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setup.py
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"""
Module to build install the azorange package.
Specific versions of dependencies are needed, eg gcc.
"""
import commands
import os
from optparse import OptionParser
import string
import sys
import traceback
import types
# Needed for modules to be loaded.
def module(command, *arguments):
#status = commands.getstatusoutput('%s/bin/modulecmd python %s %s' % (os.environ['MODULESHOME'], command, string.join(arguments)))
#print status
commands = os.popen('%s/bin/modulecmd python %s %s' % (os.environ['MODULESHOME'], command, string.join(arguments))).read()
exec commands
def checkStatus(status, output, message,check=True):
if status != 0:
print output
print "\n\n++++++++++++++++++\n\n\n", message
if check == True:
sys.exit(1)
else:
print "Above Error ignored."
def syncCPATHandINCLUDE_DIR():
""" This function should be called every time a change is made in CPATH or in INCLUDE_DIR"""
CPATH = []
INCLUDE_DIR = []
# Get the current paths in both vars
if "CPATH" in os.environ:
CPATH = os.environ["CPATH"].split(":")
if "INCLUDE_DIR" in os.environ:
INCLUDE_DIR = os.environ["INCLUDE_DIR"].split(":")
#Make CPATH handle ALL paths
for path in INCLUDE_DIR:
if path not in CPATH:
CPATH.insert(0,path)
#Assign the same paths to both variables (all are now present in CPATH)
paths = ""
#remove any empty paths
INCLUDE_DIR=[]
for idx,path in enumerate(CPATH):
if path: INCLUDE_DIR.insert(0,path)
for idx,path in enumerate(INCLUDE_DIR):
if idx: paths += ":"
paths += path
os.environ["CPATH"] = paths
os.environ["INCLUDE_DIR"] = paths
class Installer:
ACTION_ENUM = ["build"]
OPEN_INSTALL_ENUM = [False, True]
PLATFORM_ENUM = ["workstation", "cluster", "GAS-pyX.Y"]
VERBOSED_LOGGING_ENUM = [False, True]
def __init__(self, commandLineArguments):
# buildDir is the current Build dir where this script is executed!
# Dirs definition
self.commandLineArguments = commandLineArguments
self.buildDir = None
self.dependencies = {}
self.installDir = None
self.orangeDir = None
self.azorangeDir = None
self.orngCRSDir = None
self.mpichDir = None
# The boost source path is the dir created when uncompressing the orangeDependencies/src/boost_1_34_1.tar.gz
self.orngBoostDir = None
self.APPSPackDir = None
self.opencvDir = None
self.oasaDir = None
self.cinfonyDir = None
self.rdkitDir = None
self.cdkDir = None
self.ftmDir = None
self.structClustDir = None
self.fminerDir = None
#self.plearnDir = None
self.R8Dir = None
self.ctoolsDir = None
self.trainingDir = None
# dir to install all other orange dependencies packages as opencv, fann, PLearn, etc...
self.orangeDependenciesDir = None
#Variables
self.buildPythonPath = None
self.envFile = None # new input argument to define additional envVars needed at runtime back to the mail install script
self.mpiCVerOK=False # used for MPI compatibility check
self.modulesToLoad = None
self.platform = None
self.logFile = None
self.detailsLogFile = None
self.verbosedLogging = False
def __addLog(self,status,create=False):
if not ( self.logFile and self.detailsLogFile):
return
if create:
log = open(self.logFile,"w")
detailsLog = open(self.detailsLogFile,"w")
logStr = status + " (" +time.asctime() + ")\n" +"="*60
log.write(logStr+"\n")
detailsLog.write(logStr+"\n")
print logStr
log.close()
detailsLog.close()
return
#status can be the output of comands.getstatusoutput: (0, "something")
#If status is a string, it can be a new log section if started by "*" or a
# simply line if started by "#"
log = open(self.logFile,"a")
detailsLog = open(self.detailsLogFile,"a")
if type(status) in types.StringTypes:
if status[0]=="#":
logStr = status[1:]
elif status[0]=="*":
logStr = "-"*60 + "\n"+ status[1:] + " (" + time.asctime() + ")\n"+"-"*60
else:
logStr ="-"*60 + "\n"+ status + " (" + time.asctime() + ")\n"+"-"*60
log.write(logStr+"\n")
detailsLog.write(logStr+"\n")
print logStr
else:
if status[0]==0:
if not status[1]:
log.close()
detailsLog.close()
return
else:
logStr = "Detail Code: OK" + "_"+str(time.time())
detailsLogStr = logStr+"\n\t\t" + status[1].replace("\n","\n\t\t")
else:
self.successInstall = False
logStr = "ERROR: Detail Code: " + str(status[0]) + "_"+str(time.time())
detailsLogStr=logStr+"\n\t\t" + status[1].replace("\n","\n\t\t")
log.write(logStr+"\n")
detailsLog.write(detailsLogStr+"\n")
print logStr
log.close()
detailsLog.close()
def __build(self):
"""Install azorange in buildDir. """
#os.system("env")
#sys.exit(1)
if "LOADEDMODULES" in os.environ:
print "Loaded modules: %s"%os.environ["LOADEDMODULES"]
else:
print "No Modules loaded!"
