diff --git a/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c b/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c
index 61b7a3bc50c615204037b7f1b92255c973f9b039..4c2d3fea34dee8334c77ff0a2b70518e7d5f95ab 100644
--- a/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c
+++ b/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c
@@ -6,7 +6,7 @@
* Copyright (C) 2013 Bull S. A. S.
* Bull, Rue Jean Jaures, B.P.68, 78340, Les Clayes-sous-Bois.
*
- * Copyright (C) 2013 SchedMD LLC
+ * Copyright (C) 2013-2016 SchedMD LLC
*
* Initially written by Rod Schultz <rod.schultz@bull.com> @ Bull
* and Danny Auble <da@schedmd.com> @ SchedMD.
@@ -142,42 +142,40 @@ static bool _has_batch_step(char *, char *);
static void _help_msg(void)
{
- printf("\
-Usage sh5util [<OPTION>] -j <job[.stepid]>\n"
-"\n"
-"Valid <OPTION> values are:\n"
-" -L, --list Print the items of a series contained in a job file.\n"
-" -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
-" -s, --series Name of series:\n"
-" Energy | Lustre | Network | Tasks\n"
-" -E, --extract Extract data series from job file.\n"
-" -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
-" -N, --node Node name to extract (default is all)\n"
-" -l, --level Level to which series is attached\n"
-" [Node:Totals|Node:TimeSeries] (default Node:Totals)\n"
-" -s, --series Name of series:\n"
-" Energy | Lustre | Network | Tasks | Task_#\n"
-" 'Tasks' is all tasks, Task_# is task_id (default is all)\n"
-" -I, --item-extract Extract data item from one series from \n"
-" all samples on all nodes from thejob file.\n"
-" -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
-" -s, --series Name of series:\n"
-" Energy | Lustre | Network | Task\n"
-" -d, --data Name of data item in series (see man page) \n"
-" -j, --jobs Format is <job(.step)>. Merge this job/step.\n"
-" or comma-separated list of job steps. This option is\n"
-" required. Not specifying a step will result in all\n"
-" steps found to be processed.\n"
-" -h, --help Print this description of use.\n"
-" -o, --output Path to a file into which to write.\n"
-" Default for merge is ./job_$jobid.h5\n"
-" Default for extract is ./extract_$jobid.csv\n"
-" -p, --profiledir Profile directory location where node-step files exist\n"
-" default is what is set in acct_gather.conf\n"
-" -S, --savefiles Don't remove node-step files after merging them \n"
-" --user User who profiled job. (Handy for root user, defaults to \n"
-" user running this command.)\n"
-" --usage Display brief usage message\n");
+ printf("Usage sh5util [<OPTION>] -j <job[.stepid]>\n\n"
+ "Valid <OPTION> values are:\n"
+ " -L, --list Print the items of a series contained in a job file.\n"
+ " -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
+ " -s, --series Name of series:\n"
+ " Energy | Lustre | Network | Tasks\n"
+ " -E, --extract Extract data series from job file.\n"
+ " -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
+ " -N, --node Node name to extract (default is all)\n"
+ " -l, --level Level to which series is attached\n"
+ " [Node:Totals|Node:TimeSeries] (default Node:Totals)\n"
+ " -s, --series Name of series:\n"
+ " Energy | Lustre | Network | Tasks | Task_#\n"
+ " 'Tasks' is all tasks, Task_# is task_id (default is all)\n"
+ " -I, --item-extract Extract data item from one series from \n"
+ " all samples on all nodes from thejob file.\n"
+ " -i, --input merged file to extract from (default ./job_$jobid.h5)\n"
+ " -s, --series Name of series:\n"
+ " Energy | Lustre | Network | Task\n"
+ " -d, --data Name of data item in series (see man page) \n"
+ " -j, --jobs Format is <job(.step)>. Merge this job/step.\n"
+ " or comma-separated list of job steps. This option is\n"
+ " required. Not specifying a step will result in all\n"
+ " steps found to be processed.\n"
+ " -h, --help Print this description of use.\n"
+ " -o, --output Path to a file into which to write.\n"
