Ejemplo n.º 1
0
    def run(self):
        if not self.opts.keepPostprocessing:
            self.opts.additional.append("postProcessing")

        notCleared=[]

        if self.opts.dryRun:
            self.opts.verbose=True
            self.opts.verboseClear=True

        for cName in self.parser.getArgs():
            if self.checkCase(cName,fatal=self.opts.fatal,verbose=not self.opts.silent):
                if self.opts.allcleanScript:
                    scr=path.join(cName,"Allclean")
                    if(path.exists(scr)):
                        if self.opts.verbose or self.opts.verboseClear:
                            print("Executing",scr)
                    execute(scr,workdir=cName)
                try:
                    self.addLocalConfig(cName)

                    if self.opts.verbose:
                        print_("Clearing",cName)
                    sol=SolutionDirectory(cName,
                                          archive=None,
                                          parallel=True,
                                          paraviewLink=False)
                    sol.clear(after=self.parser.getOptions().after,
                              processor=self.parser.getOptions().processor,
                              pyfoam=self.parser.getOptions().pyfoam,
                              vtk=self.parser.getOptions().vtk,
                              verbose=self.parser.getOptions().verboseClear,
                              removeAnalyzed=self.parser.getOptions().removeAnalyzed,
                              keepRegular=self.parser.getOptions().keepRegular,
                              keepParallel=self.parser.getOptions().keepParallel,
                              keepLast=self.parser.getOptions().latest,
                              keepInterval=self.parser.getOptions().keepInterval,
                              keepTimes=self.opts.keepTimes,
                              clearHistory=self.parser.getOptions().clearHistory,
                              clearParameters=self.parser.getOptions().clearParameters,
                              additional=self.parser.getOptions().additional,
                              dryRun=self.opts.dryRun,
                              functionObjectData=self.parser.getOptions().functionObjectData)

                    self.addToCaseLog(cName)
                except OSError:
                    e = sys.exc_info()[1] # compatible with 2.x and 3.x
                    self.warning("Can not clear",cName,"because of OSError",e)
                    notCleared.append(cName)

        if len(notCleared)>0:
            self.warning("These case not cleared because of OS-problems:",
                         ", ".join(notCleared))
Ejemplo n.º 2
0
    def execute(self,para,log):
        cmd=replaceValues(self.command,para)
        print_("     Executing ",cmd,end=" ")
        sys.stdout.flush()
        out=execute(cmd)

        if len(out)>0:
            print_(" -->",len(out),"lines output")
            for l in out:
                print_("---- Command:",cmd,file=log)
                print_(l,end=" ",file=log)
        else:
            print_()

        return True,None
Ejemplo n.º 3
0
    def executeScript(self, scriptName, workdir, echo):
        """Execute a script and write a corresponding logfile"""

        ret, txt = execute([scriptName],
                           workdir=workdir,
                           echo=echo,
                           getReturnCode=True)

        result = "".join(txt)
        open(scriptName + ".log", "w").write(result)

        if ret not in [0, None]:
            self.info(scriptName, "failed with code", ret)
            if self.opts.failOnScriptFailure:
                self.error("Script", scriptName, "failed with code", ret)
Ejemplo n.º 4
0
    def execute(self,para,log):
        cmd=replaceValues(self.command,para)
        print "     Executing ",cmd,
        sys.stdout.flush()
        out=execute(cmd)

        if len(out)>0:
            print " -->",len(out),"lines output"
            for l in out:
                print >>log,"---- Command:",cmd
                print >>log,l,
        else:
            print

        return True,None
Ejemplo n.º 5
0
    def run(self):
        config=ConfigParser.ConfigParser()
        files=self.parser.getArgs()

        good=config.read(files)
        # will work with 2.4
        # if len(good)!=len(files):
        #    print "Problem while trying to parse files",files
        #    print "Only ",good," could be parsed"
        #    sys.exit(-1)

        benchName=config.get("General","name")
        if self.opts.nameAddition!=None:
            benchName+="_"+self.opts.nameAddition
        if self.opts.foamVersion!=None:
            benchName+="_v"+self.opts.foamVersion
            
        isParallel=config.getboolean("General","parallel")
        lam=None

        if isParallel:
            nrCpus=config.getint("General","nProcs")
            machineFile=config.get("General","machines")
            if not path.exists(machineFile):
                self.error("Machine file ",machineFile,"needed for parallel run")
            lam=LAMMachine(machineFile,nr=nrCpus)
            if lam.cpuNr()>nrCpus:
                self.error("Wrong number of CPUs: ",lam.cpuNr())

            print "Running parallel on",lam.cpuNr(),"CPUs"

        if config.has_option("General","casesDirectory"):
            casesDirectory=path.expanduser(config.get("General","casesDirectory"))
        else:
            casesDirectory=foamTutorials()

        if not path.exists(casesDirectory):
            self.error("Directory",casesDirectory,"needed with the benchmark cases is missing")
        else:
            print "Using cases from directory",casesDirectory

        benchCases=[]
        config.remove_section("General")

        for sec in config.sections():
            print "Reading: ",sec
            skipIt=False
            skipReason=""
            if config.has_option(sec,"skip"):
                skipIt=config.getboolean(sec,"skip")
                skipReason="Switched off in file"
            if self.opts.excases!=None and not skipIt:
                for p in self.opts.excases:
                    if fnmatch(sec,p):
                        skipIt=True
                        skipReason="Switched off by pattern '"+p+"'"
            if self.opts.cases!=None:
                for p in self.opts.cases:
                    if fnmatch(sec,p):
                        skipIt=False
                        skipReason=""
                
            if skipIt:
                print "Skipping case ..... Reason:"+skipReason
                continue
            sol=config.get(sec,"solver")
            cas=config.get(sec,"case")
            pre=eval(config.get(sec,"prepare"))
            preCon=[]
            if config.has_option(sec,"preControlDict"):
                preCon=eval(config.get(sec,"preControlDict"))
            con=eval(config.get(sec,"controlDict"))
            bas=config.getfloat(sec,"baseline")
            wei=config.getfloat(sec,"weight")
            add=[]
            if config.has_option(sec,"additional"):
                add=eval(config.get(sec,"additional"))
                print "Adding: ", add
            util=[]
            if config.has_option(sec,"utilities"):
                util=eval(config.get(sec,"utilities"))
                print "Utilities: ", util    
            nr=99999
            if config.has_option(sec,"nr"):
                nr=eval(config.get(sec,"nr"))
            sp=None
            if config.has_option(sec,"blockSplit"):
                sp=eval(config.get(sec,"blockSplit"))
            toRm=[]
            if config.has_option(sec,"filesToRemove"):
                toRm=eval(config.get(sec,"filesToRemove"))
            setInit=[]
            if config.has_option(sec,"setInitial"):
                setInit=eval(config.get(sec,"setInitial"))

            parallelOK=False
            if config.has_option(sec,"parallelOK"):
                parallelOK=config.getboolean(sec,"parallelOK")

