path: root/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch

diff -ru a/cluster_tools/jobsplitter/gjs.cc b/cluster_tools/jobsplitter/gjs.cc
--- a/cluster_tools/jobsplitter/gjs.cc	2020-03-25 04:30:34.000000000 -0500
+++ b/cluster_tools/jobsplitter/gjs.cc	2020-10-10 21:01:14.376770641 -0500
@@ -30,15 +30,18 @@
 	cout<<"  -a value alias             : use any alias"<<endl;
 	cout<<"  -numberofsplits, -n   n    : the number of job splits; default=1"<<endl;
 	cout<<"  -clusterplatform, -c  name : the cluster platform, name is one of the following:"<<endl;
-	cout<<"                               openmosix - condor - openPBS - slurm - xgrid"<<endl;
+	cout<<"                               openmosix - condor - openPBS - slurm - xgrid - SGE"<<endl;
 	cout<<"                               This executable is compiled with "<<GC_DEFAULT_PLATFORM<<" as default"<<endl<<endl;
-	cout<<"  -openPBSscript, os         : template for an openPBS script "<<endl;
+	cout<<"  -openPBSscript, os script  : template for an openPBS script "<<endl;
 	cout<<"                               see the example that comes with the source code (script/openPBS.script)"<<endl;
 	cout<<"                               overrules the environment variable below"<<endl<<endl; 
-	cout<<"  -slurmscript, ss           : template for a SLURM script "<<endl;
+	cout<<"  -slurmscript, ss script    : template for a SLURM script "<<endl;
 	cout<<"                               see the example that comes with the source code (script/slurm.script)"<<endl;
 	cout<<"                               overrules the environment variable below"<<endl<<endl; 
-	cout<<"  -condorscript, cs          : template for a condor submit file"<<endl;
+	cout<<"  -SGEscript, gs script      : template for a SGE script "<<endl;
+	cout<<"                               see the example that comes with the source code (script/SGE.script)"<<endl;
+	cout<<"                               overrules the environment variable below"<<endl<<endl; 
+	cout<<"  -condorscript, cs script   : template for a condor submit file"<<endl;
 	cout<<"                               see the example that comes with the source code (script/condor.script)"<<endl;
 	cout<<"  -v                         : verbosity 0 1 2 3 - 1 default "<<endl;
 	cout<<endl;
@@ -46,6 +49,10 @@
 	cout<<"  GC_DOT_GATE_DIR  : indicates the .Gate directory for splitted mac files"<<endl;
 	cout<<"  GC_GATE_EXE_DIR  : indicates the directory with the Gate executable"<<endl;
 	cout<<"  GC_PBS_SCRIPT : the openPBS template script (!optionnal variable!)"<<endl;
+	cout<<"  GC_SLURM_SCRIPT : the Slurm template script (!optionnal variable!)"<<endl;
+	cout<<"  GC_SGE_SCRIPT : the SGE template script (!optionnal variable!)"<<endl;
+	cout<<"  GC_CONDOR_SCRIPT : the condor template script (!optionnal variable!)"<<endl;
+	cout<<"  GC_SGE_QUEUE : the SGE queue to use, defaults to all.q if unset (!optional variable!)"<<endl;
 	cout<<endl;
 	cout<<"  Usage (bash):"<<endl;
 	cout<<"    export GC_DOT_GATE_DIR=/home/user/gatedir/"<<endl;
@@ -55,6 +62,9 @@
 	cout<<"    gjs -numberofsplits 10 -clusterplatform openmosix macro.mac"<<endl;