print "Orange is being built in "+self.buildDir
# Setup the correct environment.
self.setEnv()
# Compile fminer
self.compileFMINER()
# Compile structClust
self.compileStructClust()
# Compile ftm
self.compileFTM()
# Compile cinfony
self.compileCinfony()
# Compile rdkit
self.compileRdkit()
# Compile CDK
self.compileCdk()
# Compile the Orange C++ layer
self.compileOrange()
# R8 and copy the C4.5.so to the orange dir.
self.compileR8()
# APPSPack. moved to last
# Compile and copy _orngCRS.so to the orange dir.
self.compileOrngCRS()
# Compile and install the opencv.
self.compileOpenCV()
# Compile and install the oasa.
self.compileOasa()
# Compile and install the ctools.
self.compileCtools()
# Compile and install the AZOrange C++ layer
self.compileAZOrange()
# APPSPack.
if self.platform == "workstation" or self.platform[0:3] == "GAS":
self.compileMPICH()
self.compileAPPSPack()
# Install the signSVM binaries
self.installSignSVM()
# Set the python path and install the python layer
self.__installPythonLayer()
# Copy the test directory
os.system("cp -r "+os.path.join(self.buildDir, "tests")+" "+self.installDir)
#Expand profiling Data
if not self.openInstall:
#Dir of dataSets used by profiling tools
dataDir = os.path.realpath(os.path.join(self.installDir,'tests','profiling','dataSets'))
# Zipped file containing the full set of datasets for profiling
ZippedData=os.path.realpath(os.path.join(dataDir,'profilingDataSuite.tar.gz'))
#Dir where the original datasets are going to be unzipped
fullTrunkDir=os.path.join(dataDir,'fullTrunk')
os.system("rm -rf " + fullTrunkDir)
os.system("mkdir -p " + fullTrunkDir)
os.system("tar xfz " + ZippedData + " -C " + fullTrunkDir)
def __initialize(self):
if not os.path.exists(self.buildDir):
raise Exception("Invalid or none-existing buildDir.")
if not os.path.exists(self.installDir):
raise Exception("Invalid or none-existing installDir.")
if not self.platform:
raise Exception("Missing platform.")
if not self.platform in Installer.PLATFORM_ENUM and \
not ( self.platform[:3] in [p[:3] for p in Installer.PLATFORM_ENUM] ):
raise Exception("Invalid platform.")
self.orangeDir = os.path.join(self.buildDir,"orange") # will be Orange in later revision!
self.orangeInstallDir = os.path.join(self.installDir) #It will add orange. In a latter revision it will add /Orange
self.orangeSrcDir = os.path.join(self.buildDir,"orangeDependencies/src/orange") # will be Orange in later revision!
self.azorangeDir = os.path.join(self.buildDir,"azorange")
self.orngCRSDir = os.path.join(self.buildDir,"orangeDependencies/src/orngCRS")
self.mpichDir = os.path.join(self.buildDir,"orangeDependencies/src/mpich-1.2.7p1")
# The boost source path is the dir created when uncompressing the orangeDependencies/src/boost_1_34_1.tar.gz
self.orngBoostDir = os.path.join(self.buildDir,"orangeDependencies/src/boost")
self.APPSPackDir = os.path.join(self.buildDir,"orangeDependencies/src/appspack")
self.signSVMDir = os.path.join(self.buildDir,"orangeDependencies/src/signSVM")
self.opencvDir = os.path.join(self.buildDir,"orangeDependencies/src/opencv")
self.oasaDir = os.path.join(self.buildDir,"orangeDependencies/src/oasa")
self.cinfonyDir = os.path.join(self.buildDir,"orangeDependencies/src/cinfony")
self.rdkitDir = os.path.join(self.buildDir,"orangeDependencies/src/rdkit")
self.cdkDir = os.path.join(self.buildDir,"orangeDependencies/src/cdk")
self.ftmDir = os.path.join(self.buildDir,"orangeDependencies/src/ftm")
self.structClustDir = os.path.join(self.buildDir,"orangeDependencies/src/structuralClustering")
self.fminerDir = os.path.join(self.buildDir,"orangeDependencies/src/fminer")
#self.plearnDir = os.path.join(self.buildDir,"orangeDependencies/src/plearn")
self.ctoolsDir = os.path.join(self.buildDir,"orangeDependencies/src/Ctools")
self.R8Dir = os.path.join(self.buildDir,"orangeDependencies/src/R8/Src")
self.trainingDir = os.path.join(self.buildDir,"azorange/trainingMethods")
# dir to install all other orange dependencies packages as opencv, fann, PLearn, etc...
self.orangeDependenciesDir = os.path.join(self.installDir,"orangeDependencies")
#make sure .../bin is also created
os.system("mkdir -p " + os.path.join(self.orangeDependenciesDir,"bin"))
#Variables
self.buildPythonPath = self.orangeDir+":"+self.azorangeDir
self.__loadModules()
def __installPythonLayer(self):
"""Once the orange/source directory is compiled, the python layer can be built using the
orange/setup.py script. """
print "InstallPythonLayer"
# Set the python path and install the python layer
#setupFile = os.path.join(self.orangeDir,"setup.py")
# Remove old link liborange.so
commands.getstatusoutput("rm -f "+os.path.join(self.orangeInstallDir, "orange", "liborange.so")) # will be Orange in later revision!