            deMet=["metis"]
            if config.has_option(sec,"decomposition"):
                deMet=config.get(sec,"decomposition").split()

            if deMet[0]=="metis":
                pass
            elif deMet[0]=="simple":
                if len(deMet)<2:
                    deMet.append(0)
                else:
                    deMet[1]=int(deMet[1])
            else:
                print "Unimplemented decomposition method",deMet[0],"switching to metis"
                deMet=["metis"]

            if isParallel==False or parallelOK==True:
                if path.exists(path.join(casesDirectory,sol,cas)):
                    benchCases.append( (nr,sec,sol,cas,pre,con,preCon,bas,wei,add,util,sp,toRm,setInit,deMet) )
                else:
                    print "Skipping",sec,"because directory",path.join(casesDirectory,sol,cas),"could not be found"
            else:
                print "Skipping",sec,"because not parallel"

        benchCases.sort()

        parallelString=""
        if isParallel:
            parallelString=".cpus="+str(nrCpus)

        resultFile=open("Benchmark."+benchName+"."+uname()[1]+parallelString+".results","w")

        totalSpeedup=0
        minSpeedup=None
        maxSpeedup=None
        totalWeight =0
        runsOK=0
        currentEstimate = 1.

        print "\nStart Benching\n"
        
        csv=CSVCollection("Benchmark."+benchName+"."+uname()[1]+parallelString+".csv")
        
#        csvHeaders=["description","solver","case","caseDir","base",
#                    "benchmark","machine","arch","cpus","os","version",
#                    "wallclocktime","cputime","cputimeuser","cputimesystem","maxmemory","cpuusage","speedup"]

        for nr,description,solver,case,prepare,control,preControl,base,weight,additional,utilities,split,toRemove,setInit,decomposition in benchCases:
            #    control.append( ("endTime",-2000) )
            print "Running Benchmark: ",description
            print "Solver: ",solver
            print "Case: ",case
            caseName=solver+"_"+case+"_"+benchName+"."+uname()[1]+".case"
            print "Short name: ",caseName
            caseDir=caseName+".runDir"

            csv["description"]=description
            csv["solver"]=solver
            csv["case"]=case
            csv["caseDir"]=caseDir
            csv["base"]=base

            csv["benchmark"]=benchName
            csv["machine"]=uname()[1]
            csv["arch"]=uname()[4]
            if lam==None:
                csv["cpus"]=1
            else:
                csv["cpus"]=lam.cpuNr()
            csv["os"]=uname()[0]
            csv["version"]=uname()[2]
            
            workDir=path.realpath(path.curdir)

            orig=SolutionDirectory(path.join(casesDirectory,solver,case),
                                   archive=None,
                                   paraviewLink=False)
            for a in additional+utilities:
                orig.addToClone(a)
            orig.cloneCase(path.join(workDir,caseDir))

            if oldApp():
                argv=[solver,workDir,caseDir]
            else:
                argv=[solver,"-case",path.join(workDir,caseDir)]
                
            run=BasicRunner(silent=True,argv=argv,logname="BenchRunning",lam=lam)
            runDir=run.getSolutionDirectory()
            controlFile=ParameterFile(runDir.controlDict())

            for name,value in preControl:
                print "Setting parameter",name,"to",value,"in controlDict"
                controlFile.replaceParameter(name,value)

            for rm in toRemove:
                fn=path.join(caseDir,rm)
                print "Removing file",fn
                remove(fn)

            for field,bc,val in setInit:
                print "Setting",field,"on",bc,"to",val
                SolutionFile(runDir.initialDir(),field).replaceBoundary(bc,val)

            oldDeltaT=controlFile.replaceParameter("deltaT",0)

            for u in utilities:
                print "Building utility ",u
                execute("wmake 2>&1 >%s %s" % (path.join(caseDir,"BenchCompile."+u),path.join(caseDir,u)))

            print "Preparing the case: "
            if lam!=None:
                prepare=prepare+[("decomposePar","")]
                if decomposition[0]=="metis":
                    lam.writeMetis(SolutionDirectory(path.join(workDir,caseDir)))
                elif decomposition[0]=="simple":
                    lam.writeSimple(SolutionDirectory(path.join(workDir,caseDir)),decomposition[1])

            if split:
                print "Splitting the mesh:",split
                bm=BlockMesh(runDir.blockMesh())
                bm.refineMesh(split)

            for pre,post in prepare:
                print "Doing ",pre," ...."
                post=post.replace("%case%",caseDir)
                if oldApp():
                    args=string.split("%s %s %s %s" % (pre,workDir,caseDir,post))
                else:
                    args=string.split("%s -case %s %s" % (pre,path.join(workDir,caseDir),post))
                util=BasicRunner(silent=True,argv=args,logname="BenchPrepare_"+pre)
                util.start()

            controlFile.replaceParameter("deltaT",oldDeltaT)

            #    control.append(("endTime",-1000))
            for name,value in control:
                print "Setting parameter",name,"to",value,"in controlDict"
                controlFile.replaceParameter(name,value)

            print "Starting at ",asctime(localtime(time()))
            print " Baseline is %f, estimated speedup %f -> estimated end at %s " % (base,currentEstimate,asctime(localtime(time()+base/currentEstimate)))
            print "Running the case ...."
            run.start()

            speedup=None
            cpuUsage=0
            speedupOut=-1

            try:
                speedup=base/run.run.wallTime()
                cpuUsage=100.*run.run.cpuTime()/run.run.wallTime()
            except ZeroDivisionError:
                print "Division by Zero: ",run.run.wallTime()

            if not run.runOK():
                print "\nWARNING!!!!"
                print "Run had a problem, not using the results. Check the log\n"
                speedup=None

            if speedup!=None:
                speedupOut=speedup

                totalSpeedup+=speedup*weight
                totalWeight +=weight
                runsOK+=1
                if maxSpeedup==None:
                    maxSpeedup=speedup
                elif speedup>maxSpeedup:
                    maxSpeedup=speedup
                if minSpeedup==None:
                    minSpeedup=speedup
                elif speedup<minSpeedup:
                    minSpeedup=speedup

            print "Wall clock: ",run.run.wallTime()
            print "Speedup: ",speedup," (Baseline: ",base,")"
            print "CPU Time: ",run.run.cpuTime()
            print "CPU Time User: "******"CPU Time System: ",run.run.cpuSystemTime()
            print "Memory: ",run.run.usedMemory()
            print "CPU Usage: %6.2f%%" % (cpuUsage)

            csv["wallclocktime"]=run.run.wallTime()
            csv["cputime"]=run.run.cpuTime()
            csv["cputimeuser"]=run.run.cpuUserTime()
            csv["cputimesystem"]=run.run.cpuSystemTime()
            csv["maxmemory"]=run.run.usedMemory()
            csv["cpuusage"]=cpuUsage
            if speedup!=None:
                csv["speedup"]=speedup
            else:
                csv["speedup"]="##"
                
            csv.write()
            
