Hello,
I think I am ready to return to mpirun affinity handling discussion. I have
more general solution now. It is beta-tested (just one cluster with SLURM
using cgroups plugin). But it shows my main idea and if it is worth to be
included into mainstream I am ready to polish or improove it.
The code respects SLURM cpu allocation through SLURM_JOB_CPUS_PER_NODE and
handles such cases correctly:
SLURM_JOB_CPUS_PER_NODE='12(x3),7'
SLURM_JOB_NODELIST=node[0-3]
It splits the node lists into groups having equal number of cpus. In the
example above we will have 2 groups:
1) node0, node1, node2 with 12 cpus
2) node3 with 7 cpus.
then it uses separate srun's for each group.
The weakness of this patch is that we need to deal with several srun's and
I am not sure that cleanup will perform correctly. I plan to test this case
additionaly.
2014-02-12 17:42 GMT+07:00 Artem Polyakov <artpo...@gmail.com>:
> Hello
>
> I found that SLURM installations that use cgroup plugin and
> have TaskAffinity=yes in cgroup.conf have problems with OpenMPI: all
> processes on non-launch node are assigned on one core. This leads to quite
> poor performance.
> The problem can be seen only if using mpirun to start parallel application
> in batch script. For example: *mpirun ./mympi*
> If using srun with PMI affinity is setted properly: *srun ./mympi.*
>
> Close look shows that the reason lies in the way Open MPI use srun to
> launch ORTE daemons. Here is example of the command line:
> *srun* *--nodes=1* *--ntasks=1* --kill-on-bad-exit --nodelist=node02
> *orted* -mca ess slurm -mca orte_ess_jobid 3799121920 -mca orte_ess_vpid
>
> Saying *--nodes=1* *--ntasks=1* to SLURM means that you want to start one
> task and (with TaskAffinity=yes) it will be binded to one core. Next orted
> use this affinity as base for all spawned branch processes. If I understand
> correctly the problem behind using srun is that if you say *srun*
> *--nodes=1* *--ntasks=4* - then SLURM will spawn 4 independent orted
> processes binded to different cores which is not what we really need.
>
> I found that disabling of cpu binding as a fast hack works good for cgroup
> plugin. Since job runs inside a group which has core access restrictions,
> spawned branch processes are executed under nodes scheduler control on all
> allocated cores. The command line looks like this:
> srun *--cpu_bind=none* --nodes=1 --ntasks=1 --kill-on-bad-exit
> --nodelist=node02 orted -mca ess slurm -mca orte_ess_jobid 3799121920 -mca
> orte_ess_vpid
>
> This solution will probably won't work with SLURM task/affinity plugin.
> Also it may be a bad idea when strong affinity desirable.
>
> My patch to stable Open MPI version (1.6.5) is attached to this e-mail. I
> will try to make more reliable solution but I need more time and beforehand
> would like to know opinion of Open MPI developers.
>
> --
> С Уважением, Поляков Артем Юрьевич
> Best regards, Artem Y. Polyakov
>
--
С Уважением, Поляков Артем Юрьевич
Best regards, Artem Y. Polyakov
diff -Naur openmpi-1.6.5/orte/mca/plm/slurm/plm_slurm_module.c openmpi-1.6.5_new/orte/mca/plm/slurm/plm_slurm_module.c
--- openmpi-1.6.5/orte/mca/plm/slurm/plm_slurm_module.c 2012-04-03 10:30:29.000000000 -0400
+++ openmpi-1.6.5_new/orte/mca/plm/slurm/plm_slurm_module.c 2014-03-07 08:54:12.878010513 -0500
@@ -11,7 +11,7 @@
* All rights reserved.
* Copyright (c) 2006-2007 Cisco Systems, Inc. All rights reserved.
* Copyright (c) 2007 Los Alamos National Security, LLC. All rights
- * reserved.
+ * reserved.