#Install now orange in its destination dir
installCMD = 'python setup.py install --install-base "'+self.orangeInstallDir+\
'" --install-platbase "'+self.orangeInstallDir+\
'" --install-lib "'+self.orangeInstallDir+\
'" --install-headers "'+self.orangeInstallDir+\
'" --install-scripts "'+self.orangeInstallDir+\
'" --install-data "'+self.orangeInstallDir+'"'
os.chdir(self.orangeSrcDir)
# will install in self.orangeInstallDir/orange # will be Orange in later revision!
stat, out = commands.getstatusoutput(installCMD)
checkStatus(stat, out,"Error installing orange orange.")
self.__prependEnvVar("PYTHONPATH", self.orangeInstallDir+"/")
self.__prependEnvVar("PYTHONPATH", os.path.join(self.orangeInstallDir,"orange/orng")) # will be Orange in later revision!
self.__prependEnvVar("LD_LIBRARY_PATH", self.orangeInstallDir+"/")
self.__prependEnvVar("LD_LIBRARY_PATH", os.path.join(self.orangeInstallDir,"orange/orng")) # will be Orange in later revision!
# Check that liborange.so link was created
if not os.path.isfile(os.path.join(self.orangeInstallDir, "orange", "liborange.so")): # will be Orange in later revision!
print "WARNING: Missing link liborange.so -> orange.so"
# os.symlink(os.path.join(self.orangeInstallDir, "orange", "orange.so"), os.path.join(self.orangeInstallDir, "orange", "liborange.so")) # will be Orange in later revision!
# Recover any git replaced files from the orange installation
commands.getstatusoutput("cp -Rf "+os.path.join(self.buildDir,"orange")+" "+self.orangeInstallDir)
os.chdir(self.orangeDir)
# Also copy the shared libraries that were built separately.
#print "Copying c45.so and _orngCRS.so to installation directory."
#try:
# os.system("cp c45.so %s/orange/c45.so" % self.installDir)
# os.system("cp _orngCRS.so %s/orange/_orngCRS.so" % self.installDir)
#except:
# print "Error copying c45.so and/or _orngCRS.so from orange build directory to installation directory."
print "Copying trainingMethods, AZutilities and AZOrangeConfig.py to installation directory."
sumStatus = 0
try:
##scPA Changed the source and destination of these files
sumStatus += os.system("mkdir -p %s/azorange/trainingMethods" % self.installDir)
#Not included in the sumStatus because this command will generate a warning because being skipping directories.
os.system("cp -f ../azorange/trainingMethods/* %s/azorange/trainingMethods/" % self.installDir)
#Not being used... it is still empty
#sumStatus += os.system("cp -f ../azorange/trainingMethods/bin/* %s/azorange/trainingMethods/bin/" % self.installDir)
sumStatus += os.system("cp -Rf ../azorange/AZutilities %s/azorange/." % self.installDir)
sumStatus += os.system("cp -Rf ../azorange/statlib %s/azorange/." % self.installDir)
sumStatus += os.system("cp -f ../azorange/*.py %s/azorange/." % self.installDir)
sumStatus += os.system("cp -Rf ../azorange/bin %s/azorange/." % self.installDir)
sumStatus += os.system("cp -Rf ../doc %s/." % self.installDir)
sumStatus += os.system("cp -Rf ../azorange/documentation %s/azorange/." % self.installDir)
#Copy missing from orange install script. TODO
#sumStatus += os.system("cp -Rf ../orange/Orange " + os.path.join(self.orangeInstallDir, ".") )
if self.openInstall:
sumStatus += os.system("cp -Rf ../COPYING* %s/." % self.installDir)
else:
sumStatus += os.system("cp -Rf ../azorange/etc %s/azorange/." % self.installDir)
sumStatus += os.system("cp -Rf ../exampleScripts %s/." % self.installDir)
# Added the azorange to pythonpath in order to maintain the use of modules
# inside it accessible by the same way
if "PYTHONPATH" in os.environ:
os.environ["PYTHONPATH"] = self.orangeDir + "/azorange:" + os.environ["PYTHONPATH"]
else:
os.environ["PYTHONPATH"] = self.orangeDir + "/azorange"
##ecPA
#print "copy env:"
#os.system("ls -l ")
#os.system("pwd")
except:
print "Error copying trainingMethods directory from orange build directory to installation directory."
if sumStatus:
print "Error copying azorange files to the install Dir."
sys.exit(1)
def __loadModules(self):
# Setup up the correct env using modules for each target.
##scPA
if self.modulesToLoad:
sys.stdout.write("Loading module: ")
#Check out what vital modules define in setup.ini are missing
if "LOADEDMODULES" in os.environ:
missingModules = [m for m in self.modulesToLoad if m not in (os.environ["LOADEDMODULES"]).split(":")]
else:
missingModules = self.modulesToLoad
#Load the missing modules
for mname in missingModules:
#print commands.getstatusoutput("gcc -dumpversion")
sys.stdout.write(" %s " % mname)
module("load", mname)
#print commands.getstatusoutput("gcc -dumpversion")
#Cheack if the needed modules were loaded correctly
for mname in self.modulesToLoad:
if mname not in (os.environ["LOADEDMODULES"]).split(":"):
print "\nWARNING!! Required Module '"+mname+"' was not able to be loaded...Installation may fail!"
else:
sys.stdout.write("Not using modules!")
def __logAndExecute(self, command, logOutput=False):
if self.verboseLogging:
self.__addLog("#setup - About to execute (in " + os.getcwd() + "): " + command)
status, output = commands.getstatusoutput(command)
if logOutput:
self.__addLog((status, "#setup - Output from command: " + str(output)))
return status, output
def __prependEnvVar(self,envName, value):
""" This function will add to ./env.tmp a definition of the var 'envName' with the 'value'.
