From 95b9875e959f838752f500aa89329c9241bc6c7c Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Mon, 19 Oct 2020 16:07:47 -0500
Subject: New package - Gate (#19377)

* New package - Gate

This PR adds the Gate package as well as the ITK dependency.

* Fix flake 8 errors

* Be more explicit with CMake options

Make sure Cmake values related to variants are explicitly set to either
ON/OFF.

The ITK_USE_MKL flag will turn on the following:
- USE_FFTWD=ON
- USE_FFTWF=ON
- USE_SYSTEM_FFTW=ON

Since the package depends on fftw-api, those options will always be set.
---
 .../gate/cluster_tools_filemerger_Makefile.patch   |  16 +
 .../gate/cluster_tools_jobsplitter_Makefile.patch  |  33 ++
 .../gate/cluster_tools_jobsplitter_platform.patch  | 336 +++++++++++++++++++++
 var/spack/repos/builtin/packages/gate/package.py   |  87 ++++++
 var/spack/repos/builtin/packages/itk/package.py    |  84 ++++++
 5 files changed, 556 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gate/cluster_tools_filemerger_Makefile.patch
 create mode 100644 var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_Makefile.patch
 create mode 100644 var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch
 create mode 100644 var/spack/repos/builtin/packages/gate/package.py
 create mode 100644 var/spack/repos/builtin/packages/itk/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/gate/cluster_tools_filemerger_Makefile.patch b/var/spack/repos/builtin/packages/gate/cluster_tools_filemerger_Makefile.patch
new file mode 100644
index 0000000000..8fc491f21d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gate/cluster_tools_filemerger_Makefile.patch
@@ -0,0 +1,16 @@
+Common subdirectories: a/cluster_tools/filemerger/include and b/cluster_tools/filemerger/include
+diff -u a/cluster_tools/filemerger/Makefile b/cluster_tools/filemerger/Makefile
+--- a/cluster_tools/filemerger/Makefile	2020-03-25 04:30:34.000000000 -0500
++++ b/cluster_tools/filemerger/Makefile	2020-10-10 14:52:07.181712970 -0500
+@@ -49,8 +49,8 @@
+ 
+ install:
+ 	@echo Installing ...
+-	@$(CP) $(TARGET) /usr/local/bin
++	@$(CP) $(TARGET) $(PREFIX)/bin
+ 
+ uninstall:
+ 	@echo Uninstalling...
+-	@$(RM) /usr/local/bin/$(TARGET)
++	@$(RM) $(PREFIX)/bin/$(TARGET)
+Common subdirectories: a/cluster_tools/filemerger/src and b/cluster_tools/filemerger/src
diff --git a/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_Makefile.patch b/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_Makefile.patch
new file mode 100644
index 0000000000..291b3a9d03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_Makefile.patch
@@ -0,0 +1,33 @@
+--- a/cluster_tools/jobsplitter/Makefile	2020-03-25 04:30:34.000000000 -0500
++++ b/cluster_tools/jobsplitter/Makefile	2020-10-10 15:08:33.435073993 -0500
+@@ -4,6 +4,10 @@
+ CP := cp
+ RM := rm -rf
+ 
++ifndef GC_DEFAULT_PLATFORM
++$(error GC_DEFAULT_PLATFORM must be set)
++endif
++
+ MAINSOURCES := $(wildcard *.cc)
+ SOURCES := $(wildcard ./src/*.cc)
+ MAINOBJECTS := $(patsubst %.cc, tmp/%.o, $(notdir $(MAINSOURCES)))
+@@ -12,7 +16,7 @@
+ vpath %.hh ./include
+ vpath %.cc ./src
+ 
+-CXXFLAGS := -DGC_DEFAULT_PLATFORM=\"condor\"
++CXXFLAGS := -DGC_DEFAULT_PLATFORM=\"$(GC_DEFAULT_PLATFORM)\"
+ INCLUDE := -I./include `geant4-config --cflags`
+ LDFLAGS := `geant4-config --libs`
+ 
+@@ -57,8 +61,8 @@
+ 
+ install:
+ 	@echo Installing ...
+-	@$(CP) $(TARGET) /usr/local/bin
++	@$(CP) $(TARGET) $(PREFIX)/bin
+ 
+ uninstall:
+ 	@echo Uninstalling...
+-	@$(RM) /usr/local/bin/$(TARGET)
++	@$(RM) $(PREFIX)/bin/$(TARGET)
diff --git a/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch b/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch
new file mode 100644
index 0000000000..3662fdfeee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch
@@ -0,0 +1,336 @@
+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;
+ }
+ 
diff --git a/var/spack/repos/builtin/packages/gate/package.py b/var/spack/repos/builtin/packages/gate/package.py
new file mode 100644
index 0000000000..741d472f80
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gate/package.py
@@ -0,0 +1,87 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gate(CMakePackage):
+    """Simulations of Preclinical and Clinical Scans in Emission Tomography,
+    Transmission Tomography and Radiation Therapy
+
+    GATE is an advanced opensource software developed by the international
+    OpenGATE collaboration and dedicated to numerical simulations in medical
+    imaging and radiotherapy. It currently supports simulations of Emission
+    Tomography (Positron Emission Tomography - PET and Single Photon Emission
+    Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging
+    (Bioluminescence and Fluorescence) and Radiotherapy experiments. Using an
+    easy-to-learn macro mechanism to configurate simple or highly sophisticated
+    experimental settings, GATE now plays a key role in the design of new
+    medical imaging devices, in the optimization of acquisition protocols and
+    in the development and assessment of image reconstruction algorithms and
+    correction techniques. It can also be used for dose calculation in
+    radiotherapy experiments."""
+
+    homepage = "http://opengatecollaboration.org/"
+    url      = "https://github.com/OpenGATE/Gate/archive/v9.0.tar.gz"
+
+    maintainers = ['glennpj']
+
+    version('9.0', sha256='8354f392facc0b7ae2ddf0eed61cc43136195b198ba399df25e874886b8b69cb')
+
