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New package - Gate (#19377)

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* 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.
This commit is contained in:
Glenn Johnson 2020-10-19 16:07:47 -05:00 committed by GitHub
parent 152144f17a
commit 95b9875e95
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 556 additions and 0 deletions
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16
var/spack/repos/builtin/packages/gate/cluster_tools_filemerger_Makefile.patch Normal file
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@ -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

33
var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_Makefile.patch Normal file
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@ -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)

336
var/spack/repos/builtin/packages/gate/cluster_tools_jobsplitter_platform.patch Normal file
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@ -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;
}

87
var/spack/repos/builtin/packages/gate/package.py Normal file
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@ -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)

84
var/spack/repos/builtin/packages/itk/package.py Normal file
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@ -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