If the envVar already exists in the file, it will prepend the value to the values already defined.
If the envVar already have the value, it will NOT be doubled.
"""
if not self.envFile:
self.envFile = os.path.realpath("./env.tmp")
print "WARNING!! It was not defines a file to report back new environment variables needed at run time.\n " +\
self.envFile + "will be used."
if not envName or not value or type(envName)!=types.StringType or type(value)!=types.StringType:
print "Error appending envVar, envName and value cannot be empty, and have to be strings"
sys.exit(1)
envVars = {}
envName = envName.upper()
if os.path.isfile(self.envFile):
file = open(self.envFile,"r")
lines = file.readlines()
file.close()
for line in lines:
envVars[line.split("=")[0].strip()] = line.split("=")[1].strip()
if envName in envVars:
values = [var.strip() for var in envVars[envName].split(":")]
if value not in values:
envVars[envName] = value + ":" + envVars[envName]
else:
envVars[envName] = value
file = open(self.envFile,"w")
for var in envVars:
file.write(var+"="+envVars[var]+"\n")
file.close()
def compileCinfony(self):
# this is only untill the cinfony functionality is implemented at InHouse
if ("cinfony" not in self.dependencies):
print "Not using the local cinfony"
return
cinfonyinstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.cinfonyDir)[1])
if self.dependencies["cinfony"]: #compile and install
print "Compiling cinfony"
os.chdir(self.cinfonyDir)
print "Building in: ",self.cinfonyDir
print "Installing in: ",cinfonyinstallDir
stat, out = commands.getstatusoutput("python setup.py build")
checkStatus(stat, out,"Error compiling cinfony.")
stat, out = commands.getstatusoutput("python setup.py install --prefix=\"" + cinfonyinstallDir + "\"")
checkStatus(stat, out,"Error installing cinfony")
else:
print "Not reinstalled"
status, out = commands.getstatusoutput("find \""+cinfonyinstallDir+"\" | grep webel.py | grep -v \".svn\"")
checkStatus(status, out,"Error: webel.py not found while finding site-packages of cinfony!")
sitePackagesPath = os.path.split(os.path.split(out.split("\n")[-1])[0])[0]
if not sitePackagesPath:
print "ERROR: webel.py not found while finding site-packages of cinfony"
sys.exit(1)
# At runtime we will need PYTHONPATH to include the location of new installed modules
self.__prependEnvVar("PYTHONPATH" , sitePackagesPath)
def compileCdk(self):
if ("cdk" not in self.dependencies):
print "Not using the local cdk"
return
cdkinstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.cdkDir)[1])
if self.dependencies["cdk"]: #compile and install
# The source Dir will have to be available at running time
print "Copying cdk dir to orangeDependencies"
stat, out = commands.getstatusoutput("rm -rf " + cdkinstallDir)
stat, out = commands.getstatusoutput("cp -R " + self.cdkDir+ " " + cdkinstallDir)
checkStatus(stat, out,"Error installing cdk.")
else:
print "Not reinstalled"
libjvm = os.path.join(self.getDirOfFile("libjvm.so"),"libjvm.so")
if not libjvm or not os.path.isfile(libjvm):
print "ERROR: Could not locate libjvm.so. Invalid: ", libjvm
sys.exit(1)
CDKJar = os.path.join(cdkinstallDir,[x for x in os.listdir(cdkinstallDir) if x[-4:] == ".jar"][0])
if not CDKJar or not os.path.isfile(CDKJar):
print "ERROR: cdk jar file not found at "+ cdkinstallDir
sys.exit(1)
self.__prependEnvVar("JPYPE_JVM" , libjvm)
self.__prependEnvVar("CLASSPATH" , CDKJar)
def compileStructClust(self):
if ("clustering" not in self.dependencies):
print "Not using the local structural clustering"
return
structClustinstallDir = os.path.join(self.orangeDependenciesDir,"structuralClustering")
if self.dependencies["clustering"]: #compile and install
# The source Dir will have to be available at running time
print "Copying clustering dir to orangeDependencies"
stat, out = commands.getstatusoutput("rm -rf " + structClustinstallDir)
stat, out = commands.getstatusoutput("cp -R " + self.structClustDir+ " " + structClustinstallDir)
checkStatus(stat, out, "Error copying the structural clustering")
# compile gSpan
# gspanpp g++ -o gspan3 -O2 gspan_all_BB.cpp -Iivy_mike/src/
# gSpan gcc -O2 min.c computeSymm.c gSpan.c biconn.c preprocessDB2.c -o gSpan
os.chdir(os.path.join(structClustinstallDir, "gSpan/gspanpp"))
# If not using the system installed boost, we need to point boost include files location
boost_I_flag = ""
if "boost" in self.dependencies:
boost_I_flag = " -I"+self.orngBoostDir
else:
boost_I_flag = ""
stat, out = commands.getstatusoutput("g++ -o gspan3 -O2 gspan_all_BB.cpp -Iivy_mike/src/ "+boost_I_flag)
checkStatus(stat, out, "Error compiling gspan3")
os.chdir(os.path.join(structClustinstallDir, "gSpan/gSpan/FeatureVector_nodes"))
stat, out = commands.getstatusoutput("gcc -O2 min.c computeSymm.c gSpan.c biconn.c preprocessDB2.c -o gSpan")
checkStatus(stat, out, "Error compiling gSpan")
else:
print "Not reinstalled"
def compileFTM(self):
if ("ftm" not in self.dependencies):
print "Not using the local ftm"
return
ftminstallDir = os.path.join(self.orangeDependenciesDir,"bin")
if self.dependencies["ftm"]: #compile and install
# The source Dir will have to be available at running time
#print "Copying ftm dir to orangeDependencies"
#stat, out = commands.getstatusoutput("rm -rf " + ftminstallDir)
#stat, out = commands.getstatusoutput("cp -R " + self.ftmDir+ " " + ftminstallDir)
#checkStatus(stat, out,"Error installing ftm.")
