def __init__(self, jobsDir, elements, potFile, alat):
# Initialise all the required directories' path.
baseDir = os.path.join(os.path.dirname(os.path.realpath(
inspect.getfile(inspect.currentframe()))), '..', '..')
self.templatesDir = os.path.join(baseDir, 'templates')
self.jobsDir = os.path.join(baseDir, jobsDir, 'jobs', 'new')
# Initialise the require information and settings.
self.elements = elements.split()
self.potFile = potFile
self.potPath = os.path.join(self.templatesDir, potFile + '.pot')
self.alat = alat
error = False # Error flag for exiting program.
# Check if the required directories exist
if os.path.isdir(self.templatesDir) is False:
print('Templates directory does not exists, '
'it is required to have the templates files at ')
print(self.templatesDir + '.')
error = True
if os.path.isdir(self.jobsDir) is False:
print('The directory provided does not exists.')
error = True
if (os.path.isfile(self.potPath) is False):
print('The potential file provided does not exists.')
error = True
if error:
nmod.nexit()
else:
os.chdir(self.jobsDir)
def generateConcentrations(self, num, **kwargs):
""" Generate the required permutations of concentrations """
if self.potFile == 'sc_5_elements_b2':
a, b, c, d, e = 1.0, 0.5, 0.0, 0.5, 0.0
step = b / (num - 1)
precision = len(str(step).split('.')[1])
conc = [None]*5
conc[0] = nmod.float2str(precision, a)
for i in range(0, num * num):
x, y = i % num, int(i / num)
conc[1] = nmod.float2str(precision, b - x * step)
conc[2] = nmod.float2str(precision, c + x * step)
conc[3] = nmod.float2str(precision, d - y * step)
conc[4] = nmod.float2str(precision, e + y * step)
self.create(conc[0] + '_' + conc[1] + '_' + conc[2]
+ '_' + conc[3] + '_' + conc[4], **kwargs)
elif self.potFile == 'fcc_5_elements_l21':
a, b, c, d, e = 1.0, 1.0, 0.0, 1.0, 0.0
step = b / (num - 1)
precision = len(str(step).split('.')[1])
conc = [None]*5
conc[0] = nmod.float2str(precision, a)
for i in range(0, num * num):
x, y = i % num, int(i / num)
conc[1] = nmod.float2str(precision, b - x * step)
conc[2] = nmod.float2str(precision, c + x * step)
conc[3] = nmod.float2str(precision, d - y * step)
conc[4] = nmod.float2str(precision, e + y * step)
self.create(conc[0] + '_' + conc[1] + '_' + conc[2]
+ '_' + conc[3] + '_' + conc[4], **kwargs)
else:
print(self.potFile + ' has not yet been implemented.')
nmod.nexit()
def __init__(self, jobsDir, elements, potFile, alat):
numElements = len(elements.split())
if numElements != 5:
print('Expecting 5 elements, but ' + numElements
+ ' (' + elements + ') were inputted.')
nmod.nexit()
Compound.__init__(self, jobsDir, elements, potFile, alat)
def __init__(self, mainDir):
baseDir = os.path.join(os.path.dirname(os.path.realpath(
inspect.getfile(inspect.currentframe()))), '..')
self.mainDir = os.path.join(baseDir, mainDir)
self.rawDir = os.path.join(self.mainDir, 'raw')
self.dataDir = os.path.join(self.mainDir, 'data')
self.analysisDir = os.path.join(self.mainDir, 'analysis')
self.listDataDir = []
error = False
# Check if the required directories exist
if os.path.isdir(self.mainDir) is False:
print('The directory provided does not exists.')
error = True
if (os.path.isdir(self.rawDir) is False
and os.path.isdir(self.dataDir) is False):
print('The directory provided does have a raw or data folder.')
