SEXP
lsf_job_submit(SEXP sexp_debug, SEXP sexp_command, SEXP sexp_ncpus)
{
int jobId, debug, i;
struct submit submitRequest;
struct submitReply submitReply;
debug = INTEGER(sexp_debug)[0];
memset(&submitRequest, 0, sizeof(submitRequest));
for (i = 0; i < LSF_RLIM_NLIMITS; i++)
submitRequest.rLimits[i] = DEFAULT_RLIMIT;
submitRequest.command = CHAR(STRING_ELT(sexp_command, 0));
submitRequest.options |= SUB_OUT_FILE;
if (debug) {
submitRequest.outFile = "Rlsf_job_output.%J";
} else {
submitRequest.outFile = "/dev/null";
}
submitRequest.numProcessors = INTEGER(sexp_ncpus)[0];
submitRequest.maxNumProcessors = INTEGER(sexp_ncpus)[0];
jobId = lsb_submit(&submitRequest, &submitReply);
if (jobId == -1) {
Rprintf("lsf_job_submit: lsb_submit: %s\n", lsb_sysmsg());
return AsInt(0);
}
return AsInt(jobId);
}
int
do_sub (int argc, char **argv, int option)
{
static char fname[] = "do_sub";
struct submit req;
struct submitReply reply;
LS_LONG_INT jobId = -1;
if (lsb_init (argv[0]) < 0)
{
sub_perror ("lsb_init");
fprintf (stderr, ". %s.\n", (_i18n_msg_get (ls_catd, NL_SETN, 1551, "Job not submitted"))); /* catgets 1551 */
return (-1);
}
if (logclass & (LC_TRACE | LC_SCHED | LC_EXEC))
ls_syslog (LOG_DEBUG, "%s: Entering this routine...", fname);
if (fillReq (argc, argv, option, &req) < 0)
{
fprintf (stderr, ". %s.\n",
(_i18n_msg_get (ls_catd, NL_SETN, 1551, "Job not submitted")));
return (-1);
}
memset (&reply, 0, sizeof (struct submitReply));
TIMEIT (0, (jobId = lsb_submit (&req, &reply)), "lsb_submit");
if (jobId < 0)
{
prtErrMsg (&req, &reply);
fprintf (stderr, ". %s.\n",
(_i18n_msg_get (ls_catd, NL_SETN, 1551, "Job not submitted")));
return (-1);
}
if (req.nxf)
free (req.xf);
return (0);
}
SEXP
lsf_job_submit2(SEXP ctrl) {
char *name;
char *val;
char *vals[100];
int jobId, debug, i, j;
SEXP elmt = R_NilValue;
SEXP names = getAttrib(ctrl, R_NamesSymbol);
struct submit submitRequest;
struct submitReply submitReply;
memset(&submitRequest, 0, sizeof(submitRequest));
for (i = 0; i < LSF_RLIM_NLIMITS; i++)
submitRequest.rLimits[i] = DEFAULT_RLIMIT;
for (i = 0; i < length(names); i++) {
name = CHAR(STRING_ELT(names, i));
elmt = VECTOR_ELT(ctrl, i);
val = CHAR(STRING_ELT(elmt, 0));
if (0) {
} else if (!strcmp(name, "jobName")) {
submitRequest.options |= SUB_JOB_NAME;
submitRequest.jobName = val;
} else if (!strcmp(name, "queue")) {
submitRequest.options |= SUB_QUEUE;
submitRequest.queue = val;
} else if (!strcmp(name, "askedHosts")){
submitRequest.options |= SUB_HOST;
char **chars;
chars = (char **)calloc(length(elmt), sizeof(char *));
for (j = 0; j < length(elmt); j++){
val=CHAR(STRING_ELT(elmt, j));
chars[j] = val;
}
submitRequest.numAskedHosts = length(elmt);
submitRequest.askedHosts = chars;
} else if (!strcmp(name, "resReq")){
submitRequest.options |= SUB_RES_REQ;
submitRequest.resReq = val;
} else if (!strcmp(name, "rlimit_cpu")) {
submitRequest.rLimits[LSF_RLIMIT_CPU] = atoi(val);
} else if (!strcmp(name, "rlimit_fsize")) {
submitRequest.rLimits[LSF_RLIMIT_FSIZE] = atoi(val);
} else if (!strcmp(name, "rlimit_data")) {
submitRequest.rLimits[LSF_RLIMIT_DATA] = atoi(val);
} else if (!strcmp(name, "rlimit_stack")) {
submitRequest.rLimits[LSF_RLIMIT_STACK] = atoi(val);
} else if (!strcmp(name, "rlimit_core")) {
submitRequest.rLimits[LSF_RLIMIT_CORE] = atoi(val);
} else if (!strcmp(name, "rlimit_rss")) {
submitRequest.rLimits[LSF_RLIMIT_RSS] = atoi(val);
} else if (!strcmp(name, "rlimit_nofile")) {
submitRequest.rLimits[LSF_RLIMIT_NOFILE] = atoi(val);
} else if (!strcmp(name, "rlimit_open_max")) {
submitRequest.rLimits[LSF_RLIMIT_OPEN_MAX] = atoi(val);
} else if (!strcmp(name, "rlimit_swap")) {
submitRequest.rLimits[LSF_RLIMIT_SWAP] = atoi(val);
} else if (!strcmp(name, "rlimit_run")) {