 	cout<<"    gjs -numberofsplits 10 -clusterplatform openmosix -a /somedir/rootfilename ROOT_FILE macro.mac"<<endl<<endl;
 	cout<<"    gjs -numberofsplits 10 -clusterplatform openPBS -openPBSscript /somedir/script macro.mac"<<endl<<endl;
+	cout<<"    gjs -numberofsplits 10 -clusterplatform slurm -slurmscript /somedir/script macro.mac"<<endl<<endl;
+	cout<<"    gjs -numberofsplits 10 -clusterplatform SGE -SGEscript /somedir/script macro.mac"<<endl<<endl;
+	cout<<"    gjs -numberofsplits 10 -clusterplatform condor -condorscript /somedir/script macro.mac"<<endl<<endl;
 	cout<<"    gjs -numberofsplits 10 -clusterplatform xgrid macro.mac"<<endl<<endl;
 	cout<<"    gjs -numberofsplits 10  /somedir/script macro.mac"<<endl<<endl;
 	exit(0);
@@ -67,6 +77,7 @@
 	G4String macfile;
 	G4String pbsscript;
 	G4String slurmscript;
+	G4String sgescript;
 	G4String condorscript;
 	G4int nSplits=0;
 	G4int nextArg = 1;
@@ -131,6 +142,12 @@
 			slurmscript=argv[nextArg+1];
 			if(debug)cout<<"found -slurmscript "<<slurmscript<<endl;
 		}  
+		if ((!strcmp(argv[nextArg],"-SGEscript") || !strcmp(argv[nextArg],"-gs")) && indicator==0)
+		{
+			indicator=1;
+			sgescript=argv[nextArg+1];
+			if(debug)cout<<"found -SGEscript "<<sgescript<<endl;
+		}  
 		if ((!strcmp(argv[nextArg],"-condorscript") || !strcmp(argv[nextArg],"-cs")) && indicator==0)
 		{
 			indicator=1;
@@ -168,7 +185,7 @@
 		}
 	} 
 	
-	if (platform=="" || platform=="openmosix" || platform=="openPBS" || platform=="slurm" || platform=="condor"|| platform=="xgrid")
+	if (platform=="" || platform=="openmosix" || platform=="openPBS" || platform=="slurm" || platform=="SGE" || platform=="condor"|| platform=="xgrid")
 	{  
 		if (platform=="")
 		{
@@ -180,6 +197,21 @@
 				pbsscript=getenv("GC_PBS_SCRIPT");
 				if(verb>1&&pbsscript!="")cout<<"Information : using $GC_PBS_SCRIPT="<<pbsscript<<" as default PBS template script"<<endl;
 			}}  
+		if (platform=="slurm"&&slurmscript==""){
+			if (getenv("GC_SLURM_SCRIPT")){
+				slurmscript=getenv("GC_SLURM_SCRIPT");
+				if(verb>1&&slurmscript!="")cout<<"Information : using $GC_SLURM_SCRIPT="<<slurmscript<<" as default slurm template script"<<endl;
+			}}  
+		if (platform=="SGE"&&sgescript==""){
+			if (getenv("GC_SGE_SCRIPT")){
+				sgescript=getenv("GC_SGE_SCRIPT");
+				if(verb>1&&sgescript!="")cout<<"Information : using $GC_SGE_SCRIPT="<<sgescript<<" as default SGE template script"<<endl;
+			}}  
+		if (platform=="condoe"&&condorscript==""){
+			if (getenv("GC_CONDOR_SCRIPT")){
+				condorscript=getenv("GC_CONDOR_SCRIPT");
+				if(verb>1&&condorscript!="")cout<<"Information : using $GC_CONDOR_SCRIPT="<<condorscript<<" as default condor template script"<<endl;
+			}}  
 		if (platform!="openPBS"&&pbsscript!="")
 		{
 			if(verb>0)cout<<"Warning : cluster platform is not openPBS, openPBSscript ignored!"<<endl;
@@ -189,7 +221,25 @@
 			cout<<"Error : cluster platform is openPBS but openPBSscript undefined!"<<endl;
 			exit(1);
 		}
-		if ((platform=="openPBS"&&pbsscript!="")||platform=="openmosix"||(platform=="condor"&&condorscript!=""))
