SLURM: Submit merging and ambigator jobs via script

1 files changed, 2 insertions, 181 deletions

diff --git a/src/gui_merge.c b/src/gui_merge.c
index 11d48117..d561c2da 100644
--- a/src/gui_merge.c
+++ b/src/gui_merge.c
@@ -343,187 +343,6 @@ gint merge_sig(GtkWidget *widget, struct crystfelproject *proj)
 }
 
 
-static GSList *append_arg_str(GSList *args,
-                              const char *label,
-                              const char *val)
-{
-	size_t len;
-	char *str;
-
-	len = strlen(label)+strlen(val)+4;
-	str = malloc(len);
-	if ( str == NULL ) return args;
-	snprintf(str, 63, "--%s=%s", label, val);
-
-	return g_slist_append(args, str);
-}
-
-
-static GSList *append_arg_int(GSList *args,
-                              const char *label,
-                              int val)
-{
-	char *str = malloc(64);
-	if ( str == NULL ) return args;
-	snprintf(str, 63, "--%s=%i", label, val);
-	return g_slist_append(args, str);
-}
-
-
-static GSList *append_arg_float(GSList *args,
-                                const char *label,
-                                float val)
-{
-	char *str = malloc(64);
-	if ( str == NULL ) return args;
-	snprintf(str, 63, "--%s=%f", label, val);
-	return g_slist_append(args, str);
-}
-
-
-static GSList *process_hkl_command_line(struct gui_indexing_result *input,
-                                        struct merging_params *params)
-{
-	GSList *args = NULL;
-	char *exe_path;
-	int i;
-
-	exe_path = get_crystfel_exe("process_hkl");
-	if ( exe_path == NULL ) return NULL;
-	args = g_slist_append(args, exe_path);
-
-	for ( i=0; i<input->n_streams; i++ ) {
-		args = g_slist_append(args, input->streams[i]);
-	}
-
-	args = g_slist_append(args, "-o");
-	args = g_slist_append(args, "crystfel.hkl");
-
-	args = append_arg_str(args, "symmetry", params->symmetry);
-
-	if ( params->scale ) {
-		args = g_slist_append(args, strdup("--scale"));
-	}
-
-	args = append_arg_str(args, "polarisation",
-	                      params->polarisation);
-
-	args = append_arg_int(args, "min-measurements",
-	                      params->min_measurements);
-
-	args = append_arg_float(args, "max-adu", params->max_adu);
-
-	args = append_arg_float(args, "min-res", params->min_res);
-
-	args = append_arg_float(args, "push-res", params->push_res);
-
-	return args;
-}
-
-
-static GSList *partialator_command_line(const char *n_thread_str,
-                                        struct gui_indexing_result *input,
-                                        struct merging_params *params)
-{
-	GSList *args = NULL;
-	char *exe_path;
-	int i;
-
-	exe_path = get_crystfel_exe("partialator");
-	if ( exe_path == NULL ) return NULL;
-	args = g_slist_append(args, exe_path);
-
-	for ( i=0; i<input->n_streams; i++ ) {
-		args = g_slist_append(args, input->streams[i]);
-	}
-
-	args = g_slist_append(args, "-o");
-	args = g_slist_append(args, "crystfel.hkl");
-
-	args = append_arg_str(args, "symmetry", params->symmetry);
-
-	args = g_slist_append(args, "-j");
-	args = g_slist_append(args, strdup(n_thread_str));
-
-	if ( params->twin_sym != NULL ) {
-		args = g_slist_append(args, "-w");
-		args = g_slist_append(args, strdup(params->twin_sym));
-	}
-
-	if ( params->custom_split != NULL ) {
-		args = append_arg_str(args, "custom-split",
-		                      params->custom_split);
-	}
-
-	if ( !params->scale ) {
-		args = g_slist_append(args, "--no-scale");
-	}
-
-	if ( !params->bscale ) {
-		args = g_slist_append(args, "--no-bscale");
-	}
-
-	if ( !params->postref ) {
-		args = g_slist_append(args, "--no-pr");
-	}
-
-	if ( !params->deltacchalf ) {
-		args = g_slist_append(args, "--no-deltacchalf");
-	}
-
-	args = append_arg_int(args, "iterations", params->niter);
-
-	args = append_arg_str(args, "polarisation",
-	                      params->polarisation);
-
-	args = append_arg_int(args, "min-measurements",
-	                      params->min_measurements);
-
-	args = append_arg_float(args, "max-adu", params->max_adu);
-
-	args = append_arg_float(args, "min-res", params->min_res);
-
-	args = append_arg_float(args, "push-res", params->push_res);
-
-	return args;
-}
-
-
-char **merging_command_line(const char *n_thread_str,
-                            struct gui_indexing_result *input,
-                            struct merging_params *params)
-{
-	GSList *args;
-	char **arg_strings;
-	GSList *args2;
-	int i, n;
-
-	if ( strcmp(params->model, "process_hkl") == 0 ) {
-		args = process_hkl_command_line(input, params);
-	} else {
-		args = partialator_command_line(n_thread_str,
-		                                input,
-		                                params);
-	}
-
-	if ( args == NULL ) return NULL;
-
-	n = g_slist_length(args);
-	arg_strings = malloc((n+1)*sizeof(char *));
-	if ( arg_strings == NULL ) return NULL;
-
-	args2 = args;
-	for ( i=0; i<n; i++ ) {
-		arg_strings[i] = args2->data;
-		args2 = args2->next;
-	}
-	arg_strings[n] = NULL;
-	g_slist_free(args);
-
-	return arg_strings;
-}
-
-
 static int write_partialator_script(const char *filename,
                                     struct gui_indexing_result *input,
                                     const char *n_thread_str,
@@ -537,6 +356,8 @@ static int write_partialator_script(const char *filename,
 	fh = fopen(filename, "w");
 	if ( fh == NULL ) return 1;
 
+	fprintf(fh, "#!/bin/sh\n");
+
 	exe_path = get_crystfel_exe("partialator");
 	if ( exe_path == NULL ) return 1;
 	fprintf(fh, "%s \\\n", exe_path);