os.chdir(os.path.join(self.ftmDir,"src"))
print "Building in: ",self.ftmDir
stat, out = commands.getstatusoutput("make clean")
os.chdir(os.path.join(self.ftmDir,"src/openbabel/src"))
stat, out = commands.getstatusoutput("make clean")
os.chdir(os.path.join(self.ftmDir,"src/openbabel"))
stat, out = commands.getstatusoutput("make clean")
os.chdir(os.path.join(self.ftmDir,"src"))
stat, out = commands.getstatusoutput("make clean")
os.chdir(os.path.join(self.ftmDir,"src/openbabel/src"))
stat, out = commands.getstatusoutput("make")
checkStatus(stat, out,"Error compiling ftm/src/openbabel/src")
os.chdir(os.path.join(self.ftmDir,"src"))
stat, out = commands.getstatusoutput("make ftm")
checkStatus(stat, out,"Error compiling ftm/src")
print "Installing in: ",ftminstallDir
stat, out = commands.getstatusoutput("cp "+ os.path.join(self.ftmDir,"src/ftm") +" "+ ftminstallDir)
checkStatus(stat, out,"Error installing ftm.")
else:
print "Not reinstalled"
def compileFMINER(self):
if ("fminer" not in self.dependencies):
print "Not using the local fminer"
return
fminerinstallDir = os.path.join(self.orangeDependenciesDir,"fminer")
if self.dependencies["fminer"]: #compile and install
os.chdir(os.path.join(self.fminerDir,"libbbrc"))
print "Building BBRC in: ",self.fminerDir
stat, out = commands.getstatusoutput("make python")
os.chdir(os.path.join(self.fminerDir,"liblast"))
print "Building LAST in: ",self.fminerDir
stat, out = commands.getstatusoutput("make python")
stat, out = commands.getstatusoutput("rm -rf " + fminerinstallDir)
stat, out = commands.getstatusoutput("mkdir " + fminerinstallDir)
checkStatus(stat, out,"Error creating " + fminerinstallDir)
print "Installing BBRC in: ",fminerinstallDir
_file = os.path.join(self.fminerDir,"libbbrc","bbrc.py")
stat, out = commands.getstatusoutput("cp "+ _file +" "+ fminerinstallDir)
checkStatus(stat, out,"Could not copy from " + _file)
_file = os.path.join(self.fminerDir,"libbbrc","_bbrc.so")
stat, out = commands.getstatusoutput("cp "+ _file +" "+ fminerinstallDir)
checkStatus(stat, out,"Could not copy from " + _file)
print "Installing LAST in: ",fminerinstallDir
_file = os.path.join(self.fminerDir,"liblast","last.py")
stat, out = commands.getstatusoutput("cp "+ _file +" "+ fminerinstallDir)
checkStatus(stat, out,"Could not copy from " + _file)
_file = os.path.join(self.fminerDir,"liblast","_last.so")
stat, out = commands.getstatusoutput("cp "+ _file +" "+ fminerinstallDir)
checkStatus(stat, out,"Could not copy from " + _file)
#Set Env variables
self.__prependEnvVar("PYTHONPATH" , fminerinstallDir)
self.__prependEnvVar("FMINER_LAZAR" , "1")
self.__prependEnvVar("FMINER_SMARTS" , "1")
self.__prependEnvVar("FMINER_PVALUES" , "0")
else:
print "Not reinstalled"
def compileRdkit(self):
if ("rdkit" not in self.dependencies):
print "Not using the local rdkit"
return
#rdkitinstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.rdkitDir)[1])
rdkitinstallDir = os.path.join(self.orangeDependenciesDir,"src/"+os.path.split(self.rdkitDir)[1])
if self.dependencies["rdkit"]: #compile and install
# The source Dir will have to be available at running time
print "Copying rdkit dir to orangeDependencies"
stat, out = commands.getstatusoutput("rm -rf " + rdkitinstallDir)
stat, out = commands.getstatusoutput("cp -R " + self.rdkitDir+ " " + rdkitinstallDir)
os.chdir(rdkitinstallDir)
stat, out = commands.getstatusoutput("mkdir " + os.path.join(rdkitinstallDir,"build"))
os.chdir(os.path.join(rdkitinstallDir,"build"))
print "Building in: ",os.path.join(rdkitinstallDir,"build")
stat, out = commands.getstatusoutput("cmake ../")
stat, out = commands.getstatusoutput("make")
checkStatus(stat, out,"Error compiling rdkit.")
