int
drmaa_get_vector_attribute(
drmaa_job_template_t *jt,
const char *name, drmaa_attr_values_t **out_values,
char *errmsg, size_t errlen
)
{
const drmaa_attrib_info_t *attr;
unsigned i, n_values;
char **v, **value;
attr = attr_by_drmaa_name(name);
if (attr == NULL || !drmaa_is_vector(attr))
RAISE_DRMAA(DRMAA_ERRNO_INVALID_ARGUMENT);
pthread_mutex_lock(&jt->mutex);
value = (char**)jt->attrib[ attr->code ];
pthread_mutex_unlock(&jt->mutex);
if (value == NULL)
{
*out_values = NULL;
return DRMAA_ERRNO_SUCCESS;
}
for (n_values = 0; value[n_values] != NULL; n_values++)
{}
v = (char**)calloc(n_values + 1, sizeof(char*));
if (v == NULL)
RAISE_NO_MEMORY();
for (i = 0; i < n_values; i++)
{
v[i] = strdup(value[i]);
if (v[i] == NULL)
{
drmaa_free_vector(v);
RAISE_NO_MEMORY();
}
}
v[n_values] = NULL;
*out_values = malloc(sizeof(drmaa_attr_values_t));
(*out_values)->list = (*out_values)->iter = v;
return DRMAA_ERRNO_SUCCESS;
}
int
drmaa_set_vector_attribute(
drmaa_job_template_t *jt,
const char *name, const char *value[],
char *errmsg, size_t errlen
)
{
const drmaa_attrib_info_t *attr;
char **v;
int attr_no;
unsigned i, n_values;
attr = attr_by_drmaa_name(name);
if (attr == NULL || !drmaa_is_vector(attr))
RAISE_DRMAA(DRMAA_ERRNO_INVALID_ARGUMENT);
attr_no = attr->code;
for (n_values = 0; value[n_values] != NULL; n_values++)
{}
v = (char**)calloc(n_values + 1, sizeof(char*));
if (v == NULL)
RAISE_NO_MEMORY();
for (i = 0; i < n_values; i++)
{
v[i] = strdup(value[i]);
if (v[i] == NULL)
{
drmaa_free_vector(v);
RAISE_NO_MEMORY();
}
}
v[n_values] = NULL;
pthread_mutex_lock(&jt->mutex);
if (jt->attrib[attr_no] != NULL)
drmaa_free_vector((char**)jt->attrib[attr_no]);
jt->attrib[attr_no] = v;
pthread_mutex_unlock(&jt->mutex);
return DRMAA_ERRNO_SUCCESS;
}
int
drmaa_create_submission_context(
drmaa_submission_context_t **c,
const drmaa_job_template_t *jt, int bulk_no,
char *errmsg, size_t errlen)
{
drmaa_submission_context_t *sc;
sc = (drmaa_submission_context_t*)malloc(sizeof(drmaa_submission_context_t));
if (sc == NULL)
RAISE_NO_MEMORY();
sc->jt = jt;
sc->pbs_attribs = NULL;
sc->script_filename = NULL;
sc->home_directory = strdup(getenv("HOME"));
if (jt->attrib[ATTR_JOB_WORKING_DIR] != NULL)
sc->working_directory = strdup((const char *)jt->attrib[ATTR_JOB_WORKING_DIR]);
else
sc->working_directory = strdup(sc->home_directory);
asprintf(&sc->bulk_incr_no, "%d", bulk_no);
*c = sc;
return DRMAA_ERRNO_SUCCESS;
}
int
drmaa_allocate_job_template(drmaa_job_template_t **p_jt, char *errmsg, size_t errlen)
{
drmaa_session_t *c = NULL;
drmaa_job_template_t *jt = NULL;
DEBUG(("-> drmaa_allocate_job_template"));
GET_DRMAA_SESSION(c);
jt = (drmaa_job_template_t*)malloc(sizeof(drmaa_job_template_t));
if (jt == NULL)
{
RELEASE_DRMAA_SESSION(c);
RAISE_NO_MEMORY();
}
jt->session = c;
jt->attrib = (void**)calloc(N_DRMAA_ATTRIBS, sizeof(void*));
if (jt->attrib == NULL)
{
free(jt);
RELEASE_DRMAA_SESSION(c);
RAISE_NO_MEMORY();
}
pthread_mutex_init(&jt->mutex, NULL);
pthread_mutex_lock(& c->jobs_mutex);
jt->next = c->jt_list->next;
jt->prev = c->jt_list;
jt->next->prev = jt;
jt->prev->next = jt;
pthread_mutex_unlock(& c->jobs_mutex);
*p_jt = jt;
RELEASE_DRMAA_SESSION(c);
DEBUG(("<- drmaa_allocate_job_template"));
return DRMAA_ERRNO_SUCCESS;
}
/**
* Writes temporary file.
