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Merge pull request #1493 from rhc54/topic/sing

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Update singularity support to track changes in upstream Singularity code
Этот коммит содержится в:
rhc54 2016-03-24 15:16:38 -07:00
родитель f5f1751877 8c14df2328
Коммит ba8c8700aa
6 изменённых файлов: 114 добавлений и 37 удалений
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5
opal/mca/btl/sm/btl_sm_component.c
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@ -735,11 +735,6 @@ mca_btl_sm_component_init(int *num_btls,
int rc;
#endif /* OPAL_BTL_SM_HAVE_KNEM | OPAL_BTL_SM_HAVE_CMA */
/* if we are in a container, then we must disqualify ourselves */
if (NULL != getenv("OPAL_PROC_CONTAINER")) {
return NULL;
}
*num_btls = 0;
/* lookup/create shared memory pool only when used */
mca_btl_sm_component.sm_mpool = NULL;

41
opal/util/os_dirpath.c
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@ -11,6 +11,7 @@
* All rights reserved.
* Copyright (c) 2015 Research Organization for Information Science
* and Technology (RIST). All rights reserved.
* Copyright (c) 2016 Intel, Inc. All rights reserved.
* $COPYRIGHT$
*
* Additional copyrights may follow
@ -150,9 +151,7 @@ int opal_os_dirpath_destroy(const char *path,
DIR *dp;
struct dirent *ep;
char *filenm;
#ifndef HAVE_STRUCT_DIRENT_D_TYPE
struct stat buf;
#endif
if (NULL == path) { /* protect against error */
return OPAL_ERROR;
@ -161,7 +160,7 @@ int opal_os_dirpath_destroy(const char *path,
/*
* Make sure we have access to the the base directory
*/
if( OPAL_SUCCESS != (rc = opal_os_dirpath_access(path, 0) ) ) {
if (OPAL_SUCCESS != (rc = opal_os_dirpath_access(path, 0))) {
exit_status = rc;
goto cleanup;
}
@ -172,12 +171,12 @@ int opal_os_dirpath_destroy(const char *path,
return OPAL_ERROR;
}
while (NULL != (ep = readdir(dp)) ) {
while (NULL != (ep = readdir(dp))) {
/* skip:
* - . and ..
*/
if ((0 == strcmp(ep->d_name, ".")) ||
(0 == strcmp(ep->d_name, "..")) ) {
(0 == strcmp(ep->d_name, ".."))) {
continue;
}
@ -189,22 +188,17 @@ int opal_os_dirpath_destroy(const char *path,
* allocating memory here, so we need to free it later on.
*/
filenm = opal_os_path(false, path, ep->d_name, NULL);
#ifdef HAVE_STRUCT_DIRENT_D_TYPE
if (DT_DIR == ep->d_type) {
is_dir = true;
}
#else /* have dirent.d_type */
rc = stat(filenm, &buf);
if (rc < 0 || S_ISDIR(buf.st_mode)) {
if (S_ISDIR(buf.st_mode)) {
is_dir = true;
}
#endif /* have dirent.d_type */
/*
* If not recursively decending, then if we find a directory then fail
* since we were not told to remove it.
*/
if( is_dir && !recursive) {
if (is_dir && !recursive) {
/* Set the error indicating that we found a directory,
* but continue removing files
*/
@ -214,18 +208,18 @@ int opal_os_dirpath_destroy(const char *path,
}
/* Will the caller allow us to remove this file/directory? */
if(NULL != cbfunc) {
if (NULL != cbfunc) {
/*
* Caller does not wish to remove this file/directory,
* continue with the rest of the entries
*/
if( ! (cbfunc(path, ep->d_name)) ) {
if (!(cbfunc(path, ep->d_name))) {
free(filenm);
continue;
}
}
/* Directories are recursively destroyed */
if(is_dir) {
if (is_dir) {
rc = opal_os_dirpath_destroy(filenm, recursive, cbfunc);
free(filenm);
if (OPAL_SUCCESS != rc) {
@ -233,10 +227,9 @@ int opal_os_dirpath_destroy(const char *path,
closedir(dp);
goto cleanup;
}
}
/* Files are removed right here */
else {
if( 0 != (rc = unlink(filenm) ) ) {
} else {
/* Files are removed right here */
if (0 != (rc = unlink(filenm))) {
exit_status = OPAL_ERROR;
}
free(filenm);
@ -288,20 +281,18 @@ int opal_os_dirpath_access(const char *path, const mode_t in_mode ) {
/*
* If there was no mode specified, use the default mode
*/
if( 0 != in_mode ) {
if (0 != in_mode) {
loc_mode = in_mode;
}
if (0 == stat(path, &buf)) { /* exists - check access */
if ((buf.st_mode & loc_mode) == loc_mode) { /* okay, I can work here */
return(OPAL_SUCCESS);
}
else {
} else {
/* Don't have access rights to the existing path */
return(OPAL_ERROR);
}
}
else {
} else {
/* We could not find the path */
return( OPAL_ERR_NOT_FOUND );
}

6
orte/mca/ess/singleton/ess_singleton_module.c
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@ -157,10 +157,8 @@ static int rte_init(void)
/* for convenience, push the pubsub version of this param into the environ */
opal_setenv (OPAL_MCA_PREFIX"pubsub_orte_server", orte_process_info.my_hnp_uri, true, &environ);
} else if (NULL != getenv("SINGULARITY_CONTAINER")) {
/* mark that we are in a container */
opal_setenv("OPAL_PROC_CONTAINER", "1", true, &environ);
} else if (mca_ess_singleton_component.isolated) {
} else if (NULL != getenv("SINGULARITY_CONTAINER") ||
mca_ess_singleton_component.isolated) {
/* ensure we use the isolated pmix component */
opal_setenv (OPAL_MCA_PREFIX"pmix", "isolated", true, &environ);
} else {

