# -*- coding: utf-8 -*-
from six.moves import range
import cmath
import netCDF4
import numpy
import copy
import glob, os, re
from yambopy.dbs.excitondb import *
from yambopy.dbs.savedb import *
[docs]def take_fermi_parser(file): # calc_node_pk = node_conv_wfl.outputs.last_calculation
for line in file:
if '[X]Fermi Level' in line:
print('The Fermi level is {}'.format(line.split()[3]))
ef = float(line.split()[3])
if '[X] Fermi Level' in line:
print('The Fermi level is {}'.format(line.split()[4]))
ef = float(line.split()[4])
return ef
[docs]def yambotiming_to_seconds(yt):
t = 0
th = 0
tm = 0
ts = 0
if isinstance(yt, str):
for i in yt.replace('-',' ').split():
if 'h' in i:
th = int(i.replace('h',''))*3600
if 'm' in i:
tm = int(i.replace('m',''))*60
if 's' in i:
ts = int(i.replace('s',''))
t = th+tm+ts
return t
else:
return yt
[docs]errors = {'memory_error':['\[ERROR\]Allocation','\[ERROR\] Allocation', '\[ERROR\]out of memory', '\[ERROR\] out of memory', '\[MEMORY\] Alloc','\[MEMORY\]Alloc'],
'time_most_prob':['Alloc Xo%blc_d',],
'para_error':['\[ERROR\]Incomplete','\[ERROR\]Impossible','\[ERROR\]USER parallel',
'\[NULL\]','\[ERROR\] Incomplete','\[ERROR\] Impossible','\[ERROR\] USER parallel',
],
'X_par_allocation':['\[ERROR\]Allocation of X_par%blc_d failed'],
}
[docs]errors_raw = {'memory_error':[r'[ERROR]Allocation',r'[ERROR] Allocation', r'out of memory', r'[ERROR] out of memory', r'[MEMORY] Alloc',r'[MEMORY]Alloc'],
'time_most_prob':[r'Alloc Xo%blc_d',],
'para_error':[r'[ERROR]Incomplete',r'[ERROR]Impossible',r'[ERROR]USER parallel',
r'[NULL]',r'[ERROR] Incomplete',r'[ERROR] Impossible',r'[ERROR] USER parallel',
],
'X_par_allocation':[r'[ERROR]Allocation of X_par%blc_d failed'],
}
[docs]def parse_log(log,output_params,timing):
if 'p2y' in log.filename: #just p2y...
p2y_completed = re.compile('P2Y completed')
for line in log.lines:
if p2y_completed.findall(line):
output_params['p2y_completed'] = True
elif 'l_setup' in log.filename or 'l-setup' in log.filename:
pass
else:
#Game over...
game_over = re.compile('Game')
game_over_2 = re.compile('Clock:')
for line in log.lines:
if game_over.findall(line) or game_over_2.findall(line):
output_params['game_over'] = True
break
else:
output_params['game_over'] = False
#timing sections...
timing_new = re.compile('^\s+?<([0-9a-z-]+)> ([A-Z0-9a-z-]+)[:] \[([0-9]+)\] [A-Za-z\s]+')
timing_old = re.compile('^\s+?<([0-9a-z-]+)> \[([0-9]+)\] [A-Za-z\s]+')
timing_bugs = re.compile('\[([0-9]+)\] [A-Za-z\s]+')
#if output_params['timing'] == []:
for line in log.lines:
if timing_bugs.findall(line):
output_params['timing'].append(line) #to fix for a better parsing
elif timing_new.match(line):
output_params['timing'].append(timing_new.match(line).string)
elif timing_old.match(line):
output_params['timing'].append(timing_old.match(line).string)
time = re.compile('<([0-9hms-]+)>')
try:
last_time = time.findall(log.lines[-1])[-1]
output_params['last_time'] = yambotiming_to_seconds(last_time)
except:
try:
last_time = time.findall(output_params['timing'][-1])[-1]
output_params['last_time'] = yambotiming_to_seconds(last_time)
except:
last_time = 0
output_params['last_time'] = 0
if timing:
output_params['timing'].append('verbose_output:')
t_verbose = re.compile('^\s+?<([0-9a-z-]+)> ([A-Z0-9a-z-]+)[:] (\[TIMING\])')
t_verbose_old = re.compile('^\s+?<([0-9a-z-]+)> (\[TIMING\]) ')
for line in log.lines:
if t_verbose.match(line):
output_params['timing'].append(t_verbose.match(line).string)
elif t_verbose_old.match(line):
output_params['timing'].append(t_verbose_old.match(line).string)
#warnings
warning = re.compile('\[WARNING\]')
#memstats...