* @param filename Upon successful return temporary
* file name will be stored here.
* @param content Buffer with content to write.
* @param len Buffer's length.
* @return DRMAA return code.
*/
int
drmaa_write_tmpfile(
char **filename, const char *content, size_t len,
char *errmsg, size_t errlen
)
{
char *name;
int fd;
#define TMPFILE_TEMPLATE "/tmp/pbs_drmaa.XXXXXX"
DEBUG(("-> drmaa_write_tmpfile(content=\"%.*s\")", len, content));
name = strdup(TMPFILE_TEMPLATE);
if (name == NULL)
RAISE_NO_MEMORY();
fd = mkstemp(name);
if (fd < 0)
RAISE_ERRNO(DRMAA_ERRNO_INTERNAL_ERROR);
while (len > 0)
{
size_t written = write(fd, content, len);
if (written != (size_t) - 1)
{
content += written;
len -= written;
}
else
{
free(name);
close(fd);
RAISE_ERRNO(DRMAA_ERRNO_INTERNAL_ERROR);
}
}
if (close(fd))
{
free(name);
RAISE_ERRNO(DRMAA_ERRNO_INTERNAL_ERROR);
}
DEBUG(("<- drmaa_write_tmpfile; filename=%s", name));
*filename = name;
return DRMAA_ERRNO_SUCCESS;
}
/**
* Set e-mail notification about job state.
*/
int
drmaa_set_job_email_notication(
drmaa_submission_context_t *c,
char *errmsg, size_t errlen
)
{
void **attrib = c->jt->attrib;
const char *block_email = (const char*)attrib[ATTR_BLOCK_EMAIL];
int rc;
if (block_email != NULL && !strcmp(block_email, "1"))
{
rc = drmaa_add_pbs_attr(c, ATTR_MAIL_POINTS, strdup(""), 0, errmsg, errlen);
if (rc)
return rc;
}
else
{
const char **mail_list = (const char**)attrib[ATTR_EMAIL];
char *pbs_mail_list = NULL;
if (mail_list != NULL)
{
pbs_mail_list = drmaa_explode(mail_list, ',');
if (pbs_mail_list == NULL)
RAISE_NO_MEMORY();
rc = drmaa_add_pbs_attr(c, ATTR_EMAIL, pbs_mail_list, 0, errmsg, errlen);
if (rc)
{
free(pbs_mail_list);
return rc;
}
/* a mail is sent when the job is aborted by the batch system.
b mail is sent when the job begins execution.
e mail is sent when the job terminates. */
rc = drmaa_add_pbs_attr(c, ATTR_MAIL_POINTS, strdup("ae"), 0, errmsg, errlen);
if (rc)
return rc;
}
}
return DRMAA_ERRNO_SUCCESS;
}
/**
* Adds jobs PBS attributes list.
* @param attr_code Attribute code (@ref drmaa_attribute_t).
* @param value Attribute value -- null terminated string allocated with
* malloc(); <b>callee</b> is responsible for freeing it.
* @param placeholders Placeholders to substitute inside value.
