/**
* \brief Function to submit SGE job
* \param scriptPath the path to the script containing the job characteristique
* \param options the options to submit job
* \param jobSteps The list of job steps
* \param envp The list of environment variables used by SGE submission function
* \return raises an exception on error
*/
int
SGEServer::submit(const std::string& scriptPath,
const TMS_Data::SubmitOptions& options,
TMS_Data::ListJobs& jobSteps,
char** envp) {
drmaa_job_template_t *jt = NULL;
char diagnosis[DRMAA_ERROR_STRING_BUFFER];
int drmaa_errno;
int retries = 0;
int VISHNU_MAX_RETRIES = 5;
char jobid[100];
char jobOutputPath[256] ;
char jobErrorPath[256];
char jobName[256];
char Directory[256];
bool isjobname = false;
std::string jobDIRECTORY;
boost::filesystem::path myPath(scriptPath.c_str());
string Walltime;
drmaa_errno = drmaa_init(NULL, diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!= DRMAA_ERRNO_SUCCESS
&& drmaa_errno != DRMAA_ERRNO_ALREADY_ACTIVE_SESSION) {
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
drmaa_errno = drmaa_allocate_job_template(&jt, diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS) {
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
std::string scriptContent = vishnu::get_file_content(scriptPath.c_str());
std::istringstream iss(scriptContent);
std::string line;
std::string scriptoption;
std::vector<std::string> cmdsOptions;
std::string value;
while(!iss.eof()) {
getline(iss, line);
size_t pos = line.find('#');
if(pos==string::npos) {
continue;
}
line = line.erase(0, pos);
if(boost::algorithm::starts_with(line, "#$")){
line = line.substr(std::string("#$").size());
pos = line.find("-N");
if(pos!=std::string::npos){
value = line.substr(pos+3);
drmaa_errno = drmaa_set_attribute(jt,DRMAA_JOB_NAME,value.c_str(),
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
} else {
pos = line.find("-o");
if(pos!=std::string::npos){
if(boost::algorithm::contains(line, ":")){
value = line.substr(pos+3);
boost::algorithm::trim(value);
} else{
std::string stemp =line.substr(pos+3);
boost::algorithm::trim(stemp);
value = ":"+stemp;
}
drmaa_errno = drmaa_set_attribute(jt,DRMAA_OUTPUT_PATH,value.c_str(),
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
} else {
pos = line.find("-e");
if(pos!=std::string::npos){
if(boost::algorithm::contains(line, ":")){
value = line.substr(pos+3);
boost::algorithm::trim(value);
} else{
std::string stemp = line.substr(pos+3);
boost::algorithm::trim(stemp);
value = ":"+stemp;
}
drmaa_errno = drmaa_set_attribute(jt,DRMAA_ERROR_PATH,value.c_str(),
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
} else{
scriptoption.append(line);
}
}
}
}
}
drmaa_errno = drmaa_set_attribute(jt, DRMAA_REMOTE_COMMAND, scriptPath.c_str() ,
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
replaceEnvVariables(scriptPath.c_str());
processOptions(scriptPath.c_str(),options,cmdsOptions,jt);
TMS_Data::Job_ptr jobPtr = new TMS_Data::Job();
for(int i=0; i < cmdsOptions.size(); i++) {
scriptoption += const_cast<char*>(cmdsOptions[i].c_str());
if (boost::algorithm::starts_with(cmdsOptions[i], "s_rt")){