            resultFile.write("Case %s WallTime %g CPUTime %g UserTime %g SystemTime %g Memory %g MB  Speedup %g\n" %(caseName,run.run.wallTime(),run.run.cpuTime(),run.run.cpuUserTime(),run.run.cpuSystemTime(),run.run.usedMemory(),speedupOut))

            resultFile.flush()
            
            if speedup!=None:
                currentEstimate=totalSpeedup/totalWeight

            if self.opts.removeCases:
                print "Clearing case",
                if speedup==None:
                    print "not ... because it failed"
                else:
                    print "completely"
                    rmtree(caseDir,ignore_errors=True)

            print
            print
        
        if lam!=None:
            lam.stop()

        print "Total Speedup: ",currentEstimate," ( ",totalSpeedup," / ",totalWeight, " ) Range: [",minSpeedup,",",maxSpeedup,"]"

        print runsOK,"of",len(benchCases),"ran OK"

        resultFile.write("Total Speedup: %g\n" % (currentEstimate))
        if minSpeedup and maxSpeedup:
            resultFile.write("Range: [ %g , %g ]\n" % (minSpeedup,maxSpeedup))

        resultFile.close()
Ejemplo n.º 6
0
    def run(self):
        cfgFile=self.parser.getArgs()[0]
        moduleFile=self.parser.getArgs()[1]
        useCsh = self.opts.useCshell

        if self.opts.clearEnvironment:
            self.warning("Clearing environment of variables that might come from an OpenFAOM-installation. Nevertheless it is preferable to use a clean environment")
            try:
                oldVersion=os.environ["WM_PROJECT_VERSION"]
            except KeyError:
                self.warning("Seems to be a clean environment anyway")
                oldVersion=None

            if oldVersion:
                for e in os.environ.keys():
                    for p in ["WM_","FOAM_"]:
                        if e.find(p)==0:
                            del os.environ[e]
                            break
                for p in ["PATH","DYLD_LIBRARY_PATH","LD_LIBRARY_PATH","MANPATH","PV_PLUGIN_PATH"]:
                    if p in os.environ:
                        lst=os.environ[p].split(":")
                        os.environ[p]=":".join([l for l in lst if l.find(oldVersion)<0])
                        
        if path.exists(cfgFile) and path.isfile(cfgFile) and os.access(cfgFile, os.R_OK):
            print " Using file " + cfgFile + " for loading the OpenFOAM environment"

            # Some more sanity check
            fileData = open(cfgFile).read()
            if not useCsh and "setenv" in fileData:
                self.error(" Error: Detecting 'setenv' instructions in this bash file. Please provide a configuration file compatible for bash, or use the --csh option.")
            elif useCsh and "export" in fileData:
                self.error(" Error: Detecting 'export' instructions in this csh file. Please provide a configuration file compatible for csh.")
            else:
                print " The configuration file seems ok"
        else:
            self.error(" Error: Cannot access file: " + cfgFile)

        # We choose not to run if the OpenFOAM environment is already loaded.
        # We obviously cannot diff from such an environment
        if os.getenv("WM_PROJECT") != None:
            self.error(""" Error: Cannot run with OpenFOAM environment variables already present
                       You need to run this script from a clean environment""")

        # We choose not to run under the user 'root', simply because the HOME and USER environment
        # variables are usually very similar for this user, and this will cause problem later on
        # For instance, under Centos, for the super user:
        #     HOME=/root
        #     USER=root
        # Those two are very similar
        if os.getenv("USER") == "root":
            self.error(""" Error: You should not run this script from the 'root' account.
                       Please invoke this pyFoam command from a plain OpenFOAM user account.
                       Then, make the result file available to the super user (root) of the"
                       destination host in order to install the modules configuration files.""")
            
        # Grab environment + aliases before the activation of OpenFOAM
        # We start from a minimal environment using 'env -i'    
        shellCmd = 'bash -c'
        sourceCmd = '.'

        if useCsh:
            shellCmd = 'csh -c'
            sourceCmd = 'source'
            
        oldEnv=Set(execute(shellCmd + ' "env|sort"'))
        oldAliases=Set(execute(shellCmd + ' "alias|sort"'))

        # Grab environment + aliases after the activation of OpenFOAM
        newEnv=Set(execute(shellCmd + ' \"' + sourceCmd + ' ' + cfgFile + '; env|sort"'))
        newAliases=Set(execute(shellCmd + ' \"' + sourceCmd + ' ' + cfgFile + '; alias|sort"'))

        # Handling of environment variables
        # Memorize all the PATH environment variables for later processing
        oldPath = {}
        newPath = {}
        homeVar = ""
        userVar = ""

        for v in oldEnv:
            if v.find('=') > -1:
                key, value = v.split('=', 1)

                # Memorize PATH variables
                if key.find('PATH') > -1:
                    oldPath[key] = value.replace('\n', '')

                    # We remove any reference to PyFOAM in the old PATH env. variable
                    # Since we run this script with PyFOAM, environment variables for PyFoam are
                    # present in oldPath. If the configuration file for OpenFOAM requires PyFoam too,
                    # we risk to lose these variables because they will be in common in both the
                    # 'before' and 'after'environment.
                    # This is ugly, but PyFOAM is just too useful to write this script with plain
                    # python.
                    # If you have installed PyFoam under a path where the string 'PyFoam' is not present,
                    # you will simply have to manually add the necessary PyFoam environment variables
                    # yourself in the module file. No biggie,
                    oldPath[key] = self.removeComponentWithSubstrFromPathEnvVar(oldPath[key], 'PyFoam')

                # Memorize HOME variable
                if key == 'HOME':
                    homeVar = value.replace('\n', '')

                # Memorize USER variable
                if key == 'USER':
                    userVar = value.replace('\n', '')

        # Using sets, it is trivial to remove common environment variables
        # and aliases between the two environments
        moduleEnv=newEnv - oldEnv
        moduleAliases=newAliases - oldAliases

        # Dictionary for environment variables
        envVar = {}

        # Dictionary for aliases
        aliasesVar = {}

        # Iterate through environment variables and store in dictionary
        for v in moduleEnv:
            if v.find('=') > -1:
                key, value = v.split('=')

                # Minor cleanup
                value = value.replace('\n', '')

                # Memorize PATH variables for later processing
                if key.find('PATH') > -1:
                    newPath[key] = value
                else:
                    envVar.setdefault(key, []).append(value)
    
        # Handle the PATH variables
        for v in newPath:
            if v in oldPath: 
                # Cleanup old PATH components
                newPath[v] = self.removeComponentFromPathEnvVar(newPath[v], oldPath[v])

            # Remove duplicate entries in PATH variable
            newPath[v] = self.uniqifyPathEnvVar(newPath[v])
            envVar.setdefault(v, []).append(newPath[v])

        # Iterate through aliases variables and store them in dictionary 
        for v in moduleAliases:
            if v.find('=') > -1:
                key, value = v.split('=', 1)

                # Minor cleanup
                key = key.replace("alias ", "")
                value = value.replace('\n', "")
                value = value.replace('\'', "")
                aliasesVar.setdefault(key, []).append(value)