* $COPYRIGHT$
*
* Additional copyrights may follow
@@ -107,12 +107,26 @@
/*
* Local variables
*/
-static pid_t primary_srun_pid = 0;
-static bool primary_pid_set = false;
+static pid_t *primary_srun_pids = NULL;
+static int primary_srun_pids_cnt = 0;
+static bool primary_pids_set = false;
static orte_jobid_t active_job = ORTE_JOBID_INVALID;
static bool launching_daemons;
static bool local_launch_available = false;
+struct pml_slurm_node_group_t {
+ char **nodelist;
+ unsigned int nodelist_size;
+ unsigned int cpus_per_node;
+};
+
+static int plm_slurm_group_nodes(orte_job_map_t *map,
+ struct pml_slurm_node_group_t **grpout,
+ int *grpcnt);
+static void plm_slurm_groups_free(struct pml_slurm_node_group_t **groups,
+ int grpcnt);
+
+
/**
* Init the module
*/
@@ -152,7 +166,7 @@
char *tmp;
char** env = NULL;
char* var;
- char *nodelist_flat;
+ char *nodelist_flat, *nodelist_full;
char **nodelist_argv;
char *name_string;
char **custom_strings;
@@ -163,11 +177,14 @@
orte_jobid_t failed_job;
bool failed_launch=true;
bool using_regexp=false;
+ struct pml_slurm_node_group_t *groups = NULL;
+ int grpcnt, grpnum;
+ int vpid_offset = 0;
if (NULL == jdata) {
- /* just launching debugger daemons */
- active_job = ORTE_JOBID_INVALID;
- goto launch_apps;
+ /* just launching debugger daemons */
+ active_job = ORTE_JOBID_INVALID;
+ goto launch_apps;
}
if (jdata->controls & ORTE_JOB_CONTROL_DEBUGGER_DAEMON) {
@@ -205,7 +222,7 @@
opal_output(0, "plm_slurm: could not obtain job start time");
launchstart.tv_sec = 0;
launchstart.tv_usec = 0;
- }
+ }
}
/* indicate the state of the launch */
@@ -223,7 +240,7 @@
ORTE_JOBID_PRINT(jdata->jobid)));
/* set the active jobid */
- active_job = jdata->jobid;
+ active_job = jdata->jobid;
/* Get the map for this job */
if (NULL == (map = orte_rmaps.get_job_map(active_job))) {
@@ -233,7 +250,7 @@
}
apps = (orte_app_context_t**)jdata->apps->addr;
nodes = (orte_node_t**)map->nodes->addr;
-
+
if (0 == map->num_new_daemons) {
/* no new daemons required - just launch apps */
OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
@@ -242,44 +259,12 @@
goto launch_apps;
}
+
/* need integer value for command line parameter */
asprintf(&jobid_string, "%lu", (unsigned long) jdata->jobid);
-
- /*
- * start building argv array
- */
- argv = NULL;
- argc = 0;
-
- /*
- * SLURM srun OPTIONS
- */
-
- /* add the srun command */
- opal_argv_append(&argc, &argv, "srun");
-
- /* Append user defined arguments to srun */
- if ( NULL != mca_plm_slurm_component.custom_args ) {
- custom_strings = opal_argv_split(mca_plm_slurm_component.custom_args, ' ');
- num_args = opal_argv_count(custom_strings);
- for (i = 0; i < num_args; ++i) {
- opal_argv_append(&argc, &argv, custom_strings[i]);
- }
- opal_argv_free(custom_strings);
- }
-
- asprintf(&tmp, "--nodes=%lu", (unsigned long) map->num_new_daemons);
- opal_argv_append(&argc, &argv, tmp);
- free(tmp);
-
- asprintf(&tmp, "--ntasks=%lu", (unsigned long) map->num_new_daemons);
- opal_argv_append(&argc, &argv, tmp);
- free(tmp);
-
- /* alert us if any orteds die during startup */
- opal_argv_append(&argc, &argv, "--kill-on-bad-exit");
-
- /* create nodelist */
+
+
+ // prepare full node list
nodelist_argv = NULL;
for (n=0; n < map->num_nodes; n++ ) {
@@ -300,117 +285,192 @@
rc = ORTE_ERR_FAILED_TO_START;
goto cleanup;
}
- nodelist_flat = opal_argv_join(nodelist_argv, ',');
+ nodelist_full = opal_argv_join(nodelist_argv, ',');
opal_argv_free(nodelist_argv);
- asprintf(&tmp, "--nodelist=%s", nodelist_flat);
- opal_argv_append(&argc, &argv, tmp);
- free(tmp);
-
- OPAL_OUTPUT_VERBOSE((2, orte_plm_globals.output,
- "%s plm:slurm: launching on nodes %s",
- ORTE_NAME_PRINT(ORTE_PROC_MY_NAME), nodelist_flat));
-
+
+
/*