+		if (platform!="slurm"&&slurmscript!="")
+		{
+			if(verb>0)cout<<"Warning : cluster platform is not slurm, slurmscript ignored!"<<endl;
+		}
+		if (platform=="slurm"&&slurmscript=="")
+		{
+			cout<<"Error : cluster platform is slurm but slurmscript undefined!"<<endl;
+			exit(1);
+		}
+		if (platform!="SGE"&&sgescript!="")
+		{
+			if(verb>0)cout<<"Warning : cluster platform is not SGE, sgescript ignored!"<<endl;
+		}
+		if (platform=="SGE"&&sgescript=="")
+		{
+			cout<<"Error : cluster platform is SGE but sgescript undefined!"<<endl;
+			exit(1);
+		}
+		if ((platform=="openPBS"&&pbsscript!="")||(platform=="slurm"&&slurmscript!="")||(platform=="SGE"&&sgescript!="")||platform=="openmosix"||(platform=="condor"&&condorscript!=""))
 		{
 			if(verb>1)cout<<"Information : using  "<<platform<<" as cluster platform!"<<endl;
 		}
@@ -216,7 +266,7 @@
 	}
 	//create a splitmanager to coordinate it all  
 	GateSplitManager* manager;
-	manager=new GateSplitManager(nAliases,aliases,platform,pbsscript,slurmscript,condorscript,macfile,nSplits,time);
+	manager=new GateSplitManager(nAliases,aliases,platform,pbsscript,slurmscript,sgescript,condorscript,macfile,nSplits,time);
 	manager->SetVerboseLevel(verb);
 	manager->StartSplitting();
 	
diff -ru a/cluster_tools/jobsplitter/include/GateSplitManager.hh b/cluster_tools/jobsplitter/include/GateSplitManager.hh
--- a/cluster_tools/jobsplitter/include/GateSplitManager.hh	2020-03-25 04:30:34.000000000 -0500
+++ b/cluster_tools/jobsplitter/include/GateSplitManager.hh	2020-10-10 21:02:25.136728953 -0500
@@ -21,7 +21,7 @@
 {
 public:
 
-  GateSplitManager(G4int nAliases,G4String* aliases,G4String platform,G4String pbsscript,G4String slurmscript,G4String condorscript,G4String macfile,G4int nSplits,G4int time);
+  GateSplitManager(G4int nAliases,G4String* aliases,G4String platform,G4String pbsscript,G4String slurmscript,G4String sgescript,G4String condorscript,G4String macfile,G4int nSplits,G4int time);
   ~GateSplitManager();
   void SetVerboseLevel(G4int value) { m_verboseLevel = value; };
   void StartSplitting();
diff -ru a/cluster_tools/jobsplitter/include/GateToPlatform.hh b/cluster_tools/jobsplitter/include/GateToPlatform.hh
--- a/cluster_tools/jobsplitter/include/GateToPlatform.hh	2020-03-25 04:30:34.000000000 -0500
+++ b/cluster_tools/jobsplitter/include/GateToPlatform.hh	2020-10-10 21:11:45.910390030 -0500
@@ -20,7 +20,7 @@
 {
 public:
   GateToPlatform();
-  GateToPlatform(G4int numberOfSplits, G4String thePlatform, G4String pbsscript,G4String slurmscript,G4String theCondorScript,G4String outputMacName,G4int time);
+  GateToPlatform(G4int numberOfSplits, G4String thePlatform, G4String pbsscript,G4String slurmscript,G4String sgescript,G4String theCondorScript,G4String outputMacName,G4int time);
   ~GateToPlatform();
   void SetVerboseLevel(G4int value) { m_verboseLevel = value; };
   int GenerateSubmitfile(G4String outputMacDir);
@@ -31,6 +31,8 @@
   int GenerateOpenPBSScriptfile();
   int GenerateSlurmSubmitfile();
   int GenerateSlurmScriptfile();
+  int GenerateSGESubmitfile();
+  int GenerateSGEScriptfile();