        # Generate module entries
        print " Generating modulefile: " , moduleFile

        f = open(moduleFile, 'w')
        
        self.writeModuleFileHeader(f, envVar["WM_PROJECT_VERSION"][0])
        self.writeModuleEnvironmentEntry(f, envVar, homeVar, userVar)
        self.writeModuleAliasEntry(f, aliasesVar, homeVar, userVar)
        self.writeModuleFileFooter(f)

        f.close()
        print " Done\n"
Ejemplo n.º 7
0
    def run(self):
        cfgFile = self.parser.getArgs()[0]
        moduleFile = self.parser.getArgs()[1]
        useCsh = self.opts.useCshell

        if self.opts.clearEnvironment:
            self.warning(
                "Clearing environment of variables that might come from an OpenFAOM-installation. Nevertheless it is preferable to use a clean environment"
            )
            try:
                oldVersion = os.environ["WM_PROJECT_VERSION"]
            except KeyError:
                self.warning("Seems to be a clean environment anyway")
                oldVersion = None

            if oldVersion:
                for e in list(os.environ.keys()):
                    for p in ["WM_", "FOAM_"]:
                        if e.find(p) == 0:
                            del os.environ[e]
                            break
                for p in [
                        "PATH", "DYLD_LIBRARY_PATH", "LD_LIBRARY_PATH",
                        "MANPATH", "PV_PLUGIN_PATH"
                ]:
                    if p in os.environ:
                        lst = os.environ[p].split(":")
                        os.environ[p] = ":".join(
                            [l for l in lst if l.find(oldVersion) < 0])

        if path.exists(cfgFile) and path.isfile(cfgFile) and os.access(
                cfgFile, os.R_OK):
            print_(" Using file " + cfgFile +
                   " for loading the OpenFOAM environment")

            # Some more sanity check
            fileData = open(cfgFile).read()
            if not useCsh and "setenv" in fileData:
                self.error(
                    " Error: Detecting 'setenv' instructions in this bash file. Please provide a configuration file compatible for bash, or use the --csh option."
                )
            elif useCsh and "export" in fileData:
                self.error(
                    " Error: Detecting 'export' instructions in this csh file. Please provide a configuration file compatible for csh."
                )
            else:
                print_(" The configuration file seems ok")
        else:
            self.error(" Error: Cannot access file: " + cfgFile)

        # We choose not to run if the OpenFOAM environment is already loaded.
        # We obviously cannot diff from such an environment
        if os.getenv("WM_PROJECT") != None:
            self.error(
                """ Error: Cannot run with OpenFOAM environment variables already present
                       You need to run this script from a clean environment""")

        # We choose not to run under the user 'root', simply because the HOME and USER environment
        # variables are usually very similar for this user, and this will cause problem later on
        # For instance, under Centos, for the super user:
        #     HOME=/root
        #     USER=root
        # Those two are very similar
        if os.getenv("USER") == "root":
            self.error(
                """ Error: You should not run this script from the 'root' account.
                       Please invoke this pyFoam command from a plain OpenFOAM user account.
                       Then, make the result file available to the super user (root) of the"
                       destination host in order to install the modules configuration files."""
            )

        # Grab environment + aliases before the activation of OpenFOAM
        # We start from a minimal environment using 'env -i'
        shellCmd = 'bash -c'
        sourceCmd = '.'

        if useCsh:
            shellCmd = 'csh -c'
            sourceCmd = 'source'

        oldEnv = Set(execute(shellCmd + ' "env|sort"'))
        oldAliases = Set(execute(shellCmd + ' "alias|sort"'))

        # Grab environment + aliases after the activation of OpenFOAM
        newEnv = Set(
            execute(shellCmd + ' \"' + sourceCmd + ' ' + cfgFile +
                    '; env|sort"'))
        newAliases = Set(
            execute(shellCmd + ' \"' + sourceCmd + ' ' + cfgFile +
                    '; alias|sort"'))

        # Handling of environment variables
        # Memorize all the PATH environment variables for later processing
        oldPath = {}
        newPath = {}
        homeVar = ""
        userVar = ""

        for v in oldEnv:
            if v.find('=') > -1:
                key, value = v.split('=', 1)

                # Memorize PATH variables
                if key.find('PATH') > -1:
                    oldPath[key] = value.replace('\n', '')

                    # We remove any reference to PyFOAM in the old PATH env. variable
                    # Since we run this script with PyFOAM, environment variables for PyFoam are
                    # present in oldPath. If the configuration file for OpenFOAM requires PyFoam too,
                    # we risk to lose these variables because they will be in common in both the
                    # 'before' and 'after'environment.
                    # This is ugly, but PyFOAM is just too useful to write this script with plain
                    # python.
                    # If you have installed PyFoam under a path where the string 'PyFoam' is not present,
                    # you will simply have to manually add the necessary PyFoam environment variables
                    # yourself in the module file. No biggie,
                    oldPath[
                        key] = self.removeComponentWithSubstrFromPathEnvVar(
                            oldPath[key], 'PyFoam')

                # Memorize HOME variable
                if key == 'HOME':
                    homeVar = value.replace('\n', '')

                # Memorize USER variable
                if key == 'USER':
                    userVar = value.replace('\n', '')

        # Using sets, it is trivial to remove common environment variables
        # and aliases between the two environments
        moduleEnv = newEnv - oldEnv
        moduleAliases = newAliases - oldAliases

        # Dictionary for environment variables
        envVar = {}

        # Dictionary for aliases
        aliasesVar = {}

        # Iterate through environment variables and store in dictionary
        for v in moduleEnv:
            if v.find('=') > -1:
                key, value = v.split('=')

                # Minor cleanup
                value = value.replace('\n', '')

                # Memorize PATH variables for later processing
                if key.find('PATH') > -1:
                    newPath[key] = value
                else:
                    envVar.setdefault(key, []).append(value)

        # Handle the PATH variables
        for v in newPath:
            if v in oldPath:
                # Cleanup old PATH components
                newPath[v] = self.removeComponentFromPathEnvVar(
                    newPath[v], oldPath[v])

            # Remove duplicate entries in PATH variable
            newPath[v] = self.uniqifyPathEnvVar(newPath[v])
            envVar.setdefault(v, []).append(newPath[v])

        # Iterate through aliases variables and store them in dictionary
        for v in moduleAliases:
            if v.find('=') > -1:
                key, value = v.split('=', 1)

                # Minor cleanup
                key = key.replace("alias ", "")
                value = value.replace('\n', "")
                value = value.replace('\'', "")
                aliasesVar.setdefault(key, []).append(value)