+ * start building argv array
+ */
+ if( rc = plm_slurm_group_nodes(map, &groups, &grpcnt) ){
+ goto cleanup;
+ }
+
+ argv = NULL;
+ argc = 0;
+ primary_srun_pids = malloc(sizeof(int)*grpcnt);
+ if( primary_srun_pids == NULL ){
+ ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
+ rc = ORTE_ERR_OUT_OF_RESOURCE;
+ goto cleanup;
+ }
+
+ grpnum = 0;
+ vpid_offset = 0;
+ while( grpnum < grpcnt ){
+ /*
+ * SLURM srun OPTIONS
+ */
+
+ /* add the srun command */
+ opal_argv_append(&argc, &argv, "srun");
+
+ /* Append user defined arguments to srun */
+ if ( NULL != mca_plm_slurm_component.custom_args ) {
+ custom_strings = opal_argv_split(mca_plm_slurm_component.custom_args, ' ');
+ num_args = opal_argv_count(custom_strings);
+ for (i = 0; i < num_args; ++i) {
+ opal_argv_append(&argc, &argv, custom_strings[i]);
+ }
+ opal_argv_free(custom_strings);
+ }
+
+ asprintf(&tmp, "--nodes=%lu", (unsigned long) groups[grpnum].nodelist_size);
+ opal_argv_append(&argc, &argv, tmp);
+ free(tmp);
+
+ asprintf(&tmp, "--ntasks=%lu", (unsigned long) groups[grpnum].nodelist_size);
+ opal_argv_append(&argc, &argv, tmp);
+ free(tmp);
+
+ if( groups[grpnum].cpus_per_node > 1 ){
+ asprintf(&tmp, "--cpus-per-task=%lu", (unsigned long) groups[grpnum].cpus_per_node);
+ opal_argv_append(&argc, &argv, tmp);
+ free(tmp);
+ }
+
+ /* alert us if any orteds die during startup */
+ opal_argv_append(&argc, &argv, "--kill-on-bad-exit");
+
+ /* create nodelist */
+ if (0 == groups[grpnum].nodelist_size ) {
+ orte_show_help("help-plm-slurm.txt", "no-hosts-in-list", true);
+ rc = ORTE_ERR_FAILED_TO_START;
+ goto cleanup;
+ }
+ nodelist_flat = opal_argv_join(groups[grpnum].nodelist, ',');
+ asprintf(&tmp, "--nodelist=%s", nodelist_flat);
+ opal_argv_append(&argc, &argv, tmp);
+ free(tmp);
+
+ OPAL_OUTPUT_VERBOSE((2, orte_plm_globals.output,
+ "%s plm:slurm: launching on nodes %s",
+ ORTE_NAME_PRINT(ORTE_PROC_MY_NAME), nodelist_flat));
+
+ /*
* ORTED OPTIONS
*/
- /* add the daemon command (as specified by user) */
- orte_plm_base_setup_orted_cmd(&argc, &argv);
-
- /* Add basic orted command line options, including debug flags */
- orte_plm_base_orted_append_basic_args(&argc, &argv,
- "slurm", &proc_vpid_index,
- false, nodelist_flat);
- free(nodelist_flat);
+ /* add the daemon command (as specified by user) */
+ orte_plm_base_setup_orted_cmd(&argc, &argv);
- /* tell the new daemons the base of the name list so they can compute
+ /* Add basic orted command line options, including debug flags */
+ orte_plm_base_orted_append_basic_args(&argc, &argv,
+ "slurm", &proc_vpid_index,
+ false, nodelist_full);
+ free(nodelist_flat);
+
+ /* tell the new daemons the base of the name list so they can compute
* their own name on the other end
*/
- rc = orte_util_convert_vpid_to_string(&name_string, map->daemon_vpid_start);
- if (ORTE_SUCCESS != rc) {
- opal_output(0, "plm_slurm: unable to get daemon vpid as string");
- goto cleanup;
- }
+ rc = orte_util_convert_vpid_to_string(&name_string, map->daemon_vpid_start + vpid_offset);
+ if (ORTE_SUCCESS != rc) {
+ opal_output(0, "plm_slurm: unable to get daemon vpid as string");
+ goto cleanup;
+ }
- free(argv[proc_vpid_index]);
- argv[proc_vpid_index] = strdup(name_string);
- free(name_string);
+ free(argv[proc_vpid_index]);
+ argv[proc_vpid_index] = strdup(name_string);
+ free(name_string);
- /* Copy the prefix-directory specified in the
+ /* Copy the prefix-directory specified in the
corresponding app_context. If there are multiple,
different prefix's in the app context, complain (i.e., only
allow one --prefix option for the entire slurm run -- we
don't support different --prefix'es for different nodes in
the SLURM plm) */
- cur_prefix = NULL;
- for (n=0; n < jdata->num_apps; n++) {
