/*
* BatchManager_ePBS.cxx : emulation of PBS client
*
- * Auteur : Bernard SECHER - CEA DEN
+ * Auteur : Bernard SECHER - CEA DEN, André RIBES - EDF R&D
* Mail : mailto:bernard.secher@cea.fr
* Date : Thu Apr 24 10:17:22 2008
* Projet : PAL Salome
#include <sstream>
#include <sys/stat.h>
+#include <stdlib.h>
+#include <string.h>
#include <Batch_config.h>
#ifdef MSVC
namespace Batch {
BatchManager_ePBS::BatchManager_ePBS(const FactBatchManager * parent, const char * host,
- CommunicationProtocolType protocolType, const char * mpiImpl)
- : BatchManager_eClient(parent, host, protocolType, mpiImpl)
+ CommunicationProtocolType protocolType, const char * mpiImpl,
+ int nb_proc_per_node)
+ : BatchManager_eClient(parent, host, protocolType, mpiImpl),
+ BatchManager(parent, host)
{
// Nothing to do
+ _nb_proc_per_node = nb_proc_per_node;
}
// Destructeur
{
int status;
Parametre params = job.getParametre();
- const std::string dirForTmpFiles = params[TMPDIR];
+ const std::string workDir = params[WORKDIR];
const string fileToExecute = params[EXECUTABLE];
string::size_type p1 = fileToExecute.find_last_of("/");
string::size_type p2 = fileToExecute.find_last_of(".");
string logFile = generateTemporaryFileName("PBS-submitlog");
// define command to submit batch
- string subCommand = string("cd ") + dirForTmpFiles + "; qsub " +
- fileNameToExecute + "_Batch.sh";
+ string subCommand = string("cd ") + workDir + "; qsub " + fileNameToExecute + "_Batch.sh";
string command = _protocol.getExecCommand(subCommand, _hostname, _username);
command += " > ";
command += logFile;
+ command += " 2>&1";
cerr << command.c_str() << endl;
status = system(command.c_str());
if(status)
- throw EmulationException("Error of connection on remote host");
+ {
+ ifstream error_message(logFile.c_str());
+ std::string mess;
+ std::string temp;
+ while(std::getline(error_message, temp))
+ mess += temp;
+ error_message.close();
+ throw EmulationException("Error of connection on remote host, error was: " + mess);
+ }
// read id of submitted job in log file
ifstream idfile(logFile.c_str());
void BatchManager_ePBS::buildBatchScript(const Job & job)
{
+ std::cerr << "BuildBatchScript" << std::endl;
Parametre params = job.getParametre();
Environnement env = job.getEnvironnement();
- const long nbproc = params[NBPROC];
- const long edt = params[MAXWALLTIME];
- const long mem = params[MAXRAMSIZE];
- const string workDir = params[WORKDIR];
- const std::string dirForTmpFiles = params[TMPDIR];
- const string fileToExecute = params[EXECUTABLE];
- const string home = params[HOMEDIR];
- const std::string queue = params[QUEUE];
- std::string rootNameToExecute;
- std::string fileNameToExecute;
- std::string filelogtemp;
- if( fileToExecute.size() > 0 ){
- string::size_type p1 = fileToExecute.find_last_of("/");
- string::size_type p2 = fileToExecute.find_last_of(".");
- rootNameToExecute = fileToExecute.substr(p1+1,p2-p1-1);
-
-#ifdef MSVC
- char fname[_MAX_FNAME];
- char ext[_MAX_EXT];
- _splitpath_s(fileToExecute.c_str(), NULL, 0, NULL, 0, fname, _MAX_FNAME, ext, _MAX_EXT);
- string execBaseName = string(fname) + ext;
-#else
- char* basec=strdup(fileToExecute.c_str());
- string execBaseName = string(basename(basec));
- free(basec);
-#endif
- fileNameToExecute = "~/" + dirForTmpFiles + "/" + execBaseName;
+ // Job Parameters
+ string workDir = "";
+ string fileToExecute = "";
+ int nbproc = 0;
+ int edt = 0;
+ int mem = 0;
+ string queue = "";
+
+ // Mandatory parameters
+ if (params.find(WORKDIR) != params.end())
+ workDir = params[WORKDIR].str();
+ else
+ throw EmulationException("params[WORKDIR] is not defined ! Please defined it, cannot submit this job");
+ if (params.find(EXECUTABLE) != params.end())
+ fileToExecute = params[EXECUTABLE].str();
+ else
+ throw EmulationException("params[EXECUTABLE] is not defined ! Please defined it, cannot submit this job");