memory = re.compile('^\s+?<([0-9a-z-]+)> ([A-Z0-9a-z-]+)[:] (\[MEMORY\]) ')
memory_old = re.compile('^\s+?<([0-9a-z-]+)> (\[MEMORY\]) ')
alloc1_error = re.compile('\[ERROR\]Allocation')
alloc2_error = re.compile('\[MEMORY\] Alloc')
alloc3_error = re.compile('\[MEMORY\]out of memory')
alloc4_error = re.compile('\[MEMORY\] out of memory')
incomplete_para_error = re.compile('\[ERROR\]Incomplete')
impossible_para_error = re.compile('\[ERROR\]Impossible')
impossible_para_error2 = re.compile('\[ERROR\]USER parallel')
incomplete_para_error_ = re.compile('\[ERROR\] Incomplete')
impossible_para_error_ = re.compile('\[ERROR\] Impossible')
impossible_para_error2_ = re.compile('\[ERROR\] USER parallel')
corrupted_fragment = re.compile('\[ERROR\] Writing File')
time_probably = re.compile('Alloc Xo%blc_d')
X_par_mem = re.compile('\[ERROR\]Allocation of X_par%blc_d failed')
X_par_mem_ = re.compile('\[ERROR\] Allocation of X_par%blc_d failed')
reading_explosion_of_memory = re.compile('Reading')
for line in log.lines:
if warning.match(line):
output_params['warnings'].append(warning.match(line).string)
if memory.match(line):
output_params['memstats'].append(memory.match(line).string)
if memory_old.match(line):
output_params['memstats'].append(memory_old.match(line).string)
if alloc1_error.findall(line):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
if alloc3_error.findall(line):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
if alloc4_error.findall(line):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
if incomplete_para_error.findall(line) or impossible_para_error.findall(line) or impossible_para_error2.findall(line):
output_params['para_error'] = True
if incomplete_para_error_.findall(line) or impossible_para_error_.findall(line) or impossible_para_error2_.findall(line):
output_params['para_error'] = True
if time_probably.findall(line):
output_params['errors'].append('time_most_prob')
if corrupted_fragment.findall(line):
output_params['errors'].append('corrupted_fragment')
output_params['corrupted_fragment'] = re.findall("ndb.pp_fragment_[0-9]+",line)
try:
if reading_explosion_of_memory.findall(log.lines[-1]):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
except:
pass
try:
if alloc2_error.findall(log.lines[-1]):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
except:
pass
try:
if alloc3_error.findall(log.lines[-1]):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
except:
pass
try:
if alloc4_error.findall(log.lines[-1]):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
except:
pass
try:
if X_par_mem.findall(log.lines[-1]) or X_par_mem_.findall(log.lines[-1]):
output_params['memory_error'] = True
output_params['errors'].append('X_par_allocation')
except:
pass
if 'out of memory' in log.lines[-1]:
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
return output_params
[docs]def parse_report(report, output_params):
try:
output_params['Fermi(eV)'] = take_fermi_parser(report.lines)
except:
pass
if 'setup' in report.filename:
pass
else:
#Game over...
game_over = re.compile('Game')
game_over_2 = re.compile('Clock:')
gpu_support = re.compile('CUDA')
for line in report.lines:
if game_over.findall(line) or game_over_2.findall(line):
output_params['game_over'] = True
if gpu_support.findall(line):
output_params['has_gpu'] = True
[docs]def parse_scheduler_stderr(stderr, output_params):
m1 = re.compile('out of memory')
m1_1 = re.compile('out-of-memory')
m2 = re.compile('Segmentation')
m3 = re.compile('dumped')
t1 = re.compile('walltime')
t2 = re.compile('time')
t3 = re.compile('TIME')
for line in stderr.readlines():
if m1.findall(line) or m1_1.findall(line) or m2.findall(line) or m3.findall(line):
output_params['memory_error'] = True
output_params['errors'].append('memory_general')
elif t1.findall(line) or t2.findall(line) or t3.findall(line):
output_params['time_error'] = True
[docs]def yambo_wrote_dbs(output_params):
if len(output_params['timing']) > 4:
for step in output_params['timing']:
if '[05]' in step:
output_params['yambo_wrote_dbs'] = True
else:
output_params['yambo_wrote_dbs'] = False
[docs]def get_yambo_version(report, output_params):
pass
[docs]def parse_BS(folder,filename, save_dir):
q = filename[13:]
lat = YamboLatticeDB.from_db_file(filename=save_dir+'/ns.db1')
ydb = YamboExcitonDB.from_db_file(filename=filename,folder=folder,lattice=lat)
chi = ydb.get_chi(emin=0, emax=20, estep=0.01, broad=0.15,)
chi_ = {'eV':chi[0],'eps_2':chi[1].imag,'eps_1':chi[1].real}
excitons = {'energies':ydb.eigenvalues.real,
'intensities':ydb.get_intensities().real}
return q, chi_, excitons