- char * app_prefix_dir = apps[n]->prefix_dir;
- /* Check for already set cur_prefix_dir -- if different,
+ cur_prefix = NULL;
+ for (n=0; n < jdata->num_apps; n++) {
+ char * app_prefix_dir = apps[n]->prefix_dir;
+ /* Check for already set cur_prefix_dir -- if different,
complain */
- if (NULL != app_prefix_dir) {
- if (NULL != cur_prefix &&
- 0 != strcmp (cur_prefix, app_prefix_dir)) {
- orte_show_help("help-plm-slurm.txt", "multiple-prefixes",
- true, cur_prefix, app_prefix_dir);
- return ORTE_ERR_FATAL;
- }
+ if (NULL != app_prefix_dir) {
+ if (NULL != cur_prefix &&
+ 0 != strcmp (cur_prefix, app_prefix_dir)) {
+ orte_show_help("help-plm-slurm.txt", "multiple-prefixes",
+ true, cur_prefix, app_prefix_dir);
+ return ORTE_ERR_FATAL;
+ }
- /* If not yet set, copy it; iff set, then it's the
+ /* If not yet set, copy it; iff set, then it's the
* same anyway
*/
- if (NULL == cur_prefix) {
- cur_prefix = strdup(app_prefix_dir);
- OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
- "%s plm:slurm: Set prefix:%s",
- ORTE_NAME_PRINT(ORTE_PROC_MY_NAME),
- cur_prefix));
+ if (NULL == cur_prefix) {
+ cur_prefix = strdup(app_prefix_dir);
+ OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
+ "%s plm:slurm: Set prefix:%s",
+ ORTE_NAME_PRINT(ORTE_PROC_MY_NAME),
+ cur_prefix));
+ }
}
}
- }
- /* setup environment */
- env = opal_argv_copy(orte_launch_environ);
+ /* setup environment */
+ env = opal_argv_copy(orte_launch_environ);
- /* enable local launch by the orteds */
- var = mca_base_param_environ_variable("plm", NULL, NULL);
- opal_setenv(var, "rsh", true, &env);
- free(var);
-
- /* if we can do it, use the regexp to launch the apps - this
+ /* enable local launch by the orteds */
+ var = mca_base_param_environ_variable("plm", NULL, NULL);
+ opal_setenv(var, "rsh", true, &env);
+ free(var);
+
+ /* if we can do it, use the regexp to launch the apps - this
* requires that the user requested this mode, that we were
* provided with static ports, and that we only have one
* app_context
*/
- if (orte_use_regexp && orte_static_ports && jdata->num_apps < 2) {
- char *regexp;
- regexp = orte_regex_encode_maps(jdata);
- opal_argv_append(&argc, &argv, "--launch");
- opal_argv_append(&argc, &argv, regexp);
- free(regexp);
- using_regexp = true;
- }
-
- if (0 < opal_output_get_verbosity(orte_plm_globals.output)) {
- param = opal_argv_join(argv, ' ');
- OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
- "%s plm:slurm: final top-level argv:\n\t%s",
- ORTE_NAME_PRINT(ORTE_PROC_MY_NAME),
- (NULL == param) ? "NULL" : param));
- if (NULL != param) free(param);
- }
-
- /* exec the daemon(s) */
- if (ORTE_SUCCESS != (rc = plm_slurm_start_proc(argc, argv, env, cur_prefix))) {
- ORTE_ERROR_LOG(rc);
- goto cleanup;
+ if (orte_use_regexp && orte_static_ports && jdata->num_apps < 2) {
+ char *regexp;
+ regexp = orte_regex_encode_maps(jdata);
+ opal_argv_append(&argc, &argv, "--launch");
+ opal_argv_append(&argc, &argv, regexp);
+ free(regexp);
+ using_regexp = true;
+ }
+
+ if (0 < opal_output_get_verbosity(orte_plm_globals.output)) {
+ param = opal_argv_join(argv, ' ');
+ OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
+ "%s plm:slurm: final top-level argv:\n\t%s",
+ ORTE_NAME_PRINT(ORTE_PROC_MY_NAME),
+ (NULL == param) ? "NULL" : param));
+ if (NULL != param) free(param);
+ }
+
+ //param = opal_argv_join(argv, ' ');
+ //printf("Final command line: %s\n",param);
+
+ /* exec the daemon(s) */
+ if (ORTE_SUCCESS != (rc = plm_slurm_start_proc(argc, argv, env, cur_prefix))) {
+ ORTE_ERROR_LOG(rc);
+ goto cleanup;
+ }
+
+ vpid_offset += groups[grpnum].nodelist_size;
+ grpnum++;
+ argc = 0;
+ opal_argv_free(argv);
+ argv = NULL;
}
+
+ primary_pids_set = true;