print "Installing in: ",rdkitinstallDir
stat, out = commands.getstatusoutput("make install")
checkStatus(stat, out,"Error installing rdkit.")
else:
print "Not reinstalled"
# At runtime we will need PYTHONPATH to include the location of new installed modules
self.__prependEnvVar("PYTHONPATH" , rdkitinstallDir)
# At runtime we will need LD_LIBRARY_PATH to include the location of shared objects
self.__prependEnvVar("LD_LIBRARY_PATH" , os.path.join(rdkitinstallDir,"lib"))
# At runtime we will need RDBASE to include the location of RDKit
self.__prependEnvVar("RDBASE" , rdkitinstallDir)
def compileOrange(self):
print "CompileOrange"
os.chdir(self.orangeSrcDir)
stat, out = commands.getstatusoutput("python setup.py build")
checkStatus(stat, out,"Error building orange.")
#install in the current build Structure to be used by other software on build if needed
#stat, out = commands.getstatusoutput('python setup.py install --prefix "'+self.orangeDir+'"')
#checkStatus(stat, out,"Error installing orange in build dir.")
def compileOrngCRS(self):
if "orngcrs" not in self.dependencies:
print "Not using the local orngCRS"
return
if self.dependencies["orngcrs"]: # compile and install
print "compile OrngCRS"
os.chdir(self.orngCRSDir+"/src")
stat,out = commands.getstatusoutput("make")
checkStatus(stat, out,"Error compiling _orngCRS.")
stat, out = commands.getstatusoutput("cp -f _orngCRS.so " + self.orangeDir + "/_orngCRS.so")
checkStatus(stat, out,"Error copying _orngCRS.so to orange build directory.")
else:
print "Not reinstalled"
def compileR8(self):
if "r8" not in self.dependencies:
print "Not using the local R8"
return
if self.dependencies["r8"]: # compile and install
print "compileR8"
print "Need to tell the buildC45 script where orange resides."
if "PYTHONPATH" in os.environ:
os.environ["PYTHONPATH"] = self.orangeDir + ":" + os.environ["PYTHONPATH"]
else:
os.environ["PYTHONPATH"] = self.orangeDir
if "LD_LIBRARY_PATH" in os.environ:
os.environ["LD_LIBRARY_PATH"] = self.orangeDir + ":" + os.environ["LD_LIBRARY_PATH"]
else:
os.environ["LD_LIBRARY_PATH"] = self.orangeDir
os.chdir(self.R8Dir)
stat, out = commands.getstatusoutput("cp -f %s/orange/buildC45.py ." % self.orangeDir)
checkStatus(stat, out,"Error copying build script for R8 (buildC45.py).")
stat, out = commands.getstatusoutput("cp -f %s/orange/ensemble.c ." % self.orangeDir)
checkStatus(stat, out,"Error copying ensemble.c.")
print "Build c45 start"
stat, out = commands.getstatusoutput("python buildC45.py")
checkStatus(stat, out,"Error compiling R8 (c45).")
print "Build c45 end"
else:
print "Not reinstalled"
def compileMPICH(self):
if "mpich.tar.gz" not in self.dependencies:
print "Not using the local mpich"
return
mpichInstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.mpichDir)[1])
if self.dependencies["mpich.tar.gz"]: # compile and install
# uncompress the .tar.gz in the <buildDir>/orangeDependencies/src dir,
#which will create a dir with name self.mpichDir
os.chdir(os.path.join(self.buildDir,"orangeDependencies/src"))
stat,out = commands.getstatusoutput("tar xfz mpich.tar.gz")
checkStatus(stat, out,"Error extracting 'MPICH' source files")
#Compile
print "Compiling MPICH"
os.chdir(self.mpichDir)
print "Building in: ",self.mpichDir
print "Installing in: ",mpichInstallDir
stat, out = commands.getstatusoutput("./configure --prefix=\"" + mpichInstallDir + "\"")
checkStatus(stat, out,"Error configuring mpich.")
stat, out = commands.getstatusoutput("make")
checkStatus(stat, out,"Error compiling mpich.")
stat, out = commands.getstatusoutput("make install")
checkStatus(stat, out,"Error installing mpich.")
else:
print "Not reinstalled"
# At runtime we will need PATH to include the location of new installed mpich
self.__prependEnvVar("PATH" , os.path.join(mpichInstallDir,"bin"))
#The version will also be tested when compiling appspack
os.environ["PATH"] = os.path.join(mpichInstallDir,"bin") + ":" + os.environ["PATH"]
sys.path.insert(0 , os.path.join(mpichInstallDir,"bin"))
def installSignSVM(self):
if "signsvm" not in self.dependencies or self.openInstall:
print "Not using the local signSVM"
return
if not self.dependencies["signsvm"]:
print "Not reinstalled"
return
# Cp the binaries to the install bin dir
os.system("cp "+os.path.join(self.signSVMDir,"*.jar") +" " + os.path.join(self.orangeDependenciesDir,"bin"))
def compileAPPSPack(self):
if "appspack" not in self.dependencies:
print "Not using the local appspack"
return
if not self.dependencies["appspack"]:
print "Not reinstalled"
return
# Also copy appspack that was built separately.
if self.platform != "workstation" and self.platform[0:3] != "GAS":
print "No installation of APPSPACK on the cluster."