96
orte/mca/schizo/singularity/schizo_singularity.c
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@ -31,18 +31,20 @@
static int setup_app(char **personality,
orte_app_context_t *context);
static int setup_fork(orte_job_t *jdata,
orte_app_context_t *context);
orte_schizo_base_module_t orte_schizo_singularity_module = {
.setup_app = setup_app
.setup_app = setup_app,
.setup_fork = setup_fork
};
static int setup_app(char **personality,
orte_app_context_t *app)
{
int i;
char *newenv, *pth;
char *newenv, *pth, *t2;
bool takeus = false;
char *t2;
/* see if we are included */
for (i=0; NULL != personality[i]; i++) {
@ -90,6 +92,12 @@ static int setup_app(char **personality,
break;
}
}
free(pth);
if (0 == strcmp(app->argv[0], "singularity")) {
/* we don't want the backend to setup a cache dir */
orte_set_attribute(&app->attributes, ORTE_APP_NO_CACHEDIR, ORTE_ATTR_GLOBAL, NULL, OPAL_BOOL);
}
/* export an envar to permit shared memory operations */
opal_setenv("SINGULARITY_NO_NAMESPACE_PID", "1", true, &app->env);
@ -97,3 +105,85 @@ static int setup_app(char **personality,
return ORTE_SUCCESS;
}
static int setup_fork(orte_job_t *jdata,
orte_app_context_t *app)
{
int i;
bool takeus = false;
char *p, *t2;
char dir[MAXPATHLEN];
/* see if we are included */
for (i=0; NULL != jdata->personality[i]; i++) {
if (0 == strcmp(jdata->personality[i], "singularity")) {
takeus = true;
break;
}
}
if (!takeus) {
/* even if they didn't specify, check to see if
* this involves a singularity container */
if (0 != strcmp(app->argv[0],"singularity") &&
0 != strcmp(app->argv[0],"sapprun") &&
NULL == strstr(app->argv[0], ".sapp")) {
/* guess not! */
return ORTE_ERR_TAKE_NEXT_OPTION;
}
}
/* set the singularity cache dir, unless asked not to do so */
if (!orte_get_attribute(&app->attributes, ORTE_APP_NO_CACHEDIR, NULL, OPAL_BOOL)) {
opal_setenv("SINGULARITY_CACHEDIR", orte_process_info.job_session_dir, true, &app->env);
opal_setenv("SINGULARITY_CACHEDIR", orte_process_info.job_session_dir, true, &environ);
}
/* save our current directory */
getcwd(dir, sizeof(dir));
/* change to the working directory for this context */
chdir(app->cwd);
/* if the app contains .sapp, then we need to strip that
* extension so singularity doesn't bark at us */
if (NULL != strstr(app->argv[0], ".sapp")) {
/* ensure the app is installed */
opal_output_verbose(1, orte_schizo_base_framework.framework_output,
"%s schizo:singularity: installing app %s",
ORTE_NAME_PRINT(ORTE_PROC_MY_NAME), app->argv[0]);
t2 = opal_basename(app->argv[0]);
p = strstr(t2, ".sapp");
*p = '\0'; // strip the extension
if (0 < opal_output_get_verbosity(orte_schizo_base_framework.framework_output)) {
(void)asprintf(&p, "singularity -vv install --runkey %s %s", t2, app->argv[0]);
} else {
(void)asprintf(&p, "singularity --quiet install --runkey %s %s", t2, app->argv[0]);
}
system(p);
free(p);
free(app->argv[0]);
app->argv[0] = t2;
}
/* ensure that we use "singularity run" to execute this app */
if (0 != strcmp(app->app, "singularity")) {
opal_output_verbose(1, orte_schizo_base_framework.framework_output,
"%s schizo:singularity: adding singularity cmd",
ORTE_NAME_PRINT(ORTE_PROC_MY_NAME));
/* change the app to the "singularity" command */
free(app->app);
app->app = strdup("singularity");
opal_argv_prepend_nosize(&app->argv, "run");
if (0 < opal_output_get_verbosity(orte_schizo_base_framework.framework_output)) {
opal_argv_prepend_nosize(&app->argv, "-vv");
} else {
opal_argv_prepend_nosize(&app->argv, "--quiet");
}
opal_argv_prepend_nosize(&app->argv, "singularity");
}
/* return to the original directory */
chdir(dir);
return ORTE_SUCCESS;
}

2
orte/util/attr.c
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@ -167,6 +167,8 @@ const char *orte_attr_key_to_str(orte_attribute_key_t key)
return "APP-MAX-PPN";
case ORTE_APP_PREFIX_DIR:
return "APP-PREFIX-DIR";
case ORTE_APP_NO_CACHEDIR:
return "ORTE_APP_NO_CACHEDIR";
case ORTE_NODE_USERNAME:
return "NODE-USERNAME";

1
orte/util/attr.h
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@ -44,6 +44,7 @@ typedef uint8_t orte_app_context_flags_t;
#define ORTE_APP_MANDATORY 13 // bool - flag if nodes requested in -host are "mandatory" vs "optional"
#define ORTE_APP_MAX_PPN 14 // uint32 - maximum number of procs/node for this app
#define ORTE_APP_PREFIX_DIR 15 // string - prefix directory for this app, if override necessary
#define ORTE_APP_NO_CACHEDIR 16 // bool - flag that a cache dir is not to be specified for a Singularity container
#define ORTE_APP_MAX_KEY 100