+ " Default for merge is ./job_$jobid.h5\n"
+ " Default for extract is ./extract_$jobid.csv\n"
+ " -p, --profiledir Profile directory location where node-step files exist\n"
+ " default is what is set in acct_gather.conf\n"
+ " -S, --savefiles Don't remove node-step files after merging them \n"
+ " --user User who profiled job. (Handy for root user, defaults to \n"
+ " user running this command.)\n"
+ " --usage Display brief usage message\n");
}
@@ -196,29 +194,29 @@ main(int argc, char **argv)
goto ouch;
switch (params.mode) {
- case SH5UTIL_MODE_MERGE:
- info("Merging node-step files into %s",
- params.output);
- cc = _merge_step_files();
- break;
- case SH5UTIL_MODE_EXTRACT:
- info("Extracting job data from %s into %s",
- params.input, params.output);
- cc = _extract_series();
- break;
- case SH5UTIL_MODE_ITEM_EXTRACT:
- info("Extracting '%s' from '%s' data from %s into %s",
- params.data_item, params.series,
- params.input, params.output);
- cc = _extract_item();
- break;
- case SH5UTIL_MODE_ITEM_LIST:
- info("Listing items from %s", params.input);
- cc = _list_items();
- break;
- default:
- error("Unknown type %d", params.mode);
- break;
+ case SH5UTIL_MODE_MERGE:
+ info("Merging node-step files into %s",
+ params.output);
+ cc = _merge_step_files();
+ break;
+ case SH5UTIL_MODE_EXTRACT:
+ info("Extracting job data from %s into %s",
+ params.input, params.output);
+ cc = _extract_series();
+ break;
+ case SH5UTIL_MODE_ITEM_EXTRACT:
+ info("Extracting '%s' from '%s' data from %s into %s",
+ params.data_item, params.series,
+ params.input, params.output);
+ cc = _extract_item();
+ break;
+ case SH5UTIL_MODE_ITEM_LIST:
+ info("Listing items from %s", params.input);
+ cc = _list_items();
+ break;
+ default:
+ error("Unknown type %d", params.mode);
+ break;
}
if (cc == SLURM_PROTOCOL_VERSION_ERROR)
@@ -335,82 +333,82 @@ static int _set_options(const int argc, char **argv)
while ((cc = getopt_long(argc, argv, "d:Ehi:Ij:l:LN:o:p:s:Su:UvV",
long_options, &option_index)) != EOF) {
switch (cc) {
- case 'd':
- params.data_item = xstrdup(optarg);
- /* params.data_item =
- xstrtolower(params.data_item); */
- break;
- case 'E':
- params.mode = SH5UTIL_MODE_EXTRACT;
- break;
- case 'I':
- params.mode = SH5UTIL_MODE_ITEM_EXTRACT;
- break;
- case 'L':
- params.mode = SH5UTIL_MODE_ITEM_LIST;
- break;
- case 'h':
- _help_msg();
- return -1;
- break;
- case 'i':
- params.input = xstrdup(optarg);
- break;
- case 'j':
- params.job_id = strtol(optarg, &next_str, 10);
- if (next_str[0] == '.')
- params.step_id =
- strtol(next_str + 1, NULL, 10);
- break;
- case 'l':
- params.level = xstrdup(optarg);
- break;
- case 'N':
- params.node = xstrdup(optarg);
- break;
- case 'o':
- params.output = xstrdup(optarg);
- break;
- case 'p':
- params.dir = xstrdup(optarg);
- break;
- case 's':
- if (xstrcmp(optarg, GRP_ENERGY)
- && xstrcmp(optarg, GRP_LUSTRE)
- && xstrcmp(optarg, GRP_NETWORK)
- && xstrncmp(optarg,GRP_TASK,
- strlen(GRP_TASK))) {
- error("Bad value for --series=\"%s\"",
- optarg);
- return -1;
- }
- params.series = xstrdup(optarg);
- break;
- case 'S':
- params.keepfiles = 1;
- break;
- case 'u':
- if (uid_from_string(optarg, &u) < 0) {
- error("No such user --uid=\"%s\"",
- optarg);
- return -1;
- }
- params.user = uid_to_string(u);
- break;
- case 'U':
- _help_msg();
- return -1;
- break;
- case 'v':
- params.verbose++;
- break;
- case 'V':
- print_slurm_version();
+ case 'd':
+ params.data_item = xstrdup(optarg);
+ /* params.data_item =
+ xstrtolower(params.data_item); */
+ break;
+ case 'E':
+ params.mode = SH5UTIL_MODE_EXTRACT;
+ break;
+ case 'I':
+ params.mode = SH5UTIL_MODE_ITEM_EXTRACT;
+ break;
+ case 'L':
+ params.mode = SH5UTIL_MODE_ITEM_LIST;
+ break;
+ case 'h':
+ _help_msg();
+ return -1;
+ break;
+ case 'i':
+ params.input = xstrdup(optarg);
+ break;
+ case 'j':
+ params.job_id = strtol(optarg, &next_str, 10);
+ if (next_str[0] == '.')
