def generate(self):
# Parent config dict is none
configDicts = [None]
if self.cCluster.jobIdxParent >= self.cCluster.nJobs-1:
raise ValueError("jobIdxParent=%i not feasible, since you generate %i jobs from idx 0 till %i !" % (self.cCluster.jobIdxParent,self.cCluster.nJobs, self.cCluster.nJobs-1) )
for jobIdx in range(0,self.cCluster.nJobs):
CE.printHeader("Generating Simple Job: ====================================")
CE.printKeyMessage("JobIndex","%i" % jobIdx + (" (not files because parent job!)" if jobIdx <= self.cCluster.jobIdxParent else "") )
# first make a new self.config
self.config = self.makeInterpolationConfig();
# setting the jobIdx
self.config["Job"]["jobIdx"] = str(jobIdx)
# final interpolation of all automatic generated options and conversion to self.configDict
# and checking of feasible values before template writting
# from now self.cCluster , self.cJob and self.cRigidBodySim are available (reference to self.configDict)
self.convertValues()
# only generate files for the job for jobIndices which are greater then jobIdxParent
# jobIdxParent is the parent job, which we base our nJobs on
if jobIdx > self.cCluster.jobIdxParent :
self.checkConfig(interact=self.cCluster.interact)
self.printOptions()
# make job script dir (if exists, try to remove it, if no -> abort)
cF.makeDirectory( self.cJob.scriptDir, name="Job script dir", defaultMakeEmpty=False, interact= self.cCluster.interact)
self.writeJobScriptArgs( os.path.join(self.cJob.scriptDir, "configureScriptArgs.txt" ) )
# write all templates
self.writeTemplates(self, configDicts);
# save conficDict for next jobIdx (possibly)
configDicts.append(self.configDict)
CE.printHeader("==========================================================")
def __checkConfig(self, interact):
# Check all values
cF.makeDirectory(self.cCluster.jobGeneratorOutputDir, interact=False, name="Job output dir")
self.cCluster.jobGeneratorOutputDir = os.path.abspath(self.cCluster.jobGeneratorOutputDir);
if not path.exists(self.cCluster.jobGeneratorConfig):
raise NameError("Job config file: %s does not exist!" % self.cCluster.jobGeneratorConfig)
else:
self.cCluster.jobGeneratorConfig = os.path.abspath(self.cCluster.jobGeneratorConfig);
if(self.cCluster.nProcesses < 1):
raise NameError("Process number: %i wrong (>1)!" % self.cCluster.nProcesses )
if(self.cCluster.runTime < 0):
raise NameError("Run time value: %i wrong (>1)!" % self.cCluster.runTime )
if(self.cCluster.ramPerCore < 1):
raise NameError("Ram per core value: %i wrong (>1)!" % self. cCluster.ramPerCore )
if(self.cCluster.localScratchPerCore < 1):
raise NameError("Local scratch per core value: %i wrong (>1)!" % self.cCluster.localScratchPerCore )
if(self.cCluster.nJobs < 1):
raise NameError("Number of jobs to generate: %i wrong (>1)!" % self.cCluster.nJobs )
def main():
""" {old validatation file infos} is compared
to { new validation file infos} ==> outputs new file validation info
"""
parser = MyOptParser()
parser.add_argument("-s", "--searchDirNew", dest="searchDirNew",
help="""This is the search directory where it is looked for output files (.tiff,.exr,.rib.gz). """,
metavar="<path>", default=None, required=False)
parser.add_argument("--valFileInfoGlobNew", dest="valFileInfoGlobNew",
help="""
The globbing expression for all input xmls with file status which
are consolidated into a new file info under --output. The found and validated files in --searchDir (if specified) are
added to the set of new files.
""", default=None, metavar="<glob>", required=False)
parser.add_argument("--valFileInfoGlobOld", dest="valFileInfoGlobOld",
help="""
The globbing expression for all old input xmls with file status which
are consolidated with the new files into a combined file info under --output.
""", default=None, metavar="<glob>", required=False)
parser.add_argument("--pipelineSpecs", dest="pipelineSpecs", default="",
help="""Json file with info about the pipeline, fileValidation, fileValidationTools.
""", metavar="<string>", required=True)
parser.add_argument("--statusFolder", dest="statusFolder", default=None,
help="""The output status folder which contains links to files which are finished, or can be recovered.