return
# Compile only APPSPACK with gcc 3 (system default) as we have not been able to build mpi version with gcc 4
# Find the GCC correct module name on this system if any.
gccModuleName = None
if self.modulesToLoad:
for moduleName in self.modulesToLoad:
if "gcc" in moduleName.lower():
gccModuleName = moduleName
#Unload the GCC module
print "Unloading module ",gccModuleName
module("unload", gccModuleName)
break
if self.appsPackGccModule:
print "Loading module ",self.appsPackGccModule
module("load", self.appsPackGccModule)
print "Compiling APPSPack."
print commands.getstatusoutput("env")[1]
print commands.getstatusoutput("which mpicxx")[1]
os.chdir(self.APPSPackDir)
print "Building in: ",self.APPSPackDir
#minVer = "4.1.2" # Version of mpich. This should be controlled by the gcc version selected for appspack. To be done
minVer = "3.4.6"
mpiC = "mpicxx"
status = commands.getstatusoutput(mpiC + " -dumpversion")
if status[0]!=0:
self.mpiCVerOK=False
version = None
else:
self.mpiCVerOK=True
version = status[1]
minVerList = minVer.split(".")
runningVerList = version.split(".")
subVerN = min(len(minVerList),len(runningVerList))
for idx in range(subVerN):
if runningVerList[idx] < minVerList[idx]:
print "MPI set to false here"
self.mpiCVerOK = False
break
elif runningVerList[idx] > minVerList[idx]:
break
print "************* Config APPSPACK without MPI (would need gcc 3) !!!!!!!!!!**********************"
self.mpiCVerOK=False
################################################################
# Report
################################################################
print "####### appspack MPI compiler #######"
if self.mpiCVerOK :
print "Running version '"+version+"' of "+mpiC+" (This version should be compatible!)"
else:
if not version:
print "WARNING: "+mpiC+" was not found: "+str(status)
else:
print "WARNING: Running version '"+version+"' of "+mpiC+"\n At least version ",minVer, " is required!"
print "WARNING: MPI version of APPSPACK for the optimizer will not be available!"
if self.mpiCVerOK:
mpiFlags = "--with-mpi-compilers"
else:
mpiFlags = ""
compileFlags = " CC=gcc CXX=g++ "
if self.openInstall:
compileFlags += " F77=gfortran "
if self.platform[0:3] == "GAS":
stat, out = commands.getstatusoutput("./configure "+compileFlags+" --prefix=%s --with-blas=%s --with-lapack=%s %s" % (self.orangeDependenciesDir,os.environ["ATLAS"],os.environ["ATLAS"],mpiFlags))
else:
#print "./configure "+compileFlags+" --prefix="+self.orangeDependenciesDir+" "+mpiFlags
stat, out = commands.getstatusoutput("./configure "+compileFlags+" --prefix=%s %s" % (self.orangeDependenciesDir,mpiFlags))
checkStatus(stat, out,"Error configuring APPSPack.")
# Make sure we are clean at the start.
stat, out = commands.getstatusoutput("make clean")
checkStatus(stat, out,"Error cleaning APPSPack")
# Appspack cant be built in paralell
stat, out = commands.getstatusoutput("make -j1 ")
checkStatus(stat, out,"Error compiling APPSPack")
# Cp the binaries to the install bin dir
os.system("cp "+self.APPSPackDir + "/src/appspack_serial " + os.path.join(self.orangeDependenciesDir,"bin"))
# make it executable
stat, out = commands.getstatusoutput("chmod a+x %s" % os.path.join(self.orangeDependenciesDir,"bin/appspack_serial"))
checkStatus(stat, out,"Error making APPSPack_serial executable")
if self.mpiCVerOK:
os.system("cp "+self.APPSPackDir + "/src/appspack_mpi " + os.path.join(self.orangeDependenciesDir,"bin"))
# make it executable
stat, out = commands.getstatusoutput("chmod a+x %s" % os.path.join(self.orangeDependenciesDir,"bin/appspack_mpi"))
checkStatus(stat, out,"Error making APPSPack_mpi executable")
# Compile the rest of the code with gcc 4
# Unload the module used to compile appspack
if self.appsPackGccModule:
print "Unloading module ",self.appsPackGccModule
module("unload", self.appsPackGccModule)
# Load the gcc module if it was unloaded before
if gccModuleName:
print "Reloading module ",gccModuleName
module("load", gccModuleName)
def getDirOfFile(self, fileName):
"""Return the directory in which fileName resides (as returned by the locate command)"""
try:
filePath = commands.getoutput("locate "+fileName).split("\n")[-1]
except:
print "Unable to locate the file."
return None
dirPath = os.path.dirname(filePath)
if os.path.isdir(dirPath):
return dirPath
else:
print "WARNING: The search of '"+fileName+"' returned:",filePath
print " Try to update your DB first by running: sudo updatedb"
return None
def setEnv(self):
print "The buildDir: ",self.buildDir
# Add nspr directory to CPATH # Used by plearn (PLS)
if self.platform[0:3] == "GAS":
try:
pcfile=open("/usr/lib/pkgconfig/mozilla-nspr.pc")
line=pcfile.readline()
while(line):
if line.find("Cflags:") == 0:
nsprPath=line[10:].rstrip()
line=pcfile.readline()
pcfile.close()
except:
nsprPath = self.getDirOfFile("prlong.h")
if not nsprPath:
print "ERROR: NSPR is missing! Please install NSPR and try again."