* It have following bits:
* - @ref DRMAA_PLACEHOLDER_MASK_HD -- replaces @ref DRMAA_PLACEHOLDER_HD with
* user's home direcotry,
* - @ref DRMAA_PLACEHOLDER_MASK_WD -- replaces @ref DRMAA_PLACEHOLDER_WD with
* job's working direcotry,
* - @ref DRMAA_PLACEHOLDER_MASK_INCR -- replaces @ref DRMAA_PLACEHOLDER_INCR
* with bulk job index.
*/
int
drmaa_add_pbs_attr(
drmaa_submission_context_t *c,
int attr_code, char *value,
unsigned placeholders,
char *errmsg, size_t errlen
)
{
struct attropl *attr = NULL;
value = drmaa_expand_placeholders(c, value, placeholders);
if (value == NULL)
goto cleanup;
attr = (struct attropl*)malloc(sizeof(*attr));
if (attr == NULL)
goto cleanup;
attr->next = c->pbs_attribs;
attr->name = strdup(drmaa_attr_table[attr_code].pbs_name);
if (attr->name == NULL)
goto cleanup;
attr->value = value;
attr->resource = NULL;
attr->op = SET;
c->pbs_attribs = attr;
return DRMAA_ERRNO_SUCCESS;
cleanup:
if (value != NULL)
free(value);
if (attr != NULL)
free(attr);
RAISE_NO_MEMORY();
}
/** Sets job environment variables. */
int
drmaa_set_job_environment(
drmaa_submission_context_t *c,
char *errmsg, size_t errlen
)
{
void **attrib = c->jt->attrib;
size_t s;
char *env;
char *tmp = NULL;
int rc;
env = strdup("");
s = strlen(env);
if (attrib[ATTR_ENV] != NULL)
{
char *value = drmaa_explode((const char **)attrib[ATTR_ENV], ',');
if (value == NULL)
{
free(env);
RAISE_NO_MEMORY();
}
tmp = (char *)realloc(env, s + strlen(value) + 1);
if (tmp == NULL)
{
free(env);
return DRMAA_ERRNO_NO_MEMORY;
}
env = tmp;
strcpy(env + s, value);
free(value);
}
else env[s-1] = 0;
rc = drmaa_add_pbs_attr(c, ATTR_ENV, env,
DRMAA_PLACEHOLDER_MASK_INCR, errmsg, errlen);
if (rc)
return rc;
return DRMAA_ERRNO_SUCCESS;
}
/** Creates DRMAA session and opens connection with DRM. */
int
drmaa_create(drmaa_session_t **pc, const char *contact, char *errmsg, size_t errlen)
{
drmaa_session_t *c;
c = malloc(sizeof(drmaa_session_t));
if (c == NULL)
RAISE_NO_MEMORY();
c->pbs_conn = -1;
c->contact = NULL;
c->jt_list = NULL;
c->job_hashtab = NULL;
c->next_time_label = 0;
pthread_mutex_init(&c->conn_mutex, NULL);
pthread_mutex_init(&c->jobs_mutex, NULL);
c->jt_list = (drmaa_job_template_t*)malloc(sizeof(drmaa_job_template_t));
if (c->jt_list == NULL)
{
drmaa_destroy(c, errmsg, errlen);
RAISE_NO_MEMORY();
}
c->jt_list->next = c->jt_list->prev = c->jt_list;
c->job_hashtab = (drmaa_job_t**)calloc(HASHTAB_SIZE, sizeof(drmaa_job_t*));
if (c->job_hashtab == NULL)
{
drmaa_destroy(c, errmsg, errlen);
RAISE_NO_MEMORY();
}
c->pbs_conn = pbs_connect((char*)contact);
DEBUG(("pbs_connect(%s)=%d", contact, c->pbs_conn));
if (c->pbs_conn < 0)
{
drmaa_destroy(c, errmsg, errlen);
RAISE_PBS();
}
if (contact)
c->contact = strdup(contact);
else
c->contact = strdup(pbs_server);
if (c->contact == NULL)
{
drmaa_destroy(c, errmsg, errlen);
RAISE_NO_MEMORY();
}
*pc = c;
return DRMAA_ERRNO_SUCCESS;
}
int
drmaa_run_bulk_jobs(
drmaa_job_ids_t **job_ids,
const drmaa_job_template_t *jt,
int start, int end, int incr,
char *errmsg, size_t errlen
)
{
unsigned n_jobs;
unsigned i;
char **j;
int rc = DRMAA_ERRNO_SUCCESS;
DEBUG(("-> drmaa_run_bulk_jobs(start=%d,end=%d,incr=%d)", start, end, incr));
/* Be conform with general DRMAA specifiaction
* -- accept negative incr with end <= start.