        # Generate module entries
        print_(" Generating modulefile: ", moduleFile)

        f = open(moduleFile, 'w')

        self.writeModuleFileHeader(f, envVar["WM_PROJECT_VERSION"][0])
        self.writeModuleEnvironmentEntry(f, envVar, homeVar, userVar)
        self.writeModuleAliasEntry(f, aliasesVar, homeVar, userVar)
        self.writeModuleFileFooter(f)

        f.close()
        print_(" Done\n")
Ejemplo n.º 8
0
    def prepare(self, sol, cName=None, overrideParameters=None):
        if cName == None:
            cName = sol.name

        if self.opts.onlyVariables:
            self.opts.verbose = True

        vals = {}
        vals["casePath"] = '"' + path.abspath(cName) + '"'
        vals["caseName"] = '"' + path.basename(path.abspath(cName)) + '"'
        vals["foamVersion"] = foamVersion()
        vals["foamFork"] = foamFork()

        if self.opts.verbose:
            print_("Looking for template values", cName)
        for f in self.opts.valuesDicts:
            if self.opts.verbose:
                print_("Reading values from", f)
            vals.update(
                ParsedParameterFile(f, noHeader=True,
                                    doMacroExpansion=True).getValueDict())
        for v in self.opts.values:
            if self.opts.verbose:
                print_("Updating values", v)
            vals.update(eval(v))

        if overrideParameters:
            vals.update(overrideParameters)

        if self.opts.verbose and len(vals) > 0:
            print_("\nUsed values\n")
            nameLen = max(len("Name"), max(*[len(k) for k in vals.keys()]))
            format = "%%%ds - %%s" % nameLen
            print_(format % ("Name", "Value"))
            print_("-" * 40)
            for k, v in sorted(iteritems(vals)):
                print_(format % (k, v))
            print_("")
        elif self.opts.verbose:
            print_("\nNo values specified\n")

        if self.opts.onlyVariables:
            return

        if self.opts.doClear:
            if self.opts.verbose:
                print_("Clearing", cName)
            sol.clear(processor=True,
                      pyfoam=True,
                      vtk=True,
                      removeAnalyzed=True,
                      keepParallel=False,
                      clearHistory=False,
                      clearParameters=True,
                      additional=["postProcessing"])

        if self.opts.writeParameters:
            fName = path.join(cName, self.parameterOutFile)
            if self.opts.verbose:
                print_("Writing parameters to", fName)
            with WriteParameterFile(fName, noHeader=True) as w:
                w.content.update(vals, toString=True)
                w["foamVersion"] = vals["foamVersion"]
                w.writeFile()

        self.addToCaseLog(cName)

        for over in self.opts.overloadDirs:
            if self.opts.verbose:
                print_("Overloading files from", over)
                self.overloadDir(sol.name, over)

        zeroOrig = path.join(sol.name, "0.org")

        hasOrig = path.exists(zeroOrig)
        if not hasOrig:
            if self.opts.verbose:
                print_("Not going to clean '0'")
            self.opts.cleanDirectories.remove("0")

        if self.opts.doCopy:
            if hasOrig:
                if self.opts.verbose:
                    print_("Found 0.org. Clearing 0")
                zeroDir = path.join(sol.name, "0")
                if path.exists(zeroDir):
                    rmtree(zeroDir)
                elif self.opts.verbose:
                    print_("No 0-directory")

            if self.opts.verbose:
                print_("")

        if self.opts.doTemplates:
            self.searchAndReplaceTemplates(sol.name, vals,
                                           self.opts.templateExt)

            if self.opts.verbose:
                print_("")

        if self.opts.doMeshCreate:
            if self.opts.meshCreateScript:
                scriptName = path.join(sol.name, self.opts.meshCreateScript)
                if not path.exists(scriptName):
                    self.error("Script", scriptName, "does not exist")
            elif path.exists(path.join(sol.name, self.defaultMeshCreate)):
                scriptName = path.join(sol.name, self.defaultMeshCreate)
            else:
                scriptName = None

            if scriptName:
                if self.opts.verbose:
                    print_("Executing", scriptName, "for mesh creation")
                if self.opts.verbose:
                    echo = "Mesh: "
                else:
                    echo = None
                result = "".join(
                    execute([scriptName], workdir=sol.name, echo=echo))
                open(scriptName + ".log", "w").write(result)
            else:
                if self.opts.verbose:
                    print_(
                        "No script for mesh creation found. Looking for 'blockMeshDict'"
                    )
                if sol.blockMesh() != "":
                    if self.opts.verbose:
                        print_(sol.blockMesh(), "found. Executing 'blockMesh'")
                    bm = BasicRunner(argv=["blockMesh", "-case", sol.name])
                    bm.start()
                    if not bm.runOK():
                        self.error("Problem with blockMesh")
            if self.opts.verbose:
                print_("")

        if self.opts.doCopy:
            self.copyOriginals(sol.name)

            if self.opts.verbose:
                print_("")

        if self.opts.doPostTemplates:
            self.searchAndReplaceTemplates(sol.name, vals,
                                           self.opts.postTemplateExt)

            if self.opts.verbose:
                print_("")

        if self.opts.doCaseSetup:
            if self.opts.caseSetupScript:
                scriptName = path.join(sol.name, self.opts.caseSetupScript)
                if not path.exists(scriptName):
                    self.error("Script", scriptName, "does not exist")
            elif path.exists(path.join(sol.name, self.defaultCaseSetup)):
                scriptName = path.join(sol.name, self.defaultCaseSetup)
            else:
                scriptName = None

            if scriptName:
                if self.opts.verbose:
                    print_("Executing", scriptName, "for case setup")
                if self.opts.verbose:
                    echo = "Case:"
                else:
                    echo = None
                result = "".join(
                    execute([scriptName], workdir=sol.name, echo=echo))
                open(scriptName + ".log", "w").write(result)
            else:
                if self.opts.verbose:
                    print_("No script for case-setup found. Nothing done")
            if self.opts.verbose:
                print_("")

        if self.opts.doTemplateClean:
            if self.opts.verbose:
                print_("Clearing templates")
            for d in self.opts.cleanDirectories:
                for e in [self.opts.templateExt, self.opts.postTemplateExt]:
                    self.cleanExtension(path.join(sol.name, d), e)
            if self.opts.verbose:
                print_("")

        if self.opts.verbose:
            print_("Case setup finished")
    def prepare(self,sol,
                cName=None,
                overrideParameters=None,
                numberOfProcessors=None):
        """Do the actual preparing
        @param numberOfProcessors: If set this overrides the value set in the
        command line"""

        if cName==None:
            cName=sol.name

        if self.opts.onlyVariables:
            self.opts.verbose=True

        vals={}
        vals,self.metaData=self.getDefaultValues(cName)
        vals.update(self.addDictValues("System",
                                       "Automatically defined values",
                                       {
                                           "casePath" : '"'+path.abspath(cName)+'"',
                                           "caseName" : '"'+path.basename(path.abspath(cName))+'"',
                                           "foamVersion" : foamVersion(),
                                           "foamFork" : foamFork(),
                                           "numberOfProcessors" : numberOfProcessors if numberOfProcessors!=None else self.opts.numberOfProcessors
                                       }))

