_desc_msg.env_size,
- opts->path_add);
+ job->job_ids[i] = job_id;
+ STATUS("Submitted SLURM job ID %i\n", job_id);
+ }
+ for ( i=0; i<n_env; i++ ) free(env[i]);
+ free(env);
+ free(workdir);
g_object_unref(workdir_file);
- r = slurm_submit_batch_job(&job_desc_msg, &resp);
-
- if ( r ) {
- ERROR("Couldn't submit job: %i\n", errno);
+ if ( fail ) {
+ free(job->job_ids);
free(job);
return NULL;
}
-
- STATUS("Submitted SLURM job ID %i\n", resp->job_id);
- slurm_free_submit_response_response_msg(resp);
-
return job;
}
diff --git a/src/gui_index.c b/src/gui_index.c
index a0027f82..9874fecf 100644
--- a/src/gui_index.c
+++ b/src/gui_index.c
@@ -619,6 +619,8 @@ static char *get_indexamajig_exe()
char **indexamajig_command_line(const char *geom_filename,
const char *n_thread_str,
+ const char *files_list,
+ const char *stream_filename,
struct peak_params *peak_search_params,
struct index_params *indexing_params)
{
@@ -641,11 +643,11 @@ char **indexamajig_command_line(const char *geom_filename,
/* The basics */
add_arg(args, n_args++, indexamajig_path);
add_arg(args, n_args++, "-i");
- add_arg(args, n_args++, "files.lst");
+ add_arg(args, n_args++, files_list);
add_arg(args, n_args++, "-g");
add_arg(args, n_args++, geom_filename);
add_arg(args, n_args++, "-o");
- add_arg(args, n_args++, "crystfel.stream");
+ add_arg(args, n_args++, stream_filename);
add_arg(args, n_args++, "-j");
add_arg(args, n_args++, n_thread_str);
diff --git a/src/gui_index.h b/src/gui_index.h
index f0454271..0812c3a9 100644
--- a/src/gui_index.h
+++ b/src/gui_index.h
@@ -43,6 +43,8 @@ extern void cell_explorer_sig(struct crystfelproject *proj);
extern char **indexamajig_command_line(const char *geom_filename,
const char *n_thread_str,
+ const char *files_list,
+ const char *stream_filename,
struct peak_params *peak_search_params,
struct index_params *indexing_params);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 18:27:46 +0000