*/
if (incr < 0)
{
/* swap(start,end) */
int tmp;
tmp = start;
start = end;
end = tmp;
incr = - incr;
}
if (0 < start && start <= end && 0 < incr)
{}
else return DRMAA_ERRNO_INVALID_ARGUMENT;
n_jobs = (end - start) / incr + 1;
*job_ids = (drmaa_job_ids_t*)malloc(sizeof(drmaa_job_ids_t));
if (*job_ids == NULL)
RAISE_NO_MEMORY();
(*job_ids)->list = (*job_ids)->iter = (char**) calloc(n_jobs + 1, sizeof(char*));
if ((*job_ids)->list == NULL)
{
free(*job_ids);
RAISE_NO_MEMORY();
}
j = (*job_ids)->list;
for (i = start; i <= (unsigned)end; i += incr)
{
char *job_id = (char*)malloc(DRMAA_JOBNAME_BUFFER);
if (job_id == NULL)
{
drmaa_release_job_ids(*job_ids);
RAISE_NO_MEMORY();
}
rc = drmaa_run_job_impl(job_id, DRMAA_JOBNAME_BUFFER, jt, i, errmsg, errlen);
*j++ = job_id;
if (rc)
{
drmaa_release_job_ids(*job_ids);
return rc;
}
}
*j++ = NULL;
DEBUG(("<- drmaa_run_bulk_jobs() =%d, job_ids=%p", rc, (void*)*job_ids));
return DRMAA_ERRNO_SUCCESS;
}
/** Writes job's PBS script to temporary file. */
int
drmaa_create_job_script(
drmaa_submission_context_t *c,
char *errmsg, size_t errlen
)
{
size_t script_size;
const char *job, *wd, **argv;
char *input_path;
char *script, *s;
const char **i;
int rc;
void **attrib = c->jt->attrib;
job = (const char*) attrib[ ATTR_JOB_PATH ];
wd = (const char*) attrib[ ATTR_JOB_WORKING_DIR ];
argv = (const char**)attrib[ ATTR_ARGV ];
input_path = (char *) attrib[ ATTR_INPUT_PATH ];
if (job == NULL)
RAISE_DRMAA(DRMAA_ERRNO_INVALID_ATTRIBUTE_VALUE);
/* compute script length */
script_size = 0;
if (wd != NULL)
script_size += strlen("cd ") + strlen(wd) + strlen("; ");
script_size += strlen("exec ") + strlen(job);
if (argv != NULL)
for (i = argv; *i != NULL; i++)
script_size += 1 + strlen(*i);
if (input_path != NULL)
script_size += sizeof(" <") + strlen(input_path);
script = (char*)malloc(script_size + 1);
if (script == NULL)
RAISE_NO_MEMORY();
s = script;
if (wd != NULL)
s += sprintf(s, "cd %s; ", wd);
s += sprintf(s, "exec %s", job);
if (argv != NULL)
for (i = argv; *i != NULL; i++)
s += sprintf(s, " %s", *i);
if (input_path != NULL)
{
char *colon = strchr(input_path, ':');
if (colon != NULL)
input_path = colon + 1;
s += sprintf(s, " <%s", input_path);
}
DEBUG(("script before substitution = {%s}", script));
script = drmaa_expand_placeholders(c, script,
DRMAA_PLACEHOLDER_MASK_HD |
DRMAA_PLACEHOLDER_MASK_WD |
DRMAA_PLACEHOLDER_MASK_INCR);
DEBUG(("script after substitution = {%s}", script));
rc = drmaa_write_tmpfile(&c->script_filename,
script, strlen(script), errmsg, errlen);
free(script);
return rc;
}