        if len(self.opts.extensionAddition)>0:
            vals.update(self.addDictValues("ExtensionAdditions",
                                           "Additional extensions to be processed",
                                           dict((e,True) for e in self.opts.extensionAddition)))

        valsWithDefaults=set(vals.keys())

        self.info("Looking for template values",cName)
        for f in self.opts.valuesDicts:
            self.info("Reading values from",f)
            vals.update(ParsedParameterFile(f,
                                            noHeader=True,
                                            doMacroExpansion=True).getValueDict())

        setValues={}
        for v in self.opts.values:
            self.info("Updating values",v)
            vals.update(eval(v))
            setValues.update(eval(v))

        if overrideParameters:
            vals.update(overrideParameters)

        unknownValues=set(vals.keys())-valsWithDefaults
        if len(unknownValues)>0:
            self.warning("Values for which no default was specified: "+
                         ", ".join(unknownValues))

        if self.opts.verbose and len(vals)>0:
            print_("\nUsed values\n")
            nameLen=max(len("Name"),
                        max(*[len(k) for k in vals.keys()]))
            format="%%%ds - %%s" % nameLen
            print_(format % ("Name","Value"))
            print_("-"*40)
            for k,v in sorted(iteritems(vals)):
                print_(format % (k,v))
            print_("")
        else:
            self.info("\nNo values specified\n")

        self.checkCorrectOptions(vals)

        derivedScript=path.join(cName,self.opts.derivedParametersScript)
        if path.exists(derivedScript):
            self.info("Deriving variables in script",derivedScript)
            scriptText=open(derivedScript).read()
            glob={}
            oldVals=vals.copy()
            exec_(scriptText,glob,vals)
            added=[]
            changed=[]
            for k,v in iteritems(vals):
                if k not in oldVals:
                    added.append(k)
                elif vals[k]!=oldVals[k]:
                    changed.append(k)
            if len(changed)>0 and (not self.opts.allowDerivedChanges and not configuration().getboolean("PrepareCase","AllowDerivedChanges")):
                self.error(self.opts.derivedParametersScript,
                           "changed values of"," ".join(changed),
                           "\nTo allow this set --allow-derived-changes or the configuration item 'AllowDerivedChanges'")
            if len(added)>0:
                self.info("Added values:"," ".join(added))
            if len(changed)>0:
                self.info("Changed values:"," ".join(changed))
            if len(added)==0 and len(changed)==0:
                self.info("Nothing added or changed")
        else:
            self.info("No script",derivedScript,"for derived values")

        if self.opts.onlyVariables:
            return

        if self.opts.doClear:
            self.info("Clearing",cName)
            sol.clear(processor=True,
                      pyfoam=True,
                      vtk=True,
                      removeAnalyzed=True,
                      keepParallel=False,
                      clearHistory=False,
                      clearParameters=True,
                      additional=["postProcessing"])

        if self.opts.writeParameters:
            fName=path.join(cName,self.parameterOutFile)
            self.info("Writing parameters to",fName)
            with WriteParameterFile(fName,noHeader=True) as w:
                w.content.update(vals,toString=True)
                w["foamVersion"]=vals["foamVersion"]
                w.writeFile()

        if self.opts.writeReport:
            fName=path.join(cName,self.parameterOutFile+".rst")
            self.info("Writing report to",fName)
            with open(fName,"w") as w:
                helper=RestructuredTextHelper(defaultHeading=1)
                w.write(".. title:: "+self.__strip(vals["caseName"])+"\n")
                w.write(".. sectnum::\n")
                w.write(".. header:: "+self.__strip(vals["caseName"])+"\n")
                w.write(".. header:: "+time.asctime()+"\n")
                w.write(".. footer:: ###Page### / ###Total###\n\n")

                w.write("Parameters set in case directory "+
                        helper.literal(self.__strip(vals["casePath"]))+" at "+
                        helper.emphasis(time.asctime())+"\n\n")
                w.write(".. contents::\n\n")
                if len(self.opts.valuesDicts):
                    w.write(helper.heading("Parameter files"))
                    w.write("Parameters read from files\n\n")
                    w.write(helper.enumerateList([helper.literal(f) for f in self.opts.valuesDicts]))
                    w.write("\n")
                if len(setValues)>0:
                    w.write(helper.heading("Overwritten parameters"))
                    w.write("These parameters were set from the command line\n\n")
                    w.write(helper.definitionList(setValues))
                    w.write("\n")
                w.write(helper.heading("Parameters with defaults"))
                w.write(self.makeReport(vals))
                if len(unknownValues)>0:
                    w.write(helper.heading("Unspecified parameters"))
                    w.write("If these parameters are actually used then specify them in "+
                            helper.literal(self.defaultParameterFile)+"\n\n")
                    tab=helper.table(True)
                    for u in unknownValues:
                        tab.addRow(u)
                        tab.addItem("Value",vals[u])
                    w.write(str(tab))

        self.addToCaseLog(cName)

        for over in self.opts.overloadDirs:
            self.info("Overloading files from",over)
            self.overloadDir(sol.name,over)

        zeroOrig=path.join(sol.name,"0.org")

        hasOrig=path.exists(zeroOrig)
        cleanZero=True

        if not hasOrig:
            self.info("Not going to clean '0'")
            self.opts.cleanDirectories.remove("0")
            cleanZero=False

        if self.opts.doCopy:
            if hasOrig:
                self.info("Found 0.org. Clearing 0")
                zeroDir=path.join(sol.name,"0")
                if path.exists(zeroDir):
                    rmtree(zeroDir)
                else:
                    self.info("No 0-directory")

            self.info("")
        else:
            cleanZero=False

        if self.opts.doTemplates:
            self.searchAndReplaceTemplates(sol.name,
                                           vals,
                                           self.opts.templateExt)

            self.info("")

        backupZeroDir=None

        if self.opts.doMeshCreate:
            if self.opts.meshCreateScript:
                scriptName=path.join(sol.name,self.opts.meshCreateScript)
                if not path.exists(scriptName):
                    self.error("Script",scriptName,"does not exist")
            elif path.exists(path.join(sol.name,self.defaultMeshCreate)):
                scriptName=path.join(sol.name,self.defaultMeshCreate)
            else:
                scriptName=None

            if scriptName:
                self.info("Executing",scriptName,"for mesh creation")
                if self.opts.verbose:
                    echo="Mesh: "
                else:
                    echo=None
                result="".join(execute([scriptName],workdir=sol.name,echo=echo))
                open(scriptName+".log","w").write(result)
            else:
                self.info("No script for mesh creation found. Looking for 'blockMeshDict'")
                if sol.blockMesh()!="":
                    self.info(sol.blockMesh(),"found. Executing 'blockMesh'")
                    bm=BasicRunner(argv=["blockMesh","-case",sol.name])
                    bm.start()
                    if not bm.runOK():
                        self.error("Problem with blockMesh")
                for r in sol.regions():
                    self.info("Checking region",r)
                    s=SolutionDirectory(sol.name,region=r,
                                        archive=None,paraviewLink=False)
                    if s.blockMesh()!="":
                        self.info(s.blockMesh(),"found. Executing 'blockMesh'")
                        bm=BasicRunner(argv=["blockMesh","-case",sol.name,
                                             "-region",r])
                        bm.start()
                        if not bm.runOK():
                            self.error("Problem with blockMesh")