/* do NOT wait for srun to complete. Srun only completes when the processes
* it starts - in this case, the orteds - complete. Instead, we'll catch
* any srun failures and deal with them elsewhere
*/
-
+ //plm_affinity_free(classes);
/* wait for daemons to callback */
+
if (ORTE_SUCCESS != (rc = orte_plm_base_daemon_callback(map->num_new_daemons))) {
OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
"%s plm:slurm: daemon launch failed for job %s on error %s",
@@ -460,12 +520,12 @@
if (orte_timing) {
if (0 != gettimeofday(&launchstop, NULL)) {
- opal_output(0, "plm_slurm: could not obtain stop time");
- } else {
- opal_output(0, "plm_slurm: total job launch time is %ld usec",
- (launchstop.tv_sec - launchstart.tv_sec)*1000000 +
- (launchstop.tv_usec - launchstart.tv_usec));
- }
+ opal_output(0, "plm_slurm: could not obtain stop time");
+ } else {
+ opal_output(0, "plm_slurm: total job launch time is %ld usec",
+ (launchstop.tv_sec - launchstart.tv_sec)*1000000 +
+ (launchstop.tv_usec - launchstart.tv_usec));
+ }
}
if (ORTE_SUCCESS != rc) {
@@ -474,6 +534,7 @@
}
cleanup:
+
if (NULL != argv) {
opal_argv_free(argv);
}
@@ -485,6 +546,14 @@
free(jobid_string);
}
+ if( NULL != primary_srun_pids ){
+ free(primary_srun_pids);
+ }
+
+ if( groups != NULL ){
+ plm_slurm_groups_free(&groups, grpcnt);
+ }
+
/* check for failed launch - if so, force terminate */
if (failed_launch) {
orte_plm_base_launch_failed(failed_job, -1, ORTE_ERROR_DEFAULT_EXIT_CODE, ORTE_JOB_STATE_FAILED_TO_START);
@@ -514,7 +583,7 @@
* not wait for a waitpid to fire and tell us it's okay to
* exit. Instead, we simply trigger an exit for ourselves
*/
- if (!primary_pid_set) {
+ if (!primary_pids_set) {
OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
"%s plm:slurm: primary daemons complete!",
ORTE_NAME_PRINT(ORTE_PROC_MY_NAME)));
@@ -560,6 +629,7 @@
static void srun_wait_cb(pid_t pid, int status, void* cbdata){
orte_job_t *jdata;
+ int i;
/* According to the SLURM folks, srun always returns the highest exit
code of our remote processes. Thus, a non-zero exit status doesn't
@@ -602,18 +672,20 @@
orte_plm_base_launch_failed(ORTE_PROC_MY_NAME->jobid, -1, status, ORTE_JOB_STATE_ABORTED);
}
/* otherwise, check to see if this is the primary pid */
- if (primary_srun_pid == pid) {
- /* in this case, we just want to fire the proper trigger so
- * mpirun can exit
- */
- OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
- "%s plm:slurm: primary daemons complete!",
- ORTE_NAME_PRINT(ORTE_PROC_MY_NAME)));
- jdata = orte_get_job_data_object(ORTE_PROC_MY_NAME->jobid);
- jdata->state = ORTE_JOB_STATE_TERMINATED;
- /* need to set the #terminated value to avoid an incorrect error msg */
- jdata->num_terminated = jdata->num_procs;
- orte_trigger_event(&orteds_exit);
+ for(i=0; i<primary_srun_pids_cnt; i++){
+ if (primary_srun_pids[i] == pid) {
+ /* in this case, we just want to fire the proper trigger so
+ * mpirun can exit
+ */
+ OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
+ "%s plm:slurm: primary daemons complete!",
+ ORTE_NAME_PRINT(ORTE_PROC_MY_NAME)));
+ jdata = orte_get_job_data_object(ORTE_PROC_MY_NAME->jobid);
+ jdata->state = ORTE_JOB_STATE_TERMINATED;
+ /* need to set the #terminated value to avoid an incorrect error msg */
+ jdata->num_terminated = jdata->num_procs;
+ orte_trigger_event(&orteds_exit);
+ }
}
}
}
@@ -692,7 +764,7 @@
* EXCEPT if the user has requested that we leave sessions attached
*/
if (0 >= opal_output_get_verbosity(orte_plm_globals.output) &&
- !orte_debug_daemons_flag && !orte_leave_session_attached) {
+ !orte_debug_daemons_flag && !orte_leave_session_attached) {
if (fd >= 0) {
if (fd != 1) {
dup2(fd,1);
@@ -727,9 +799,8 @@
/* if this is the primary launch - i.e., not a comm_spawn of a