error = True
else:
# Check if there are any data in the raw folder.
numTotal = 0
if os.path.isdir(self.dataDir) is True:
numData = len([dirname for dirname in os.listdir(self.dataDir)
if os.path.isdir(os.path.join(self.dataDir, dirname))])
if numData != 0:
numTotal += numData
self.listDataDir = sorted(os.listdir(self.dataDir))
if os.path.isdir(self.rawDir) is True:
numRaw = len([dirname for dirname in os.listdir(self.rawDir)
if os.path.isdir(os.path.join(self.rawDir, dirname))])
if numRaw != 0 and len(self.listDataDir) == 0:
numTotal += numRaw
self.listDataDir = sorted(os.listdir(self.dataDir))
if numTotal == 0:
print('No data in ' + os.path.join(mainDir, 'data'))
print('or in ' + os.path.join(mainDir, 'raw') + ',')
print('Make sure that your data are in one of those folders.')
error = True
if error:
nmod.nexit()
else:
os.chdir(self.mainDir)
def submitArray(mainDir, pbsFile, start, end, **kwargs):
""" Submit many array jobs without overloading the task farm """
# Define all the required directories.
baseDir = os.path.join(os.path.dirname(os.path.realpath(
inspect.getfile(inspect.currentframe()))), '..')
templatesDir = os.path.join(baseDir, 'templates')
jobsDir = os.path.join(baseDir, mainDir, 'jobs')
# Set default settings.
settings = {
'step': 10,
'interval': 300
}
# Replace default settings with user defined settings.
for key, value in kwargs.iteritems():
settings[key] = value
if checkRequired(mainDir, templatesDir, jobsDir):
nmod.nexit()
else:
os.chdir(jobsDir)
iterations = int(math.ceil((end - start) / settings['step']))
last = iterations - 1 # Last iteration point for checks later.
subCmd = ['qsub', pbsFile]
checkInterval = settings['interval']
timeStart = int(time.time())
timePrev = timeStart
# Submit the first batch of jobs.
reps = {
'tmpTSTART' : start,
'tmpTEND' : settings['step'] + start - 1
}
nmod.modFile(pbsFile,
os.path.join(templatesDir, pbsFile), reps)
subprocess.Popen(subCmd)
for i in range(1, iterations):
# Check if any jobs are still idle or blocked.
# If there are, check again after an interval.
# Only submit the next batch of jobs when there are no queued jobs.
time.sleep(3) # Sleep to make sure the jobs are submitted.
while True:
# Read in the showq command as an array separated by newline.
p = subprocess.Popen(['showq', '-u', 'phukgm'],
stdout = subprocess.PIPE,
stderr = subprocess.PIPE)
stdout, _ = p.communicate()
stdout = stdout.decode()
stdout = stdout.split('\n')
# Check if queued jobs are non-zero.
if ('Idle Jobs: 0' in stdout[-2]
and 'Blocked Jobs: 0' in stdout[-2]):
timePrev = time.time()
break
else:
print('There are still idle and blocked jobs after '
+ nmod.seconds2str(time.time() - timePrev) + '.')
timePrev = time.time()
time.sleep(checkInterval) # Check jobs interval.
# Submit the next batch of jobs.
# Make sure the last iteration has the correct
# ending point of -t (tempTEND).
if i == last:
print('Submitting -t ' + str(i * settings['step'] + start)
+ '-' + str(end) + '...')
reps = {
'tmpTSTART' : i * settings['step'] + start,
'tmpTEND' : end
}
else:
print('Submitting -t ' + str(i * settings['step'] + start)
+ '-' + str((i+1) * settings['step'] + start - 1) + '...')
reps = {
'tmpTSTART' : i * settings['step'] + start,
'tmpTEND' : (i+1) * settings['step'] + start - 1
}
nmod.modFile(pbsFile,
os.path.join(templatesDir, pbsFile), reps)
subprocess.Popen(subCmd)
timeTaken = nmod.seconds2str(time.time() - timeStart)
print('All jobs submitted. Time taken: ' + timeTaken + '.')