   int GenerateCondorSubmitfile();
   int GenerateXgridSubmitfile();    
   G4int m_verboseLevel;  
@@ -38,6 +40,7 @@
   G4String platform;
   G4String pbsScript;
   G4String slurmScript;
+  G4String sgeScript;
   G4String condorScript;
   G4String outputMacfilename;
   G4String outputDir;
Only in b/cluster_tools/jobsplitter/script: SGE.script
diff -ru a/cluster_tools/jobsplitter/src/GateSplitManager.cc b/cluster_tools/jobsplitter/src/GateSplitManager.cc
--- a/cluster_tools/jobsplitter/src/GateSplitManager.cc	2020-03-25 04:30:34.000000000 -0500
+++ b/cluster_tools/jobsplitter/src/GateSplitManager.cc	2020-10-10 21:15:14.371255628 -0500
@@ -17,9 +17,10 @@
 using std::endl;
 
 GateSplitManager::GateSplitManager(G4int nAliases,G4String* aliases,G4String platform,G4String pbsscript,
-                                   G4String slurmscript,G4String condorscript,G4String macfile,G4int nSplits,G4int time)
+                                   G4String slurmscript,G4String sgescript,G4String condorscript,
+				   G4String macfile,G4int nSplits,G4int time)
 {
- toPlatform = new GateToPlatform(nSplits,platform,pbsscript,slurmscript,condorscript,macfile,time);
+ toPlatform = new GateToPlatform(nSplits,platform,pbsscript,slurmscript,sgescript,condorscript,macfile,time);
  macParser  = new GateMacfileParser(macfile,nSplits,nAliases,aliases);
  numberOfSplits=nSplits;
 }
diff -ru a/cluster_tools/jobsplitter/src/GateToPlatform.cc b/cluster_tools/jobsplitter/src/GateToPlatform.cc
--- a/cluster_tools/jobsplitter/src/GateToPlatform.cc	2020-03-25 04:30:34.000000000 -0500
+++ b/cluster_tools/jobsplitter/src/GateToPlatform.cc	2020-10-10 22:04:46.108197968 -0500
@@ -25,12 +25,13 @@
 using std::ifstream;
 using std::ostringstream;
               
-GateToPlatform::GateToPlatform(G4int numberOfSplits, G4String thePlatform, G4String thePbsscript, G4String theSlurmScript, G4String theCondorScript, G4String outputMacName, G4int time)
+GateToPlatform::GateToPlatform(G4int numberOfSplits, G4String thePlatform, G4String thePbsScript, G4String theSlurmScript,  G4String theSgeScript,G4String theCondorScript, G4String outputMacName, G4int time)
 {
 	nSplits=numberOfSplits;
 	platform=thePlatform;
-	pbsScript=thePbsscript;
+	pbsScript=thePbsScript;
 	slurmScript=theSlurmScript;
+	sgeScript=theSgeScript;
 	condorScript=theCondorScript;
 	useTiming=time;
 	outputMacfilename=outputMacName.substr(0,outputMacName.length()-4);
@@ -60,6 +61,11 @@
 		err+=GenerateSlurmSubmitfile();
 		if (err>0) return 1;
 	}
+	if (platform=="SGE"){
+		err+=GenerateSGEScriptfile();
+		err+=GenerateSGESubmitfile();
+		if (err>0) return 1;
+	}
 	if (platform=="condor"){
 		err+=GenerateCondorSubmitfile();
 		if (err>0) return 1;
@@ -262,6 +268,111 @@
 	}
 	submitFile.close();
 	chmod( submitFilename.c_str() , S_IRWXU|S_IRGRP );
+	return 0;
+}
+
+int GateToPlatform::GenerateSGEScriptfile()
+{
+        G4String queue="";
+        if (!getenv("GC_SGE_QUEUE")) {
+                queue="all.q";
+        } else {
+                queue=getenv("GC_SGE_QUEUE");
+        }
+ 
+	G4String dir=getenv("GC_GATE_EXE_DIR");