Walltime = cmdsOptions[i].substr(5);
jobPtr->setWallClockLimit(vishnu::convertStringToWallTime(Walltime));
}
}
scriptoption += " -b no ";
drmaa_errno = drmaa_set_attribute(jt, DRMAA_NATIVE_SPECIFICATION,
scriptoption.c_str(),diagnosis,
sizeof(diagnosis)-1);
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
//To submit the job
while ((drmaa_errno=drmaa_run_job(jobid, sizeof(jobid)-1, jt, diagnosis,
sizeof(diagnosis)-1)) == DRMAA_ERRNO_DRM_COMMUNICATION_FAILURE) {
retries++;
if(retries == VISHNU_MAX_RETRIES){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
"SGE ERROR: Submit retries over");
}
sleep(1);
}
if (drmaa_errno!=DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
std::string jobidstring(jobid);
int size=256;
drmaa_errno = drmaa_get_attribute(jt,DRMAA_JOB_NAME,jobName,size,diagnosis,
sizeof(diagnosis)-1);
if (drmaa_errno==DRMAA_ERRNO_SUCCESS){
jobPtr->setJobName(jobName);
isjobname = true;
}
drmaa_errno = drmaa_get_attribute(jt,DRMAA_WD,Directory, size,diagnosis,
sizeof(diagnosis)-1);
if (drmaa_errno==DRMAA_ERRNO_SUCCESS){
jobDIRECTORY = Directory;
} else{
jobDIRECTORY = getenv("HOME");
}
jobPtr->setJobWorkingDir(jobDIRECTORY);
drmaa_errno = drmaa_get_attribute(jt,DRMAA_ERROR_PATH,jobErrorPath, size,
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno==DRMAA_ERRNO_SUCCESS){
std::string jobErrorPathStr = jobErrorPath;
vishnu::replaceAllOccurences(jobErrorPathStr,"$JOB_ID",jobid);
if(boost::algorithm::contains(jobErrorPathStr, "$")){
drmaa_exit(NULL, 0);
throw UserException(ERRCODE_INVALID_PARAM,
"Conflict: You can't use another environment variable than $JOB_ID.\n");
}
size_t pos = jobErrorPathStr.find_last_of(':');
if((pos!=string::npos)&& (pos!=0)){
std::string part1 = jobErrorPathStr.substr(0,pos+1);
std::string part2 = jobErrorPathStr.substr(pos+1);
if(!boost::algorithm::starts_with(part2, "/")){
jobErrorPathStr = part1+jobDIRECTORY+"/"+part2;
}
}else if (pos==0){
jobErrorPathStr = jobErrorPathStr.substr(1);
if(!boost::algorithm::starts_with(jobErrorPathStr, "/")){
jobErrorPathStr = jobDIRECTORY +"/"+jobErrorPathStr;
}
} else if(pos==string::npos){
if(!boost::algorithm::starts_with(jobErrorPathStr, "/")){
jobErrorPathStr = jobDIRECTORY +"/"+jobErrorPathStr;
}
}
jobPtr->setErrorPath(jobErrorPathStr);
} else{
if(isjobname){
std::string jobErrorFile(jobDIRECTORY+"/"+jobPtr->getJobName()+".e"+jobidstring);//default path
jobPtr->setErrorPath(jobErrorFile);
}else{
std::string jobErrorFile(jobDIRECTORY+"/"+myPath.filename().c_str()+".e"+jobidstring);//default path
jobPtr->setErrorPath(jobErrorFile);
}
}
drmaa_errno = drmaa_get_attribute(jt,DRMAA_OUTPUT_PATH,jobOutputPath, size,
diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno==DRMAA_ERRNO_SUCCESS){
std::string jobOutputPathStr = jobOutputPath;
vishnu::replaceAllOccurences(jobOutputPathStr,"$JOB_ID",jobid);
if(boost::algorithm::contains(jobOutputPathStr, "$")){
drmaa_exit(NULL, 0);
throw UserException(ERRCODE_INVALID_PARAM,
"Conflict: You can't use another environment variable than $JOB_ID.\n");
}
size_t pos = jobOutputPathStr.find_last_of(':');
