def submitProtocol(script, **params):
'''Launch a protocol, to a queue or executing directly.
If the queue options are found, it will be launched with
configuration (command and file template) found in project settings
This function should be called from ProjectDir
'''
#Load the config module
launch = loadLaunchModule()
launchFilename = script.replace('.py', '.job')
# This is for make a copy of nodes files
nodesFile = script.replace('.py', '.nodes')
params['nodesfileBackup'] = nodesFile
params['file'] = launchFilename
params['XMIPP_HOME'] = os.environ['XMIPP_HOME']
#create launch file
launchfile = open(launchFilename, 'w')
launchfile.write(launch.FileTemplate % params)
launchfile.close()
command = launch.Program + " " + launch.ArgsTemplate % params
from protlib_xmipp import greenStr, redStr
from protlib_sql import SqliteDb
print "** Submiting to queue: '%s'" % greenStr(command)
ps = Popen(command, shell=True, stdout=PIPE)
out = ps.communicate()[0]
import re
s = re.search('(\d+)', out)
if s:
return int(s.group(0))
else:
print "** Couldn't parse %s ouput: %s" % (greenStr(launch.Program), redStr(out))
return SqliteDb.UNKNOWN_JOBID
def runJob(log,
programname,
params,
NumberOfMpi = 1,
NumberOfThreads = 1,
RunInBackground=False):
command = buildRunCommand(log,
programname,
params,
NumberOfMpi,
NumberOfThreads,
RunInBackground)
if log:
from protlib_xmipp import greenStr
printLog("Running command: %s" % greenStr(command),log)
from subprocess import call
retcode = 1000
try:
retcode = call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr)
if log:
printLog("Process returned with code %d" % retcode,log)
if retcode != 0:
raise Exception("Process returned with code %d, command: %s" % (retcode,command))
except OSError, e:
raise Exception("Execution failed %s, command: %s" % (e, command))
def _endSingleStep(self, _connection, _cursor, stepRow, info):
# Report step finish and update database
msg = greenStr(" Step finished: %s" % info.stepStr)
printLog(msg, self.Log, out=True, err=True)
sqlCommand = (
"""UPDATE %(TableSteps)s SET finish = CURRENT_TIMESTAMP
WHERE step_id=%(step_id)d
AND run_id=%(run_id)d"""
% info.dict
)
_cursor.execute(sqlCommand)
_connection.commit()
def submitProgram(script, **params):
''' Same function as submitProtocol but just for single
programs, not need to be inside a Project '''
#Load the config module
launch = loadLaunchModule()
launchFilename = script.replace('.py', '.job')
nodesFile = script.replace('.py', '.nodes')
params['nodesfileBackup'] = nodesFile
params['file'] = launchFilename
#create launch file
launchfile = open(launchFilename, 'w')
launchfile.write(launch.FileTemplate % params)
launchfile.close()
command = launch.Program + " " + launch.ArgsTemplate % params
from protlib_xmipp import greenStr
print "** Submiting to queue: '%s'" % greenStr(command)
os.system(command)
def runProgramTests(self, program):
tests = self.progDict[program]
n = len(tests)
outPath = join(self.fnDir, program)
outDir = outPath
testName = ""
testNo = 1
md = MetaData(self._statistics)
for test, mpi, random, preruns, postruns, changeDirectory, testfiles, owner in tests:
# for test, mpi, random, preruns, postruns, changeDirectory, testfiles in tests:
objid = md.addObject()
if n > 1:
outDir = outPath + "_%02d" % testNo
testName = "(%d of %d)" % (testNo, n)
# test num
md.setValue(MDL_BLOCK_NUMBER, testNo, objid)
# program name
# print type(program)
md.setValue(MDL_PROGRAM, str(program), objid)
dtBegin = datetime.now()
timeStr = str(dtBegin)
# beginning time
md.setValue(MDL_DATE, str(timeStr), objid)
print "------------------------------------------------------------------------------------"
print warnStr(">>> Running test %(testName)s of %(program)s (%(timeStr)s)" % locals())
print " Output dir: "
print " ", outDir
print " Statistics file: "
print " ", self._statistics
print " Timeout: "
print " %d seconds" % self._timeout
if exists(outDir):
shutil.rmtree(outDir)
os.makedirs(outDir)
self.outDir = outDir
self.program = program
test = self.expandFormat(test)
self.runCommands(preruns, "prerun")
if mpi:
cmd = (
"mpirun -np 3 `which %s`" % program
) ##DO NOT REPLACE SO WE CAN TEST MPI EASILY.replace("xmipp_", "xmipp_mpi_")
else:
cmd = program
if changeDirectory:
cmd = "cd %s ; " % outDir + cmd + " %s > stdout.txt 2> stderr.txt" % test
else:
cmd += " %s > %s/stdout.txt 2> %s/stderr.txt" % (test, outDir, outDir)
print " Command: "
print " ", greenStr(cmd)
# run the test itself
command = Command(cmd)
self._command = command
try:
command.run(timeout=self._timeout)
except KeyboardInterrupt:
command.terminate()
# result = os.system(cmd)
# result = subprocess.call(cmd, shell=True)
self.runCommands(postruns, "postrun")
tdEnd = (datetime.now() - dtBegin).total_seconds()
# elapsed time
md.setValue(MDL_TIME, tdEnd, objid)
print " Elapsed time: %d seconds" % tdEnd
error = self.checkResult(testfiles, outDir, random)
if len(error):
self.error += error
self.errorFlag = True
print redStr("ERRORS:\n" + error)
md.setValue(MDL_ENABLED, -1, objid)
else:
md.setValue(MDL_ENABLED, 1, objid)
testNo += 1
md.setValue(MDL_USER, str(owner), objid)
md.write(self._statistics)