* child job - then save the pid
*/
- if (!primary_pid_set) {
- primary_srun_pid = srun_pid;
- primary_pid_set = true;
+ if (!primary_pids_set) {
+ primary_srun_pids[ primary_srun_pids_cnt++] = srun_pid;
}
/* setup the waitpid so we can find out if srun succeeds! */
@@ -739,3 +810,136 @@
return ORTE_SUCCESS;
}
+
+
+static int plm_slurm_group_nodes(orte_job_map_t *map,
+ struct pml_slurm_node_group_t **grpout,
+ int *grpcnt)
+{
+ int estimsize = sizeof(int)*orte_node_pool->size;
+ int *grp_cpus, *grp_ncount;
+ int group_n = 0, groups_size;
+ orte_node_t **nodes = (orte_node_t**)map->nodes->addr;
+ int n,j;
+ struct pml_slurm_node_group_t *groups;
+ int *cur_grpcnt;
+
+ grp_cpus = malloc(estimsize);
+ grp_ncount = malloc(estimsize);
+ memset(grp_ncount, 0, estimsize);
+ if( grp_cpus == NULL || grp_ncount == NULL ){
+ ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
+ return ORTE_ERR_OUT_OF_RESOURCE;
+ }
+
+ for (n=0; n < map->num_nodes; n++ ) {
+ int found = 0;
+ if (nodes[n]->daemon_launched) {
+ continue;
+ }
+ for(j=0; j<group_n; j++){
+ if( grp_cpus[j] == nodes[n]->cpus ) {
+ found = 1;
+ grp_ncount[j]++;
+ break;
+ }
+ }
+ if( found )
+ continue;
+ grp_cpus[group_n] = nodes[n]->cpus;
+ grp_ncount[group_n] = 1;
+ group_n++;
+ }
+/*
+ {
+ int i;
+ printf("\tclass_cnt = %d, class content is:\n",class_n);
+ for(i=0;i<class_n;i++){
+ printf("\t\tval = %d, count = %d\n",classval[i], classcnt[i]);
+ }
+ }
+*/
+ OPAL_OUTPUT_VERBOSE((1, orte_plm_globals.output,
+ "%s plm:slurm: foud %d node groups",
+ group_n));
+
+ groups_size = sizeof(struct pml_slurm_node_group_t)*group_n;
+ *grpout = groups = malloc(groups_size);
+ *grpcnt = group_n;
+ cur_grpcnt = malloc(sizeof(int)*group_n);
+ if( groups == NULL || cur_grpcnt == NULL )
+ {
+ ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
+ return ORTE_ERR_OUT_OF_RESOURCE;
+ }
+ memset(groups, 0, groups_size);
+ memset(cur_grpcnt, 0, sizeof(int)*group_n);
+
+ //printf("\tStart classes fillup\n");
+ for (n=0; n < map->num_nodes; n++ ) {
+ int found = 0;
+ if (nodes[n]->daemon_launched) {
+ //printf("\tSkip %s\n",nodes[n]->name);
+ continue;
+ }
+ for(j=0; j<group_n; j++){
+ //printf("\tCompare classval[%d] = %d with nodes[%d]->cpus = %d\n",
+ // j, classval[j], n, nodes[n]->cpus);
+ if( grp_cpus[j] == nodes[n]->cpus ) {
+ found = 1;
+ break;
+ }
+ }
+ if( !found ){
+ printf("Something is wrong, class for node %s with %d cpus not found\n",
+ nodes[n]->name, nodes[n]->cpus);
+ return -1;
+ }
+ //printf("\tprocess %s, class #%d\n",nodes[n]->name, j);
+ if( cur_grpcnt[j] == 0 ){
+ int i, size = sizeof(char*)*(grp_ncount[j] + 1);
+ //printf("\t\tneed to initialize: nodes = %d, cpu per node = %d\n",
+ // classcnt[j], classval[j]);
+ groups[j].cpus_per_node = grp_cpus[j];
+ groups[j].nodelist_size = grp_ncount[j];
+ // reserve 1 element for NULL
+ groups[j].nodelist = malloc( size );
+ for(i=0; i<(grp_ncount[j] + 1); i++){
+ groups[j].nodelist[i] = NULL;
+ }
+ }
+ groups[j].nodelist[cur_grpcnt[j]] = nodes[n]->name;
+ cur_grpcnt[j]++;
+ }
+/*
+ {
+ int i, j;
+ printf("\tclasses is filled!:\n");
+ for(i=0;i<class_n;i++){
+ printf("\t\tcpus per node = %d, nodes: ", classes[i].cpus_per_node);
+ j = 0;
+ while( classes[i].nodelist[j] != NULL ){
+ printf("%s ", classes[i].nodelist[j] );
+ j++;
+ }
+ printf("\n");
+ }
+ }
+*/
+ // Free temp data structures
+ free(grp_cpus);
+ free(grp_ncount);
+ free(cur_grpcnt);
+ return 0;
+}
+
+static void plm_slurm_groups_free(struct pml_slurm_node_group_t **groups,
+ int grpcnt)
+{
+ int i;
+ for(i=0; i < grpcnt; i++){
+ free( (*groups)[i].nodelist );
+ }
+ free(*groups);
+ *groups = NULL;
+}
diff -Naur openmpi-1.6.5/orte/mca/ras/slurm/ras_slurm_module.c openmpi-1.6.5_new/orte/mca/ras/slurm/ras_slurm_module.c