+ params.step_id =
+ strtol(next_str + 1, NULL, 10);
+ break;
+ case 'l':
+ params.level = xstrdup(optarg);
+ break;
+ case 'N':
+ params.node = xstrdup(optarg);
+ break;
+ case 'o':
+ params.output = xstrdup(optarg);
+ break;
+ case 'p':
+ params.dir = xstrdup(optarg);
+ break;
+ case 's':
+ if (xstrcmp(optarg, GRP_ENERGY)
+ && xstrcmp(optarg, GRP_LUSTRE)
+ && xstrcmp(optarg, GRP_NETWORK)
+ && xstrncmp(optarg,GRP_TASK,
+ strlen(GRP_TASK))) {
+ error("Bad value for --series=\"%s\"",
+ optarg);
return -1;
- break;
- case ':':
- case '?': /* getopt() has explained it */
+ }
+ params.series = xstrdup(optarg);
+ break;
+ case 'S':
+ params.keepfiles = 1;
+ break;
+ case 'u':
+ if (uid_from_string(optarg, &u) < 0) {
+ error("No such user --uid=\"%s\"",
+ optarg);
return -1;
+ }
+ params.user = uid_to_string(u);
+ break;
+ case 'U':
+ _help_msg();
+ return -1;
+ break;
+ case 'v':
+ params.verbose++;
+ break;
+ case 'V':
+ print_slurm_version();
+ return -1;
+ break;
+ case ':':
+ case '?': /* getopt() has explained it */
+ return -1;
}
}
@@ -464,7 +462,8 @@ _check_params(void)
fatal("Must specify series option --series");
if (!params.input)
- params.input = xstrdup_printf("./job_%d.h5", params.job_id);
+ params.input = xstrdup_printf("./job_%d.h5",
+ params.job_id);
if (!params.output)
params.output = xstrdup_printf("./%s_%s_%d.csv",
@@ -560,7 +559,8 @@ static int _merge_step_files(void)
while (max_step == -1 || stepx <= max_step) {
if (!(dir = opendir(step_dir))) {
- error("Cannot open %s job profile directory: %m", step_dir);
+ error("Cannot open %s job profile directory: %m",
+ step_dir);
return -1;
}
@@ -609,36 +609,43 @@ static int _merge_step_files(void)
H5P_DEFAULT,
H5P_DEFAULT);
if (fid_job < 0) {
- error("Failed create HDF5 file %s", params.output);
+ error("Failed create HDF5 file %s",
+ params.output);
return -1;
}
found_files = true;
jgid_steps = make_group(fid_job, GRP_STEPS);
if (jgid_steps < 0) {
- error("Failed to create group %s", GRP_STEPS);
+ error("Failed to create group %s",
+ GRP_STEPS);
continue;
}
if (has_batch) {
- sprintf(jgrp_step_name, "/%s/batch", GRP_STEPS);
- jgid_step = make_group(fid_job, jgrp_step_name);
+ sprintf(jgrp_step_name, "/%s/batch",
+ GRP_STEPS);
+ jgid_step = make_group(
+ fid_job, jgrp_step_name);
if (jgid_step < 0) {
- error("Failed to create %s", jgrp_step_name);
+ error("Failed to create %s",
+ jgrp_step_name);
continue;
}
sprintf(jgrp_nodes_name,"%s/%s",
jgrp_step_name,
GRP_NODES);
- jgid_nodes = make_group(jgid_step,
- jgrp_nodes_name);
+ jgid_nodes = make_group(
+ jgid_step, jgrp_nodes_name);
if (jgid_nodes < 0) {
- error("Failed to create %s", jgrp_nodes_name);
+ error("Failed to create %s",
+ jgrp_nodes_name);
continue;
}
- sprintf(step_path, "%s/%s", step_dir, batch_step);
+ sprintf(step_path, "%s/%s",
+ step_dir, batch_step);
rc = _merge_node_step_data(step_path,
nodex,
jgid_nodes,
@@ -658,7 +665,8 @@ static int _merge_step_files(void)
jgid_step = make_group(fid_job, jgrp_step_name);
if (jgid_step < 0) {
- error("Failed to create %s", jgrp_step_name);
+ error("Failed to create %s",
+ jgrp_step_name);
continue;
}
@@ -668,19 +676,20 @@ static int _merge_step_files(void)
jgid_nodes = make_group(jgid_step,
jgrp_nodes_name);
if (jgid_nodes < 0) {
- error("Failed to create %s", jgrp_nodes_name);
+ error("Failed to create %s",
+ jgrp_nodes_name);
continue;
}
/*
- sprintf(jgrp_tasks_name,"%s/%s",
- jgrp_step_name,
- GRP_TASKS);
- jgid_tasks = make_group(jgid_step,
- jgrp_tasks_name);
- if (jgid_tasks < 0) {
- error("Failed to create %s", jgrp_tasks_name);
- continue;
- }
+ sprintf(jgrp_tasks_name,"%s/%s",
+ jgrp_step_name,
+ GRP_TASKS);
+ jgid_tasks = make_group(jgid_step,
+ jgrp_tasks_name);
+ if (jgid_tasks < 0) {
+ error("Failed to create %s", jgrp_tasks_name);
+ continue;
+ }
*/
}
@@ -703,7 +712,7 @@ static int _merge_step_files(void)
* bail out.