submitRequest.rLimits[LSF_RLIMIT_RUN] = atoi(val);
} else if (!strcmp(name, "rlimit_process")) {
submitRequest.rLimits[LSF_RLIMIT_PROCESS] = atoi(val);
} else if (!strcmp(name, "hostSpec")) {
submitRequest.options |= SUB_HOST_SPEC;
submitRequest.hostSpec = val;
} else if (!strcmp(name, "numProcessors")){
submitRequest.numProcessors = atoi(val);
} else if (!strcmp(name, "dependCond")){
submitRequest.options |= SUB_DEPEND_COND;
submitRequest.dependCond = val;
} else if (!strcmp(name, "beginTime")) {
submitRequest.beginTime = atoi(val);
} else if (!strcmp(name, "termTime")) {
submitRequest.termTime = atoi(val);
} else if (!strcmp(name, "sigValue")) {
submitRequest.options |= SUB_WINDOW_SIG;
submitRequest.sigValue= atoi(val);
} else if (!strcmp(name, "command")){
submitRequest.command = val;
} else if (!strcmp(name, "inFile")){
submitRequest.options |= SUB_IN_FILE;
submitRequest.inFile = val;
} else if (!strcmp(name, "outFile")){
submitRequest.options |= SUB_OUT_FILE;
submitRequest.outFile = val;
} else if (!strcmp(name, "errFile")){
submitRequest.options |= SUB_ERR_FILE;
submitRequest.errFile = val;
} else if (!strcmp(name, "chkpntPeriod")){
submitRequest.options |= SUB_CHKPNTABLE;
submitRequest.options |= SUB_CHKPNT_PERIOD;
submitRequest.chkpntPeriod = atoi(val);
} else if (!strcmp(name, "chkpntDir")){
submitRequest.options |= SUB_CHKPNTABLE;
submitRequest.options |= SUB_CHKPNT_DIR;
submitRequest.chkpntDir = val;
} else if (!strcmp(name, "xFile")){
/*not implemented*/
/* SUB_OTHER_FILES probably should be set */
/* submitRequest.nxf should be assigned */
} else if (!strcmp(name, "preExecCmd")){
submitRequest.options |= SUB_PRE_EXEC;
submitRequest.preExecCmd = val;
} else if (!strcmp(name, "mailUser")){
submitRequest.options |= SUB_MAIL_USER;
submitRequest.mailUser = val;
} else if (!strcmp(name, "delOptions")){
submitRequest.delOptions = atoi(val);
} else if (!strcmp(name, "projectName")){
submitRequest.options |= SUB_PROJECT_NAME;
submitRequest.projectName = val;
} else if (!strcmp(name, "maxNumProcessors")){
submitRequest.maxNumProcessors = atoi(val);
} else if (!strcmp(name, "loginShell")){
submitRequest.options |= SUB_LOGIN_SHELL;
submitRequest.loginShell = val; }
else if (!strcmp(name, "userGroup")){
submitRequest.options |= SUB_USER_GROUP;
submitRequest.loginShell = val;
} else if (!strcmp(name, "exceptList")){
submitRequest.exceptList = val;
} else if (!strcmp(name, "exclusive")){
submitRequest.options |= SUB_EXCLUSIVE;
} else if (!strcmp(name, "notifyBegin")){
submitRequest.options |= SUB_NOTIFY_BEGIN;
} else if (!strcmp(name, "notifyEnd")){
submitRequest.options |= SUB_NOTIFY_END;
} else if (!strcmp(name, "restart")){
submitRequest.options |= SUB_RESTART;
} else if (!strcmp(name, "restartForce")){
submitRequest.options |= SUB_RESTART_FORCE;
} else if (!strcmp(name, "rerunnable")){
submitRequest.options |= SUB_RERUNNABLE;
/*} else if (!strcmp(name, "chkpnt_copy")){
submitRequest.options |= SUB_CHKPNT_COPY;*/
/*} else if (!strcmp(name, "chkpnt_force")){
submitRequest.options |= SUB_CHKPNT_FORCE;*/
} else if (!strcmp(name, "interactive")){
submitRequest.options |= SUB_INTERACTIVE;
} else if (!strcmp(name, "pty")){
submitRequest.options |= SUB_PTY;
} else if (!strcmp(name, "pty_shell")){
submitRequest.options |= SUB_PTY_SHELL;
} else if (!strcmp(name, "hold")){
submitRequest.options2 |= SUB2_HOLD;
} else if (!strcmp(name, "wait")){
/* This will require forking */
/*submitRequest.options2 |= SUB2_BSUB_BLOCK;*/
} else if (!strcmp(name, "debug")){
/* is debug used anymore? */
if (val) debug = 1;
}
val = "";
}
jobId = lsb_submit(&submitRequest, &submitReply);
if (jobId == -1) {
Rprintf("lsf_job_submit: lsb_submit: %s\n", lsb_sysmsg());
return AsInt(0);
}
return AsInt(jobId);
}