""", metavar="<string>", required=False)
parser.add_argument("--validateOnlyLastModified", dest="validateOnlyLastModified", type=cF.toBool, default=True,
help="""The file with the moset recent modified time is only validated, all others are set to finished!.""", required=False)
parser.add_argument("-o", "--output", dest="output",
help="""The output xml which is written, which proivides validation info for each file found""", metavar="<path>", required=True)
try:
print("====================== FileValidation ===========================")
opts= AttrMap(vars(parser.parse_args()))
if not opts.searchDirNew and not opts.valFileInfoGlobNew:
raise ValueError("You need to define either searchDirNew or valFileInfoGlobNew!")
if opts.valFileInfoGlobOld == "":
opts.valFileInfoGlobOld = None
print("searchDir: %s" % opts.searchDirNew)
print("valFileInfoGlobNew: %s" % opts.valFileInfoGlobNew)
print("valFileInfoGlobOld: %s" % opts.valFileInfoGlobOld)
print("output: %s" % opts.output)
d = cF.jsonLoad(opts.pipelineSpecs)
pipelineTools = d["pipelineTools"]
fileValidationSpecs = d["fileValidationSpecs"]
fileValidationTools = d["fileValidationTools"]
valDataAllNew = dict()
deleteFiles = []
# load new validataion datas
if opts.valFileInfoGlobNew is not None:
print("Load new validation files")
valDataAllNew , valFilesNew = loadValidationFiles(opts.valFileInfoGlobNew)
preferGlobalPaths(valDataAllNew)
# add searchDir files to new set
# search files ============================================================================
if opts.searchDirNew is not None:
print("Validate all files in: %s with pipeLineSpecs: %s" % (opts.searchDirNew , opts.pipelineSpecs) )
allFiles = searchFiles(opts.searchDirNew, opts, fileValidationSpecs,fileValidationTools,pipelineTools)
for ha, f in allFiles.items():
if ha in valDataAllNew:
print("""WARNING: File %s already found in validation data set
from globbing expr. %s """ % (f["absPath"], opts.valFileInfoGlobNew))
else:
valDataAllNew[ha] = f
# ===============================================================================================
# load old validation datas
if opts.valFileInfoGlobOld is not None:
print("Load old validation files")
valDataAllOld , valFilesOld = loadValidationFiles(opts.valFileInfoGlobOld)
preferGlobalPaths(valDataAllOld)
# add old to new validatation infos
for ha, valInfo in valDataAllOld.items():
if ha not in valDataAllNew:
# this old file hash is not in our current list, so add it!
# check absPath if it exists otherwise try to extent the relPath with dir of this validation file.
if not os.path.exists(valInfo["absPath"]):
absPath = os.path.join( os.path.dirname(valInfo["validatationInfoPath"]) , valInfo["relPath"] )
if not os.path.exists(absPath):
print(valInfo["validatationInfoPath"])
raise NameError("""File path in valid. info file: %s
does not exist, extended rel. path to: %s does also not exist!""" % (valInfo["absPath"],absPath))
else:
print("Replacing inexisting path %s with %s", valInfo["absPath"], absPath)
valInfo["absPath"] = absPath
# copy element to new file info
valDataAllNew[ha] = valInfo
else:
# we have the same hash in the new info
# take our new one which is better!
# delete old file if it is not linked to by new file
if os.path.realpath(valDataAllNew[ha]["absPath"]) != os.path.realpath(valInfo["absPath"]):
deleteFiles.append(valInfo["absPath"])
# make final list
finalFiles = [ f for f in valDataAllNew.values() ]
printSummary(finalFiles,pipelineTools,False)
print("Make output validation file")
f = open(opts.output,"w+")
cF.jsonDump(finalFiles,f, sort_keys=True)
f.close();
# Renew status folder, move over new xml info
if opts.statusFolder is not None:
print("Renew status folder:")
finished = os.path.join(opts.statusFolder,"finished")
recover = os.path.join(opts.statusFolder,"recover")
cF.makeDirectory(finished,interact=False, defaultMakeEmpty=True)
cF.makeDirectory(recover ,interact=False, defaultMakeEmpty=True)
# make symlinks for all files in the appropriate folder:
paths = {"recover": recover, "finished": finished}
for f in finalFiles:
h = f["hash"]
p = os.path.relpath(f["absPath"],start=paths[f["status"]])
filename = os.path.basename(p)
head,ext = os.path.splitext(filename)
os.symlink(p, os.path.join( paths[f["status"]] , head+"-uuid-"+h+ext ) );
print("=================================================================")
except Exception as e:
print("====================================================================")
print("Exception occured: " + str(e))
print("====================================================================")
traceback.print_exc(file=sys.stdout)
parser.print_help()
return 1
def generate(self):
# Parent config dict is none
configDicts = [None]
if self.cCluster.jobIdxParent >= self.cCluster.nJobs-1:
raise ValueError("jobIdxParent=%i not feasible, since you generate %i jobs from idx 0 till %i !" % (self.cCluster.jobIdxParent,self.cCluster.nJobs, self.cCluster.nJobs-1) )
for jobIdx in range(0,self.cCluster.nJobs):
print("Generating MPI Job: SimpleExecutable =================")
print("-> JobIndex: %i" % jobIdx + (" (not files because parent job!)" if jobIdx <= self.cCluster.jobIdxParent else "") )
# first make a new self.config
self.config = self.makeInterpolationConfig();
# setting the jobIdx
self.config["Job"]["jobIdx"] = str(jobIdx)
self.config["Job"]["submitCommand"] = " ".join([self.config["Cluster"]["submitCommand"] ,
(configDicts[-1].Cluster.submitArgsChainJob if jobIdx != 0 else "") , self.config["Job"]["submitArgs"]])
# final interpolation of all automatic generated options and conversion to self.configDict
# and checking of feasible values before template writting
# from now self.cCluster , self.cJob and are available (reference to self.configDict)
self.convertValues()
# only generate files for the job for jobIndices which are greater then jobIdxParent
# jobIdxParent is the parent job, which we base our nJobs on
if jobIdx > self.cCluster.jobIdxParent :
self.checkConfig(interact=self.cCluster.interact)
self.printOptions()
# make job script dir (if exists, try to remove it, if no -> abort)
cf.makeDirectory( self.cJob.scriptDir,
name="Job script dir",
defaultMakeEmpty=False,
interact= self.cCluster.interact)
self.writeJobScriptArgs( os.path.join(self.cJob.scriptDir, "submitScriptArgs.txt" ) )
# write all templates
self.writeTemplates(self, configDicts);
# check if we submit the job
if self.cCluster.submitJobs:
print("Trying to submit job with command: \n%s" % self.cJob.submitCommand)
cf.callProcess(self.cJob.submitCommand)
#end if
# save conficDict for next jobIdx (possibly)
configDicts.append(self.configDict)
print("==========================================================")
# Write total submit file to first folder
config0 = configDicts[1];
filePath = os.path.join(config0.Job.scriptDir,"submitAll.sh")
f = open(filePath,"w+")
commands = [];
for c in configDicts:
if c:
commands.append(c.Job.submitCommand)
f.write("\n".join(commands))
cf.makeExecutable(filePath);
def generate(self):
configDicts = [None]
if self.cCluster.jobIdxParent >= self.cCluster.nJobs-1:
raise CE.MyValueError("jobIdxParent=%i not feasible, since you generate %i jobs from idx 0 till %i !" % (self.cCluster.jobIdxParent,self.cCluster.nJobs, self.cCluster.nJobs-1) )
for jobIdx in range(0,self.cCluster.nJobs):
CE.printHeader("Generating MPI Job: Tool Pipeline ========================")
CE.printKeyMessage("JobIndex","%i" % jobIdx + (" (no generating, because parent job!)" if jobIdx <= self.cCluster.jobIdxParent else "") )
# first make a new self.config
self.config = self.makeInterpolationConfig();
# setting the jobIdx
self.config["Job"]["jobIdx"] = str(jobIdx)
self.config["Job"]["submitCommand"] = " ".join([self.config["Cluster"]["submitCommand"] ,
(configDicts[-1].Cluster.submitArgsChainJob if jobIdx > self.cCluster.jobIdxParent+1 else "") , self.config["Job"]["submitArgs"]])
if configDicts[-1]:
self.config["Pipeline-PreProcess"]["validationInfoFile"] = configDicts[-1]["Pipeline-PostProcess"]["validationInfoFile"]
else:
self.config["Pipeline-PreProcess"]["validationInfoFile"] = ""
# final interpolation of all automatic generated options and conversion to self.configDict
# and checking of feasible values before template writting
# from now self.cCluster , self.cJob and self.cRigidBodySim are available (reference to self.configDict)
self.convertValues()
# only make jobs which are greater then parent!
if jobIdx > self.cCluster.jobIdxParent:
self.checkConfig(interact=self.cCluster.interact)
self.printOptions()
# make job script dir (if exists, try to remove it, if no -> abort)
cF.makeDirectory( self.cJob.scriptDir, name="Job script dir", defaultMakeEmpty=False, interact= self.cCluster.interact)
self.writeJobScriptArgs( os.path.join(self.cJob.scriptDir, "configureScriptArgs.txt" ) )
# write all templates
self.writeTemplates(self, configDicts);
# check if we submit command
# overwrite submit command by appending all submit args
if self.cCluster.submitJobs:
print("Trying to submit job with command: \n%s" % self.cJob.submitCommand)
cF.callProcess(self.cJob.submitCommand)
# save conficDict for next jobIdx (possibly)
# TODO save config dict in job script folder (json file)
configDicts.append(self.configDict)
CE.printHeader("==========================================================")
# Write total submit file to first folder
config0 = configDicts[self.cCluster.jobIdxParent+2];
filePath = os.path.join(config0.Job.scriptDir,"submitAll.sh")
f = open(filePath,"w+")
commands = [];
for c in configDicts[self.cCluster.jobIdxParent+2:]:
if c:
commands.append(c.Job.submitCommand)
f.write("\n".join(commands))
cF.makeExecutable(filePath);