            self.info("")

            if cleanZero and path.exists(zeroDir):
                self.warning("Mesh creation recreated 0-directory")
                if self.opts.keepZeroDirectoryFromMesh:
                    backupZeroDir=zeroDir+".bakByPyFoam"
                    self.info("Backing up",zeroDir,"to",backupZeroDir)
                    move(zeroDir,backupZeroDir)
                else:
                    self.info("Data in",zeroDir,"will be removed")

        if self.opts.doCopy:
            self.copyOriginals(sol.name)

            self.info("")

            if backupZeroDir:
                self.info("Copying backups from",backupZeroDir,"to",zeroDir)
                self.overloadDir(zeroDir,backupZeroDir)
                self.info("Removing backup",backupZeroDir)
                rmtree(backupZeroDir)

        if self.opts.doPostTemplates:
            self.searchAndReplaceTemplates(sol.name,
                                           vals,
                                           self.opts.postTemplateExt)

            self.info("")

        if self.opts.doCaseSetup:
            if self.opts.caseSetupScript:
                scriptName=path.join(sol.name,self.opts.caseSetupScript)
                if not path.exists(scriptName):
                    self.error("Script",scriptName,"does not exist")
            elif path.exists(path.join(sol.name,self.defaultCaseSetup)):
                scriptName=path.join(sol.name,self.defaultCaseSetup)
            else:
                scriptName=None

            if scriptName:
                self.info("Executing",scriptName,"for case setup")
                if self.opts.verbose:
                    echo="Case:"
                else:
                    echo=None
                result="".join(execute([scriptName],workdir=sol.name,echo=echo))
                open(scriptName+".log","w").write(result)
            else:
                self.info("No script for case-setup found. Nothing done")
            self.info("")

        if self.opts.doFinalTemplates:
            self.searchAndReplaceTemplates(sol.name,
                                           vals,
                                           self.opts.finalTemplateExt)

        if self.opts.doTemplateClean:
            self.info("Clearing templates")
            for d in self.opts.cleanDirectories:
                for e in [self.opts.templateExt,
                          self.opts.postTemplateExt,
                          self.opts.finalTemplateExt]:
                    self.cleanExtension(path.join(sol.name,d),e)
            self.info("")

        self.info("Case setup finished")
Ejemplo n.º 10
0
    def run(self):
        config = ConfigParser.ConfigParser()
        files = self.parser.getArgs()

        good = config.read(files)
        # will work with 2.4
        # if len(good)!=len(files):
        #    print_("Problem while trying to parse files",files)
        #    print_("Only ",good," could be parsed")
        #    sys.exit(-1)

        benchName = config.get("General", "name")
        if self.opts.nameAddition != None:
            benchName += "_" + self.opts.nameAddition
        if self.opts.foamVersion != None:
            benchName += "_v" + self.opts.foamVersion

        isParallel = config.getboolean("General", "parallel")
        lam = None

        if isParallel:
            nrCpus = config.getint("General", "nProcs")
            machineFile = config.get("General", "machines")
            if not path.exists(machineFile):
                self.error("Machine file ", machineFile,
                           "needed for parallel run")
            lam = LAMMachine(machineFile, nr=nrCpus)
            if lam.cpuNr() > nrCpus:
                self.error("Wrong number of CPUs: ", lam.cpuNr())

            print_("Running parallel on", lam.cpuNr(), "CPUs")

        if config.has_option("General", "casesDirectory"):
            casesDirectory = path.expanduser(
                config.get("General", "casesDirectory"))
        else:
            casesDirectory = foamTutorials()

        if not path.exists(casesDirectory):
            self.error("Directory", casesDirectory,
                       "needed with the benchmark cases is missing")
        else:
            print_("Using cases from directory", casesDirectory)

        benchCases = []
        config.remove_section("General")

        for sec in config.sections():
            print_("Reading: ", sec)
            skipIt = False
            skipReason = ""
            if config.has_option(sec, "skip"):
                skipIt = config.getboolean(sec, "skip")
                skipReason = "Switched off in file"
            if self.opts.excases != None and not skipIt:
                for p in self.opts.excases:
                    if fnmatch(sec, p):
                        skipIt = True
                        skipReason = "Switched off by pattern '" + p + "'"
            if self.opts.cases != None:
                for p in self.opts.cases:
                    if fnmatch(sec, p):
                        skipIt = False
                        skipReason = ""

            if skipIt:
                print_("Skipping case ..... Reason:" + skipReason)
                continue
            sol = config.get(sec, "solver")
            cas = config.get(sec, "case")
            pre = eval(config.get(sec, "prepare"))
            preCon = []
            if config.has_option(sec, "preControlDict"):
                preCon = eval(config.get(sec, "preControlDict"))
            con = eval(config.get(sec, "controlDict"))
            bas = config.getfloat(sec, "baseline")
            wei = config.getfloat(sec, "weight")
            add = []
            if config.has_option(sec, "additional"):
                add = eval(config.get(sec, "additional"))
                print_("Adding: ", add)
            util = []
            if config.has_option(sec, "utilities"):
                util = eval(config.get(sec, "utilities"))
                print_("Utilities: ", util)
            nr = 99999
            if config.has_option(sec, "nr"):
                nr = eval(config.get(sec, "nr"))
            sp = None
            if config.has_option(sec, "blockSplit"):
                sp = eval(config.get(sec, "blockSplit"))
            toRm = []
            if config.has_option(sec, "filesToRemove"):
                toRm = eval(config.get(sec, "filesToRemove"))
            setInit = []
            if config.has_option(sec, "setInitial"):
                setInit = eval(config.get(sec, "setInitial"))

            parallelOK = False
            if config.has_option(sec, "parallelOK"):
                parallelOK = config.getboolean(sec, "parallelOK")

            deMet = ["metis"]
            if config.has_option(sec, "decomposition"):
                deMet = config.get(sec, "decomposition").split()

            if deMet[0] == "metis":
                pass
            elif deMet[0] == "simple":
                if len(deMet) < 2:
                    deMet.append(0)
                else:
                    deMet[1] = int(deMet[1])
            else:
                print_("Unimplemented decomposition method", deMet[0],
                       "switching to metis")
                deMet = ["metis"]

            if isParallel == False or parallelOK == True:
                if path.exists(path.join(casesDirectory, sol, cas)):
                    benchCases.append(
                        (nr, sec, sol, cas, pre, con, preCon, bas, wei, add,
                         util, sp, toRm, setInit, deMet))
                else:
                    print_("Skipping", sec, "because directory",
                           path.join(casesDirectory, sol, cas),
                           "could not be found")
            else:
                print_("Skipping", sec, "because not parallel")

        benchCases.sort()

        parallelString = ""
        if isParallel:
            parallelString = ".cpus=" + str(nrCpus)

        resultFile = open(
            "Benchmark." + benchName + "." + uname()[1] + parallelString +
            ".results", "w")

        totalSpeedup = 0
        minSpeedup = None
        maxSpeedup = None
        totalWeight = 0
        runsOK = 0
        currentEstimate = 1.