+	if (dir.substr(dir.length()-1,dir.length())!="/") dir=dir+"/"; 
+	
+	//check if we have an existing directory
+	ifstream dirstream(dir.c_str());
+	if (!dirstream) { 
+		cout<<"Error : Failed to detect the Gate executable directory"<<endl;
+		cout<<"Please check your environment variables!"<<endl; 
+		cout<<"Generated submit file may be invalid..."<<endl;  
+		return 1;
+	}
+	dirstream.close();
+	
+	//create script file to be submitted with qsub (SGE)
+	
+	
+	char out_name[1000];
+	G4String buf;
+	for (G4int i=1;i<=nSplits;i++)
+	{
+		ostringstream cnt;
+		cnt<<i;
+		// open template script file
+		ifstream inFile(sgeScript);
+		if (!inFile) {
+			cout<< "Error : could not access SGE script template file! "<<sgeScript<< endl;
+			return(1);
+		}
+		sprintf(out_name,"%s%i%s",outputDir.c_str(),i,".sge");
+		ofstream scriptFile(out_name);
+		if (!scriptFile) {
+			cout<< "Error : could not create script file! "<<out_name<< endl;
+			return(1);
+		}
+		while(getline(inFile,buf)){
+			if(buf.find("#")!=0||buf.find("#$")==0){
+				unsigned int pos=buf.find("GC_WORKDIR");
+				if(pos<buf.length())  buf=buf.substr(0,pos)+outputDir.substr(0,outputDir.rfind("/"))+buf.substr(pos+10);
+                                pos=buf.find("GC_SGE_QUEUE");
+                                if(pos<buf.length())  buf=buf.substr(0,pos)+queue+buf.substr(pos+12);
+				pos=buf.find("GC_LOG");
+				if(pos<buf.length())  buf=buf.substr(0,pos)+"log"+cnt.str()+buf.substr(pos+6);
+				pos=buf.find("GC_ERR");
+				if(pos<buf.length())  buf=buf.substr(0,pos)+"err"+cnt.str()+buf.substr(pos+6);
+				pos=buf.find("GC_JOBNAME");
+				if(pos<buf.length())  {
+					//SGE max_jobname_length=512
+					char jobname[256]="";
+					strncpy(jobname,outputMacfilename.c_str(),255-cnt.str().length());
+					buf=buf.substr(0,pos)+jobname+cnt.str()+buf.substr(pos+10);
+				}
+				pos=buf.find("GC_GATE");
+				G4String timestr="";
+				if (useTiming==1) timestr="time ";
+				if(pos<buf.length())  buf=timestr+dir+"Gate "+outputDir+cnt.str()+".mac"+buf.substr(pos+7);
+			}
+			scriptFile<<buf<<endl;
+		}
+		scriptFile.close();
+		inFile.close();
+	}
+	return 0; 
+}
+
+int GateToPlatform::GenerateSGESubmitfile()
+{
+	G4String dir=getenv("GC_GATE_EXE_DIR");
+	if (dir.substr(dir.length()-1,dir.length())!="/") dir=dir+"/"; 
+	
+	//check if we have an existing director
+	ifstream dirstream(dir.c_str());
+	if (!dirstream) { 
+		cout<<"Error : Failed to detect the Gate executable directory"<<endl;
+		cout<<"Please check your environment variables!"<<endl; 
+		cout<<"Generated submit file may be invalid..."<<endl;  
+		return 1;
+	}
+	dirstream.close();
+	
+	G4String submitFilename=outputMacfilename+".submit";
+	ofstream submitFile(submitFilename.c_str());
+	if (!submitFile) {
+		cout<< "Error : could not create submit file! "<<submitFilename<< endl;
+		return(1);
+	}
+	submitFile<<"#! /bin/sh"<<endl;
+	for (G4int i=1;i<=nSplits;i++)
+	{
+		submitFile<<"echo qsub "<<outputDir<<i<<+".sge"<<endl;
+		submitFile<<"qsub "<<outputDir<<i<<+".sge"<<endl;
+	}
+	submitFile.close();
+	chmod( submitFilename.c_str() , S_IRWXU|S_IRGRP );
 	return 0;
 }