--- openmpi-1.6.5/orte/mca/ras/slurm/ras_slurm_module.c 2012-04-03 10:30:28.000000000 -0400
+++ openmpi-1.6.5_new/orte/mca/ras/slurm/ras_slurm_module.c 2014-03-07 08:25:45.187430530 -0500
@@ -43,8 +43,8 @@
static int orte_ras_slurm_allocate(opal_list_t *nodes);
static int orte_ras_slurm_finalize(void);
-static int orte_ras_slurm_discover(char *regexp, char* tasks_per_node,
- opal_list_t *nodelist);
+static int orte_ras_slurm_discover(char *regexp, char *tasks_per_node,
+ char *cpus_per_node, opal_list_t* nodelist);
static int orte_ras_slurm_parse_ranges(char *base, char *ranges, char ***nodelist);
static int orte_ras_slurm_parse_range(char *base, char *range, char ***nodelist);
@@ -65,9 +65,10 @@
*/
static int orte_ras_slurm_allocate(opal_list_t *nodes)
{
- int ret, cpus_per_task;
+ int ret;
char *slurm_node_str, *regexp;
- char *tasks_per_node, *node_tasks;
+ char *tasks_per_node, *cpus_per_node;
+ char *node_tasks, *node_cpus;
char * tmp;
char *slurm_jobid;
@@ -89,34 +90,22 @@
regexp = strdup(slurm_node_str);
tasks_per_node = getenv("SLURM_TASKS_PER_NODE");
- if (NULL == tasks_per_node) {
+ cpus_per_node = getenv("SLURM_JOB_CPUS_PER_NODE");
+ if (NULL == tasks_per_node || NULL == cpus_per_node ) {
/* couldn't find any version - abort */
orte_show_help("help-ras-slurm.txt", "slurm-env-var-not-found", 1,
- "SLURM_TASKS_PER_NODE");
+ "SLURM_TASKS_PER_NODE or SLURM_JOB_CPUS_PER_NODE");
return ORTE_ERR_NOT_FOUND;
}
node_tasks = strdup(tasks_per_node);
+ node_cpus = strdup(cpus_per_node);
- if(NULL == regexp || NULL == node_tasks) {
+ if( NULL == regexp || NULL == node_tasks || NULL == node_cpus ) {
ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
return ORTE_ERR_OUT_OF_RESOURCE;
}
- /* get the number of CPUs per task that the user provided to slurm */
- tmp = getenv("SLURM_CPUS_PER_TASK");
- if(NULL != tmp) {
- cpus_per_task = atoi(tmp);
- if(0 >= cpus_per_task) {
- opal_output(0, "ras:slurm:allocate: Got bad value from SLURM_CPUS_PER_TASK. "
- "Variable was: %s\n", tmp);
- ORTE_ERROR_LOG(ORTE_ERROR);
- return ORTE_ERROR;
- }
- } else {
- cpus_per_task = 1;
- }
-
- ret = orte_ras_slurm_discover(regexp, node_tasks, nodes);
+ ret = orte_ras_slurm_discover(regexp, node_tasks, node_cpus, nodes);
free(regexp);
free(node_tasks);
if (ORTE_SUCCESS != ret) {
@@ -153,6 +142,53 @@
}
+static int process_task_or_cpus(char *resource, int *elems, int num_nodes)
+{
+ char *begptr = resource, *endptr;
+ int reps, count;
+ int j = 0, i;
+
+ while (begptr) {
+ count = strtol(begptr, &endptr, 10);
+ if ((endptr[0] == '(') && (endptr[1] == 'x')) {
+ reps = strtol((endptr+2), &endptr, 10);
+ if (endptr[0] == ')') {
+ endptr++;
+ }
+ } else {
+ reps = 1;
+ }
+
+ /**
+ * TBP: it seems like it would be an error to have more slot
+ * descriptions than nodes. Turns out that this valid, and SLURM will
+ * return such a thing. For instance, if I did:
+ * srun -A -N 30 -w odin001
+ * I would get SLURM_NODELIST=odin001 SLURM_TASKS_PER_NODE=4(x30)
+ * That is, I am allocated 30 nodes, but since I only requested
+ * one specific node, that's what is in the nodelist.
+ * I'm not sure this is what users would expect, but I think it is
+ * more of a SLURM issue than a orte issue, since SLURM is OK with it,
+ * I'm ok with it
+ */
+ for (i = 0; i < reps && j < num_nodes; i++) {
+ elems[j++] = count;
+ }
+
+ if (*endptr == ',') {
+ begptr = endptr + 1;
+ } else if (*endptr == '\0' || j >= num_nodes) {
+ break;
+ } else {
+ orte_show_help("help-ras-slurm.txt", "slurm-env-var-bad-value", 1,
+ resource, "SLURM_TASKS_PER_NODE or SLURM_JOB_CPUS_PER_NODE");
+ ORTE_ERROR_LOG(ORTE_ERR_BAD_PARAM);
+ return ORTE_ERR_BAD_PARAM;
+ }
+ }
+ return 0;
+}
+
/**
* Discover the available resources.