if((pos!=string::npos)&&(pos!=0)){
std::string part1 = jobOutputPathStr.substr(0,pos+1);
std::string part2 = jobOutputPathStr.substr(pos+1);
if (! boost::algorithm::starts_with(part2, "/")){
jobOutputPathStr = boost::str(boost::format("%1%%2%/%3%") % part1 % jobDIRECTORY % part2);
}
} else if (pos==0){
jobOutputPathStr = jobOutputPathStr.substr(1);
if(!boost::algorithm::starts_with(jobOutputPathStr, "/")){
jobOutputPathStr = boost::str(boost::format("%1%/%2%") % jobDIRECTORY % jobOutputPathStr);
}
} else if(pos==string::npos){
if (!boost::algorithm::starts_with(jobOutputPathStr, "/")) {
jobOutputPathStr = boost::str(boost::format("%1%/%2%") % jobDIRECTORY % jobOutputPathStr);
}
}
jobPtr->setOutputPath(jobOutputPathStr);
} else{
if(isjobname){
jobPtr->setOutputPath( boost::str(boost::format("%1%/%2%.o%3%")
% jobDIRECTORY
% jobPtr->getJobName()
% jobidstring) );
} else {
jobPtr->setOutputPath( boost::str(boost::format("%1%/%2%.o%3%")
% jobDIRECTORY
% myPath.filename().string()
% jobidstring) );
}
}
jobPtr->setStatus(getJobState(jobid));
jobPtr->setBatchJobId(jobid);
drmaa_errno = drmaa_delete_job_template(jt, diagnosis, sizeof(diagnosis)-1);
if (drmaa_errno != DRMAA_ERRNO_SUCCESS){
drmaa_exit(NULL, 0);
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR,
boost::str(boost::format("SGE ERROR: %1%") % diagnosis));
}
drmaa_exit(NULL, 0);
jobSteps.getJobs().push_back(jobPtr);
return 0;
}
int
PosixServer::submit(const std::string& scriptPath,
const TMS_Data::SubmitOptions& options,
TMS_Data::ListJobs& jobSteps,
char** envp){
int ret;
struct trameJob resultat;
struct trameSubmit op;
std::string errorMsg;
std::string strRet;
memset(&op, 0, sizeof(op));
strncpy(op.name, options.getName().c_str(), sizeof(op.name)-1);
op.walltime = options.getWallTime();
strncpy(op.outPutPath, options.getOutputPath().c_str(), sizeof(op.outPutPath)-1);
strncpy(op.errorPath, options.getErrorPath().c_str(), sizeof(op.errorPath)-1);
strncpy(op.workDir, options.getWorkingDir().c_str(), sizeof(op.workDir)-1);
switch(fork()) {
case -1:
return -1;
case 0:
launchDaemon();
exit(0);
break;
default:
sleep(3); // TODO : fix, sleep because need synchronisation and can't wait child that has become a daemon
break;
}
TMS_Data::Job_ptr jobPtr = new TMS_Data::Job();
jobPtr->setStatus(vishnu::STATE_RUNNING);
jobPtr->setQueue("posix");
// If no name give a default job name
if (options.getName().empty()){
jobPtr->setName("posix_job");
} else {
jobPtr->setName(options.getName());
}
strncpy(op.jobName, jobPtr->getName().c_str(), sizeof(op.jobName)-1);
ret = reqSubmit(scriptPath, &resultat, &op);
if (ret == 0) {
jobPtr->setOutputPath(std::string(resultat.outPutPath));
jobPtr->setBatchJobId(std::string(resultat.jobId));
jobPtr->setErrorPath(std::string(resultat.errorPath));
jobPtr->setWallClockLimit(resultat.maxTime);
jobSteps.getJobs().push_back(jobPtr);
}
else {
strRet = boost::lexical_cast<std::string>(ret);
errorMsg = "Error submiting job error : " + strRet + " ernno :" + std::string(strerror(errno));
throw TMSVishnuException(ERRCODE_BATCH_SCHEDULER_ERROR, "POSIX ERROR: "+errorMsg);
}
return ret;
}