*/
if (stepx == 0
- && !found_files)
+ && !found_files)
break;
stepx++;
@@ -804,7 +813,8 @@ static herr_t _collect_tables_node(hid_t g_id, const char *name,
err = H5Literate(object_id, H5_INDEX_NAME, H5_ITER_INC, NULL,
_collect_tables_group, op_data);
if (err < 0) {
- debug("2 Failed to iterate through group %s", object_path);
+ debug("2 Failed to iterate through group %s",
+ object_path);
return SLURM_PROTOCOL_VERSION_ERROR;
}
} else {
@@ -970,7 +980,7 @@ static void _extract_totals(size_t nb_fields, size_t *offsets, hid_t *types,
* the content of the table and then handles both timeseries and totals levels.
*/
static int _extract_series_table(hid_t fid_job, table_t *table, List fields,
- FILE *output, bool level_total)
+ FILE *output, bool level_total)
{
char path[MAX_PROFILE_PATH];
@@ -1206,8 +1216,10 @@ error:
* @param step_name Name of the current step
*/
static void _item_analysis_uint(hsize_t nb_tables, hid_t *tables,
- hsize_t *nb_records, size_t buf_size, size_t *offsets,
- const char *names[], const char *nodes[], const char *step_name)
+ hsize_t *nb_records, size_t buf_size,
+ size_t *offsets,
+ const char *names[], const char *nodes[],
+ const char *step_name)
{
size_t i;
uint64_t min_val;
@@ -1305,8 +1317,10 @@ static void _item_analysis_uint(hsize_t nb_tables, hid_t *tables,
* See _item_analysis_uint for parameters description.
*/
static void _item_analysis_double(hsize_t nb_tables, hid_t *tables,
- hsize_t *nb_records, size_t buf_size, size_t *offsets,
- const char *names[], const char *nodes[], const char *step_name)
+ hsize_t *nb_records, size_t buf_size,
+ size_t *offsets,
+ const char *names[], const char *nodes[],
+ const char *step_name)
{
size_t i;
double min_val;
@@ -1527,7 +1541,8 @@ static herr_t _extract_item_step(hid_t g_id, const char *step_name,
if (group_mode)
fprintf(output_file, ",%s", t->node);
else
- fprintf(output_file, ",%s %s", t->name, t->node);
+ fprintf(output_file, ",%s %s",
+ t->name, t->node);
}
fputc('\n', output_file);
}
@@ -1538,7 +1553,8 @@ static herr_t _extract_item_step(hid_t g_id, const char *step_name,
_item_analysis_uint(nb_tables, tables_id, nb_records, buf_size,
offsets, names, nodes, step_name);
} else if (H5Tequal(item_type, H5T_NATIVE_DOUBLE)) {
- _item_analysis_double(nb_tables, tables_id, nb_records, buf_size,
+ _item_analysis_double(nb_tables, tables_id,
+ nb_records, buf_size,
offsets, names, nodes, step_name);
} else {
error("Unknown type");
@@ -1740,8 +1756,8 @@ _has_batch_step(char *batch_step, char *batch_node)
sprintf(step_dir, "%s/%s", params.dir, params.user);
if (!(dir = opendir(step_dir))) {
- error("\
-%s: Cannot open %s job profile directory: %m", __func__, step_dir);
+ error("%s: Cannot open %s job profile directory: %m",
+ __func__, step_dir);
return -1;
}