def find_inputs():
"""
Finds the inputs in subdirs. Verifies the appropriateness of
each input file. Returns Dictionary of {dir: inputfile}
"""
inputdirs = list()
filetree = dict()
results = list()
#find files in dirs:
for d, _, filenames in os.walk(os.curdir):
for f in filenames:
fileExt = os.path.splitext(f)[-1]
if (fileExt == '.in' or fileExt == '.gjf' or fileExt == '.com'
or fileExt == '.inp' or fileExt == '.input'):
results.append(os.path.join(d,f))
for r in results:
if os.path.dirname(r) in filetree:
filetree[os.path.dirname(r)].append(os.path.basename(r))
else:
filetree[os.path.dirname(r)] = [os.path.basename(r)]
multidir = list()
badinput = list()
logging.debug("{} potential inputs found".format(len(filetree)))
inputdirs = dict()
for key in filetree:
for v in filetree[key]:
job = check_input_file(os.path.join(key, v))
if job:
if key in inputdirs:
logging.warning("More than one valid input file in {}." \
"Please have only one input per directory.".format(key))
multidir.append(key)
else:
inputdirs[key] = [v, job]
else:
logging.warning("File {} not valid input.".format(
str(os.path.join(key, v))))
badinput.append(str(os.path.join(key, v)))
if key not in inputdirs:
logging.warning(
"Directory {} does not contain valid input.".format(key))
if len(badinput) > 0:
logging.info("Following inputs have errors:\n{}".format(
turbogo_helpers.list_str(badinput)))
if len(multidir) > 0:
logging.info("Following directories have too many inputs:\n{}".format(
turbogo_helpers.list_str(multidir)))
return inputdirs
def main():
"""First call on the code"""
logging.basicConfig(
format=('%(asctime)s - %(name)s - [%(levelname)s] - %(message)s'),
filename='turbocontrol.log',
level=logging.DEBUG)
logging.info('Started')
p = argparse.ArgumentParser()
parser = argparse.ArgumentParser(prog="TurboControl",
description="Usage: %prog [options]")
group = parser.add_mutually_exclusive_group()
group.add_argument('-v', '--verbose', action='store_true',
help='Run more verbose (show debugging info)')
group.add_argument('-q', '--quiet', action="store_true",
help='Run less verbose (show only warnings)')
parser.add_argument('-s', '--solvent', dest="solvent", action="store_true",
help='Show solvents known to Turbocontrol')
args = parser.parse_args()
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.INFO)
if args.solvent:
print "\n".join(sorted(turbogo_helpers.DIELECTRICS.keys(), key=lambda s: s.lower()))
exit()
if args.verbose:
ch.setLevel(logging.DEBUG)
elif args.quiet:
ch.setLevel(logging.WARNING)
logging.getLogger().setLevel(logging.INFO)
formatter = logging.Formatter(
'%(asctime)s - %(name)s - [%(levelname)s] - %(message)s'
)
ch.setFormatter(formatter)
logging.getLogger().addHandler(ch)
start = time()
inputdirs = find_inputs()
inputfiles = list()
for key in inputdirs:
inputfiles.append(str(os.path.join(key, inputdirs[key][0])))
logging.info("Inputs found at:\n{}".format(
turbogo_helpers.list_str(sorted(inputfiles))))
jobs = list()
for key in inputdirs:
job = Jobset(key, inputdirs[key][0], inputdirs[key][1])
job.submit()
job.curstart = time()
if not args.verbose:
try:
os.remove(os.path.join(key, 'define.log'))
except (OSError, IOError):
pass
jobs.append(job)
end = time() - start
logging.info("Set up and submitted {} jobs in {} seconds.".format(
len(jobs),end))
if len(jobs) > 0:
watch_jobs(jobs)
else:
logging.warning("No jobs submitted. Exiting.")