        print_("\nStart Benching\n")

        csv = CSVCollection("Benchmark." + benchName + "." + uname()[1] +
                            parallelString + ".csv")

        #        csvHeaders=["description","solver","case","caseDir","base",
        #                    "benchmark","machine","arch","cpus","os","version",
        #                    "wallclocktime","cputime","cputimeuser","cputimesystem","maxmemory","cpuusage","speedup"]

        for nr, description, solver, case, prepare, control, preControl, base, weight, additional, utilities, split, toRemove, setInit, decomposition in benchCases:
            #    control.append( ("endTime",-2000) )
            print_("Running Benchmark: ", description)
            print_("Solver: ", solver)
            print_("Case: ", case)
            caseName = solver + "_" + case + "_" + benchName + "." + uname(
            )[1] + ".case"
            print_("Short name: ", caseName)
            caseDir = caseName + ".runDir"

            csv["description"] = description
            csv["solver"] = solver
            csv["case"] = case
            csv["caseDir"] = caseDir
            csv["base"] = base

            csv["benchmark"] = benchName
            csv["machine"] = uname()[1]
            csv["arch"] = uname()[4]
            if lam == None:
                csv["cpus"] = 1
            else:
                csv["cpus"] = lam.cpuNr()
            csv["os"] = uname()[0]
            csv["version"] = uname()[2]

            workDir = path.realpath(path.curdir)

            orig = SolutionDirectory(path.join(casesDirectory, solver, case),
                                     archive=None,
                                     paraviewLink=False)
            for a in additional + utilities:
                orig.addToClone(a)
            orig.cloneCase(path.join(workDir, caseDir))

            if oldApp():
                argv = [solver, workDir, caseDir]
            else:
                argv = [solver, "-case", path.join(workDir, caseDir)]

            run = BasicRunner(silent=True,
                              argv=argv,
                              logname="BenchRunning",
                              lam=lam)
            runDir = run.getSolutionDirectory()
            controlFile = ParameterFile(runDir.controlDict())

            for name, value in preControl:
                print_("Setting parameter", name, "to", value,
                       "in controlDict")
                controlFile.replaceParameter(name, value)

            for rm in toRemove:
                fn = path.join(caseDir, rm)
                print_("Removing file", fn)
                remove(fn)

            for field, bc, val in setInit:
                print_("Setting", field, "on", bc, "to", val)
                SolutionFile(runDir.initialDir(),
                             field).replaceBoundary(bc, val)

            oldDeltaT = controlFile.replaceParameter("deltaT", 0)

            for u in utilities:
                print_("Building utility ", u)
                execute("wmake 2>&1 >%s %s" % (path.join(
                    caseDir, "BenchCompile." + u), path.join(caseDir, u)))

            print_("Preparing the case: ")
            if lam != None:
                prepare = prepare + [("decomposePar", "")]
                if decomposition[0] == "metis":
                    lam.writeMetis(
                        SolutionDirectory(path.join(workDir, caseDir)))
                elif decomposition[0] == "simple":
                    lam.writeSimple(
                        SolutionDirectory(path.join(workDir, caseDir)),
                        decomposition[1])

            if split:
                print_("Splitting the mesh:", split)
                bm = BlockMesh(runDir.blockMesh())
                bm.refineMesh(split)

            for pre, post in prepare:
                print_("Doing ", pre, " ....")
                post = post.replace("%case%", caseDir)
                if oldApp():
                    args = string.split("%s %s %s %s" %
                                        (pre, workDir, caseDir, post))
                else:
                    args = string.split(
                        "%s -case %s %s" %
                        (pre, path.join(workDir, caseDir), post))
                util = BasicRunner(silent=True,
                                   argv=args,
                                   logname="BenchPrepare_" + pre)
                util.start()

            controlFile.replaceParameter("deltaT", oldDeltaT)

            #    control.append(("endTime",-1000))
            for name, value in control:
                print_("Setting parameter", name, "to", value,
                       "in controlDict")
                controlFile.replaceParameter(name, value)

            print_("Starting at ", asctime(localtime(time())))
            print_(
                " Baseline is %f, estimated speedup %f -> estimated end at %s "
                % (base, currentEstimate,
                   asctime(localtime(time() + base / currentEstimate))))
            print_("Running the case ....")
            run.start()

            speedup = None
            cpuUsage = 0
            speedupOut = -1

            try:
                speedup = base / run.run.wallTime()
                cpuUsage = 100. * run.run.cpuTime() / run.run.wallTime()
            except ZeroDivisionError:
                print_("Division by Zero: ", run.run.wallTime())

            if not run.runOK():
                print_("\nWARNING!!!!")
                print_(
                    "Run had a problem, not using the results. Check the log\n"
                )
                speedup = None

            if speedup != None:
                speedupOut = speedup

                totalSpeedup += speedup * weight
                totalWeight += weight
                runsOK += 1
                if maxSpeedup == None:
                    maxSpeedup = speedup
                elif speedup > maxSpeedup:
                    maxSpeedup = speedup
                if minSpeedup == None:
                    minSpeedup = speedup
                elif speedup < minSpeedup:
                    minSpeedup = speedup

            print_("Wall clock: ", run.run.wallTime())
            print_("Speedup: ", speedup, " (Baseline: ", base, ")")
            print_("CPU Time: ", run.run.cpuTime())
            print_("CPU Time User: "******"CPU Time System: ", run.run.cpuSystemTime())
            print_("Memory: ", run.run.usedMemory())
            print_("CPU Usage: %6.2f%%" % (cpuUsage))

            csv["wallclocktime"] = run.run.wallTime()
            csv["cputime"] = run.run.cpuTime()
            csv["cputimeuser"] = run.run.cpuUserTime()
            csv["cputimesystem"] = run.run.cpuSystemTime()
            csv["maxmemory"] = run.run.usedMemory()
            csv["cpuusage"] = cpuUsage
            if speedup != None:
                csv["speedup"] = speedup
            else:
                csv["speedup"] = "##"

            csv.write()

            resultFile.write(
                "Case %s WallTime %g CPUTime %g UserTime %g SystemTime %g Memory %g MB  Speedup %g\n"
                % (caseName, run.run.wallTime(), run.run.cpuTime(),
                   run.run.cpuUserTime(), run.run.cpuSystemTime(),
                   run.run.usedMemory(), speedupOut))

            resultFile.flush()

            if speedup != None:
                currentEstimate = totalSpeedup / totalWeight

            if self.opts.removeCases:
                print_("Clearing case", end=" ")
                if speedup == None:
                    print_("not ... because it failed")
                else:
                    print_("completely")
                    rmtree(caseDir, ignore_errors=True)

            print_()
            print_()