sys.exit(1)
else:
nsprPath = self.getDirOfFile("prlong.h")
if not nsprPath:
print "ERROR: NSPR is missing! Please install NSPR and try again."
sys.exit(1)
idx = string.rfind(nsprPath, "/")
nsprPath = nsprPath[:idx]
print "nsprPath "+nsprPath
if nsprPath.find("nspr4") != -1:
# nspr4 not what our code expect.. Make fake link in .
newnsprPath=os.path.realpath("nspr") #Find complete path
print "Faking nspr path to %s to workaround the nspr4 problem" % newnsprPath
try:
if not os.path.exists(newnsprPath):
os.symlink(nsprPath, newnsprPath) # Create a link to the nspr4 include files
nsprPath=newnsprPath+":"+os.path.realpath(".") # Set nsprPath to link... and include .
except:
print "Error creating the symlink to nspr include dir. You need to be su to create the link."
sys.exit(1)
if nsprPath:
print os.environ["CPATH"]
print nsprPath
if "CPATH" in os.environ:
os.environ["CPATH"] = nsprPath + ":"+ os.environ["CPATH"]
else:
os.environ["CPATH"] = nsprPath
syncCPATHandINCLUDE_DIR()
print "Setting env CPATH to %s to make azorange find nspr include files" % os.environ["CPATH"]
else:
print "Terminating AZOrange installation because the nspr package was not found."
sys.exit(1)
def compileOasa(self):
# Remove "or not self.openInstall" from next test if want to install oasa in the open installation
if ("oasa" not in self.dependencies) or self.openInstall:
print "Not using the local oasa"
return
oasainstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.oasaDir)[1])
if self.dependencies["oasa"]: #compile and install
print "Compiling oasa"
os.chdir(self.oasaDir)
print "Building in: ",self.oasaDir
print "Installing in: ",oasainstallDir
# for debug include: --enable-debug=\"yes\"
stat, out = commands.getstatusoutput("python setup.py build")
checkStatus(stat, out,"Error compiling oasa.")
stat, out = commands.getstatusoutput("python setup.py install --prefix=\"" + oasainstallDir + "\"")
checkStatus(stat, out,"Error installing oasa")
else:
print "Not reinstalled"
status, out = commands.getstatusoutput("find \""+oasainstallDir+"\" | grep molecule.py | grep -v \".svn\"")
checkStatus(status, out,"Error: molecule.py not found while finding site-packages of oasa!")
sitePackagesPath = os.path.split(os.path.split(out.split("\n")[-1])[0])[0]
if not sitePackagesPath:
print "ERROR: molecule.py not found while finding site-packages of oasa"
sys.exit(1)
# At runtime we will need PYTHONPATH to include the location of new installed modules
self.__prependEnvVar("PYTHONPATH" , sitePackagesPath)
def compileOpenCV(self):
if ("opencv" not in self.dependencies):
print "Not using the local openCV"
return
openCVinstallDir = os.path.join(self.orangeDependenciesDir,os.path.split(self.opencvDir)[1])
if self.dependencies["opencv"]: #compile and install
print "Compiling openCV"
os.chdir(self.opencvDir)
print "Building in: ",self.opencvDir
print "Installing in: ",openCVinstallDir
# for debug include: --enable-debug=\"yes\"
#stat, out = commands.getstatusoutput("./configure --prefix=\"" + openCVinstallDir + "\" --with-openmp --enable-apps=\"no\"")
# Disabled openmp because of too many cores used in SGE
print "**************** OpenCV Config statement *********************"
print "./configure --prefix=\"" + openCVinstallDir + "\" --disable-openmp --enable-apps=\"no\""
stat, out = commands.getstatusoutput("./configure --prefix=\"" + openCVinstallDir + "\" --disable-openmp --enable-apps=\"no\"")
checkStatus(stat, out,"Error configuring opencv.")
stat, out = commands.getstatusoutput("make")
checkStatus(stat, out,"Error compiling opencv.")
stat, out = commands.getstatusoutput("make install")
checkStatus(stat, out,"Error installing opencv.")
else:
print "Not reinstalled"
#This env var will be used for compiling AZOrange
os.environ["PKG_CONFIG_PATH"] = os.path.join(openCVinstallDir,"lib/pkgconfig")
# At runtime we will need LD_LIBRARY_PATH to include the location of new installed libs
self.__prependEnvVar("LD_LIBRARY_PATH" , os.path.join(openCVinstallDir,"lib"))
#This env var will be used for compiling AZOrange
status, out = commands.getstatusoutput("find \""+openCVinstallDir+"\" | grep cv.py | grep -v \".svn\"")
checkStatus(status, out,"Error: cv.py not found while finding site-packages of opencv!")
sitePackagesPath = os.path.split(os.path.split(out.split("\n")[-1])[0])[0]
if not sitePackagesPath:
print "ERROR: cv.py not found while finding site-packages of opencv"
sys.exit(1)
if "PYTHONPATH" not in os.environ:
os.environ["PYTHONPATH"] = sitePackagesPath
else:
os.environ["PYTHONPATH"] = sitePackagesPath+":"+os.environ["PYTHONPATH"]
# At runtime we will need PYTHONPATH to include the location of new installed modules
self.__prependEnvVar("PYTHONPATH" , sitePackagesPath)