exit()
def watch_jobs(jobs):
"""
Monitors jobs running. If jobs request frequency, then submits to frequency
calculation
"""
orunning = list()
frunning = list()
ocomplete = list()
fcomplete = list()
ocrashed = list()
fcrashed = list()
crashed = list()
completed = list()
failed_submit = list()
stuck = list()
allcomplete = False
jobdict = dict()
starttime = time()
for job in jobs:
if job.status == 'Opt Submitted' or job.status == 'TS Submitted':
orunning.append(job.jobid)
jobdict[job.jobid] = job
elif job.status == 'Freq Submitted':
frunning.append(job.jobid)
jobdict[job.jobid] = job
else:
failed_submit.append(job.name + ' - ' + job.status)
logging.info('There are {} jobs being watched.'.format(
len(jobdict)
))
if len(failed_submit) > 0:
logging.warning('There are {} jobs that failed to launch:\n{}'.format(
len(failed_submit),
turbogo_helpers.list_str(failed_submit)
))
if len(jobdict) == 0:
exit()
loopcount = 0
change = False
#delay to ensures all jobs are in queue, and catch first moment fails
sleep(60)
while not allcomplete:
alljobs = turbogo_helpers.get_all_active_jobs()
if len(alljobs) == 0 and (len(orunning) > 0 or len(frunning) > 0):
#possible fail at getting jobs from queue
sleep(60)
alljobs = turbogo_helpers.get_all_active_jobs()
if len(alljobs) == 0:
#One more try
sleep(300)
alljobs = turbogo_helpers.get_all_active_jobs()
checkojobs = list(orunning)
checkfjobs = list(frunning)
for job in alljobs:
if job in checkojobs:
checkojobs.remove(job)
elif job in checkfjobs:
checkfjobs.remove(job)
if len(checkojobs) != 0:
#Some jobs not running
for ojob in checkojobs:
job = jobdict[ojob]
del jobdict[ojob]
orunning.remove(job.jobid)
#find out what happened to the job & deal with it
status = check_opt(job)
if status == 'freq':
ocomplete.append(job.name)
frunning.append(job.jobid)
jobdict[job.jobid] = job
logging.debug(
"Job {} submitted for freq with jobid {}.".format(
job.name, job.jobid
))
elif status == 'fcrashed':
fcrashed.append(job.name)
crashed.append(job.name)
logging.debug("Job {} crashed starting freq.".format(
job.name
))
elif status == 'ocrashed':
ocrashed.append(job.name)
crashed.append(job.name)
logging.debug("Job {} crashed in opt.".format(
job.name
))
else:
completed.append(job.name)
write_stats(job)
logging.debug("Job {} completed opt.".format(
job.name
))
change = True
if len(checkfjobs) != 0:
#some freq not running
for fjob in checkfjobs:
job = jobdict[fjob]
del jobdict[fjob]
frunning.remove(job.jobid)
#find out what happened to the job and deal with it
status = check_freq(job)
if status == 'opt':
#job was resubmitted with new geometry to avoid saddle point
orunning.append(job.jobid)
jobdict[job.jobid] = job
logging.debug(
"Job {} resubmitted for opt with jobid {}.".format(
job.name, job.jobid
))
elif status == 'fcrashed':
fcrashed.append(job.name)
crashed.append(job.name)
logging.debug("Job {} crashed starting freq.".format(
job.name
))
elif status == 'ocrashed':
ocrashed.append(job.name)
crashed.append(job.name)
logging.debug("Job {} crashed restarting opt.".format(
job.name
))
elif status == 'same' or status == 'imaginary':
stuck.append(job.name)
write_stats(job)
logging.info(
"Job {} stuck on transition state with freq {}.".format(
job.name, job.firstfreq))
elif status == 'ts':
write_stats(job)
completed.append(job.name)
logging.debug("Job {} completed ts.".format(
job.name
))
else:
write_stats(job)
completed.append(job.name)
logging.debug("Job {} completed freq.".format(
job.name
))
change = True
if len(orunning) == 0 and len(frunning) == 0:
#all jobs finished or crashed:
allcomplete = True
else:
if loopcount % (3*6) == 0 and change == True:
#3-Hourly status update if a change happened
logstring = "\n----------------------------------------------" \
"------\n"
logstring += "At {}:\n".format(strftime("%d/%m/%y %H:%M:%S"))
if len(orunning) > 0:
logstring += "There are {} running opt jobs:\n{}\n".format(
len(orunning), turbogo_helpers.list_str(orunning))
if len(frunning) > 0:
logstring += "There are {} running freq jobs:\n{}\n".format(
len(frunning), turbogo_helpers.list_str(frunning))
if len(crashed) > 0:
logstring += "There are {} crashed jobs:\n{}\n".format(
len(crashed),
turbogo_helpers.list_str(crashed))
if len(stuck) > 0:
logstring += "There are {} stuck jobs:\n{}\n".format(
len(stuck), turbogo_helpers.list_str(stuck))
if len(completed) > 0:
logstring += "There are {} completed jobs:\n{}\n".format(
len(completed), turbogo_helpers.list_str(completed))
logstring += "-----------------------------------------------" \
"-----"
logging.info(logstring)
change = False
loopcount += 1
sleep(10*60)
#after job finished/crashed logging
elapsed = turbogo_helpers.time_readable(time()-starttime)
logging.warning("{} jobs completed. {} jobs crashed.".format(
len(fcomplete),len(crashed)))
logstring = "\n----------------------------------------------------\n"
logstring += "Completed at {} after {}:\n".format(
strftime("%d/%m/%y %H:%M:%S"), elapsed)
if len(completed) > 0:
logstring += "There are {} completed jobs:\n{}\n".format(
len(completed), turbogo_helpers.list_str(completed))
if len(stuck) > 0:
logstring += "There are {} stuck jobs:\n{}\n".format(
len(stuck), turbogo_helpers.list_str(stuck))
if len(crashed) > 0:
logstring += "There are {} crashed jobs:\n{}\n".format(
len(crashed), turbogo_helpers.list_str(crashed))
if len(failed_submit) > 0:
logstring += "There are {} jobs that failed to start:\n{}\n".format(
len(failed_submit), turbogo_helpers.list_str(failed_submit))
logstring += "----------------------------------------------------"
logging.info(logstring)