+
+ // Optional parameters
+ if (params.find(NBPROC) != params.end())
+ nbproc = params[NBPROC];
+ if (params.find(MAXWALLTIME) != params.end())
+ edt = params[MAXWALLTIME];
+ if (params.find(MAXRAMSIZE) != params.end())
+ mem = params[MAXRAMSIZE];
+ if (params.find(QUEUE) != params.end())
+ queue = params[QUEUE].str();
- int idx = dirForTmpFiles.find("Batch/");
- filelogtemp = dirForTmpFiles.substr(idx+6, dirForTmpFiles.length());
- }
- else{
- rootNameToExecute = "command";
- }
+ string::size_type p1 = fileToExecute.find_last_of("/");
+ string::size_type p2 = fileToExecute.find_last_of(".");
+ string rootNameToExecute = fileToExecute.substr(p1+1,p2-p1-1);
+ string fileNameToExecute = fileToExecute.substr(p1+1);
+ // Create batch submit file
ofstream tempOutputFile;
std::string TmpFileName = createAndOpenTemporaryFile("PBS-script", tempOutputFile);
tempOutputFile << "#! /bin/sh -f" << endl;
+ if (nbproc > 0)
+ {
+ // Division - arrondi supérieur
+ int nodes_requested = (nbproc + _nb_proc_per_node -1) / _nb_proc_per_node;
+ tempOutputFile << "#PBS -l nodes=" << nodes_requested << ":ppn=" << _nb_proc_per_node << endl;
+ }
if (queue != "")
- tempOutputFile << "#BSUB -q " << queue << endl;
+ tempOutputFile << "#PBS -q " << queue << endl;
if( edt > 0 )
- tempOutputFile << "#PBS -l walltime=" << edt*60 << endl ;
+ tempOutputFile << "#PBS -l walltime=" << edt*60 << endl;
if( mem > 0 )
- tempOutputFile << "#PBS -l mem=" << mem << "mb" << endl ;
- if( fileToExecute.size() > 0 ){
- tempOutputFile << "#PBS -o " << home << "/" << dirForTmpFiles << "/output.log." << filelogtemp << endl ;
- tempOutputFile << "#PBS -e " << home << "/" << dirForTmpFiles << "/error.log." << filelogtemp << endl ;
- }
- else{
- tempOutputFile << "#PBS -o " << dirForTmpFiles << "/" << env["LOGFILE"] << ".output.log" << endl ;
- tempOutputFile << "#PBS -e " << dirForTmpFiles << "/" << env["LOGFILE"] << ".error.log" << endl ;
- }
- if( workDir.size() > 0 )
- tempOutputFile << "cd " << workDir << endl ;
- if( fileToExecute.size() > 0 ){
- tempOutputFile << _mpiImpl->boot("${PBS_NODEFILE}",nbproc);
- tempOutputFile << _mpiImpl->run("${PBS_NODEFILE}",nbproc,fileNameToExecute);
- tempOutputFile << _mpiImpl->halt();
- }
- else{
- tempOutputFile << "source " << env["SOURCEFILE"] << endl ;
- tempOutputFile << env["COMMAND"];
+ tempOutputFile << "#PBS -l mem=" << mem << "kb" << endl;
+ tempOutputFile << "#PBS -o " << workDir << "/logs/output.log." << rootNameToExecute << endl;
+ tempOutputFile << "#PBS -e " << workDir << "/logs/error.log." << rootNameToExecute << endl;
+
+ // Define environment for the job
+ if (!env.empty()) {
+ tempOutputFile << "#PBS -v ";
+ Environnement::const_iterator iter;
+ for (iter = env.begin() ; iter != env.end() ; ++iter) {
+ tempOutputFile << iter->first << "=" << iter->second << ",";
+ }
+ tempOutputFile << endl;
}
+ // Abstraction of PBS_NODEFILE - TODO
+ tempOutputFile << "export LIBBATCH_NODEFILE=$PBS_NODEFILE" << endl;
+
+ // Launch the executable
+ tempOutputFile << "cd " << workDir << endl;
+ tempOutputFile << "./" + fileNameToExecute << endl;
tempOutputFile.flush();
tempOutputFile.close();
-#ifdef WIN32
- _chmod(
-#else
- chmod(
-#endif
- TmpFileName.c_str(), 0x1ED);
- cerr << TmpFileName.c_str() << endl;
+
+ BATCH_CHMOD(TmpFileName.c_str(), 0x1ED);
+ cerr << "Batch script file generated is: " << TmpFileName.c_str() << endl;
int status = _protocol.copyFile(TmpFileName, "", "",
- dirForTmpFiles + "/" + rootNameToExecute + "_Batch.sh",
+ workDir + "/" + rootNameToExecute + "_Batch.sh",
_hostname, _username);
if (status)
- throw EmulationException("Error of connection on remote host");
-
- remove(TmpFileName.c_str());
+ throw EmulationException("Error of connection on remote host, cannot copy batch submission file");
}
-
}