+    variant('rtk', default=False,
+            description='build support for the Reconstruction Toolkit')
+    variant('default_platform', default='condor',
+            description='select default platform for the cluster tools',
+            values=('SGE', 'condor', 'openPBS', 'openmosix', 'slurm', 'xgrid'),
+            multi=False)
+
+    depends_on('geant4~threads')  # Gate needs a non-threaded geant4
+    depends_on('root')
+    depends_on('itk+rtk', when='+rtk')
+
+    patch('cluster_tools_filemerger_Makefile.patch')
+    patch('cluster_tools_jobsplitter_Makefile.patch')
+    patch('cluster_tools_jobsplitter_platform.patch')
+
+    def cmake_args(self):
+        args = []
+
+        if '+rtk' in self.spec:
+            args.append('-DGATE_USE_RTK=ON')
+        else:
+            args.append('-DGATE_USE_RTK=OFF')
+
+        return args
+
+    def setup_build_environment(self, env):
+        gc_default_platform = self.spec.variants['default_platform'].value
+        env.set('GC_DEFAULT_PLATFORM', gc_default_platform)
+
+    def setup_run_environment(self, env):
+        env.set('GC_GATE_EXE_DIR', self.prefix.bin)
+        env.set('GC_CONDOR_SCRIPT', join_path(self.prefix, 'share',
+                                              'jobsplitter', 'condor.script'))
+        env.set('GC_PBS_SCRIPT', join_path(self.prefix, 'share',
+                                           'jobsplitter', 'openPBS.script'))
+        env.set('GC_SGE_SCRIPT', join_path(self.prefix, 'share',
+                                           'jobsplitter', 'SGE.script'))
+        env.set('GC_SLURM_SCRIPT', join_path(self.prefix, 'share',
+                                             'jobsplitter', 'slurm.script'))
+
+    @run_after('install')
+    def cluster_tools(self):
+        with working_dir('cluster_tools/filemerger'):
+            make()
+            make('install', 'PREFIX={0}'.format(self.prefix))
+
+        with working_dir('cluster_tools/jobsplitter'):
+            make()
+            make('install', 'PREFIX={0}'.format(self.prefix))
+
+        script_path = join_path(self.prefix, 'share', 'jobsplitter')
+        mkdirp(script_path)
+        install_tree('cluster_tools/jobsplitter/script', script_path)
+        install('*.xml', self.prefix.share)
+        install('*.db', self.prefix.share)
diff --git a/var/spack/repos/builtin/packages/itk/package.py b/var/spack/repos/builtin/packages/itk/package.py
new file mode 100644
index 0000000000..ef0f129318
--- /dev/null
+++ b/var/spack/repos/builtin/packages/itk/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Itk(CMakePackage):
+    """The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for
+    N-dimensional scientific image processing, segmentation, and registration.
+
+    The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for
+    N-dimensional scientific image processing, segmentation, and registration.
+    Segmentation is the process of identifying and classifying data found in a
+    digitally sampled representation. Typically the sampled representation is
+    an image acquired from such medical instrumentation as CT or MRI scanners.
+    Registration is the task of aligning or developing correspondences between
+    data. For example, in the medical environment, a CT scan may be aligned
+    with a MRI scan in order to combine the information contained in both."""
+
+    homepage = "https://itk.org/"
+    url      = "https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.1/InsightToolkit-5.1.1.tar.gz"
+
+    maintainers = ['glennpj']
+
+    version('5.1.1', sha256='39e2a63840054361b728878a35b21bbe38374682ffb4b5c4f8f8f7514dedb58e')
+
+    variant('review', default=False, description='enable modules under review')
+    variant('rtk', default=False,
+            description='build the RTK (Reconstruction Toolkit module')
+
+    # TODO: This will not work if the resource is pulled from a spack mirror.
+    # The build process will checkout the appropriate commit but it needs to be
+    # a git repository. The copy pulled from the mirror is not a git
+    # repository.
+    # NOTE: This problem is reflected in issues #8746 and #14344 and PR #9436.
+    # resource(
+    #     name='RTK',
+    #     git='https://github.com/SimonRit/RTK.git',
+    #     get_full_repo=True,
+    #     destination='Modules/Remote',
+    #     when='+rtk',
+    # )
+
+    depends_on('git', type='build')
+    depends_on('perl', type='build')
+
+    depends_on('eigen')
+    depends_on('expat')
+    depends_on('fftw-api')
+    depends_on('googletest')
+    depends_on('hdf5+cxx')
+    depends_on('jpeg')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('zlib')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_SHARED_LIBS=ON',
+            '-DITK_USE_SYSTEM_LIBRARIES=ON',
+        ]
+
+        if '+review' in self.spec:
+            args.append('-DModule_ITKReview=ON')
+        else:
+            args.append('-DModule_ITKReview=OFF')
+        if '+rtk' in self.spec:
+            args.append('-DModule_RTK=ON')
+        else:
+            args.append('-DModule_RTK=OFF')
+
+        if '^mkl' in self.spec:
+            args.append('-DITK_USE_MKL=ON')
+        else:
+            args.extend([
+                '-DITK_USE_MKL=OFF',
+                '-DUSE_FFTWD=ON',
+                '-DUSE_FFTWF=ON',
+                '-DUSE_SYSTEM_FFTW=ON',
+            ])
+
+        return args
-- 
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