*
@@ -169,12 +205,13 @@
* the found nodes in
*/
static int orte_ras_slurm_discover(char *regexp, char *tasks_per_node,
- opal_list_t* nodelist)
+ char *cpus_per_node, opal_list_t* nodelist)
{
int i, j, len, ret, count, reps, num_nodes;
char *base, **names = NULL;
char *begptr, *endptr, *orig;
int *slots;
+ int *cpus;
bool found_range = false;
bool more_to_come = false;
@@ -284,57 +321,68 @@
}
memset(slots, 0, sizeof(int) * num_nodes);
- orig = begptr = strdup(tasks_per_node);
- if (NULL == begptr) {
+ orig = strdup(tasks_per_node);
+ if (NULL == orig) {
ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
free(slots);
return ORTE_ERR_OUT_OF_RESOURCE;
}
-
- j = 0;
- while (begptr) {
- count = strtol(begptr, &endptr, 10);
- if ((endptr[0] == '(') && (endptr[1] == 'x')) {
- reps = strtol((endptr+2), &endptr, 10);
- if (endptr[0] == ')') {
- endptr++;
- }
- } else {
- reps = 1;
- }
- /**
- * TBP: it seems like it would be an error to have more slot
- * descriptions than nodes. Turns out that this valid, and SLURM will
- * return such a thing. For instance, if I did:
- * srun -A -N 30 -w odin001
- * I would get SLURM_NODELIST=odin001 SLURM_TASKS_PER_NODE=4(x30)
- * That is, I am allocated 30 nodes, but since I only requested
- * one specific node, that's what is in the nodelist.
- * I'm not sure this is what users would expect, but I think it is
- * more of a SLURM issue than a orte issue, since SLURM is OK with it,
- * I'm ok with it
- */
- for (i = 0; i < reps && j < num_nodes; i++) {
- slots[j++] = count;
- }
-
- if (*endptr == ',') {
- begptr = endptr + 1;
- } else if (*endptr == '\0' || j >= num_nodes) {
- break;
- } else {
- orte_show_help("help-ras-slurm.txt", "slurm-env-var-bad-value", 1,
- regexp, tasks_per_node, "SLURM_TASKS_PER_NODE");
- ORTE_ERROR_LOG(ORTE_ERR_BAD_PARAM);
- free(slots);
- free(orig);
- return ORTE_ERR_BAD_PARAM;
+ if( process_task_or_cpus(orig,slots,num_nodes) ){
+ free(orig);
+ free(slots);
+ orte_show_help("help-ras-slurm.txt", "slurm-env-var-bad-value", 1,
+ slots, "SLURM_TASKS_PER_NODE");
+ ORTE_ERROR_LOG(ORTE_ERR_BAD_PARAM);
+ return ORTE_ERR_BAD_PARAM;
+ }
+ free(orig);
+/*
+ {
+ int i;
+ printf("orte_ras_slurm_discover: slots are processed:\n");
+ for(i=0;i<num_nodes;i++){
+ printf("\t%s, slots = %d\n",names[i],slots[i]);
}
}
+*/
+ /* Find the number of cpus per node */
+
+ cpus = malloc(sizeof(int) * num_nodes);
+ if (NULL == cpus) {
+ ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
+ return ORTE_ERR_OUT_OF_RESOURCE;
+ }
+ memset(cpus, 0, sizeof(int) * num_nodes);
+ orig = strdup(cpus_per_node);
+ if (NULL == orig) {
+ ORTE_ERROR_LOG(ORTE_ERR_OUT_OF_RESOURCE);
+ free(slots);
+ return ORTE_ERR_OUT_OF_RESOURCE;
+ }
+
+ if( ret = process_task_or_cpus(orig,cpus,num_nodes) ){
+ free(orig);
+ free(slots);
+ free(cpus);
+ orte_show_help("help-ras-slurm.txt", "slurm-env-var-bad-value", 1,
+ cpus, "SLURM_JOB_CPUS_PER_NODE");
+ ORTE_ERROR_LOG(ORTE_ERR_BAD_PARAM);
+ return ORTE_ERR_BAD_PARAM;
+ return ret;
+ }
free(orig);
+/*
+ {
+ int i;
+ printf("orte_ras_slurm_discover: cpus are processed:\n");
+ for(i=0;i<num_nodes;i++){
+ printf("\t%s, cpus = %d\n",names[i],cpus[i]);
+ }
+ }
+*/
/* Convert the argv of node names to a list of node_t's */
for (i = 0; NULL != names && NULL != names[i]; ++i) {
@@ -356,6 +404,7 @@
node->slots_inuse = 0;
node->slots_max = 0;
node->slots = slots[i];
+ node->cpus = cpus[i];
opal_list_append(nodelist, &node->super);
}
free(slots);
diff -Naur openmpi-1.6.5/orte/runtime/orte_globals.h openmpi-1.6.5_new/orte/runtime/orte_globals.h
--- openmpi-1.6.5/orte/runtime/orte_globals.h 2012-09-07 11:48:03.000000000 -0400
+++ openmpi-1.6.5_new/orte/runtime/orte_globals.h 2014-03-07 08:24:51.439655951 -0500
@@ -260,6 +260,9 @@
specified limit. For example, if we have two processors, we
may want to allow up to four processes but no more. */
orte_std_cntr_t slots_max;
+ /** Number of allocated cpus on the node. Considers cpus per task
+ * setting of srun and friends */
+ orte_std_cntr_t cpus;
/* number of physical boards in the node - defaults to 1 */
uint8_t boards;
/* number of sockets on each board - defaults to 1 */
