def crab_hadd(working_dir, new_name=None, new_dir=None, raise_on_empty=False, chunk_size=900, pattern=None):
if working_dir.endswith('/'):
working_dir = working_dir[:-1]
if new_name is None:
new_name = '_'.join(os.path.basename(working_dir).split('_')[2:])
if not new_name.endswith('.root'):
new_name += '.root'
if new_dir is not None:
new_name = os.path.join(new_dir, new_name)
expected = crab_get_njobs(working_dir)
print '%s: expecting %i files if all jobs succeeded' % (working_dir, expected)
res = crab_command('out', '--xrootd', dir=working_dir)
if 'No files to retrieve.' in res:
files = []
else:
files = [x.strip() for x in res.split('\n') if x.strip() and '.root' in x]
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
jobs = [int(f.split('_')[-1].split('.root')[0]) for f in files]
jobs.sort()
expected = range(1, expected+1)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (len(jobs), crabify_list(jobs))
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(str(j) for j in missing))
l = len(files)
if l == 0:
msg = 'crab_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CRABToolsException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
cmd = 'xrdcp -s %s %s' % (files[0], new_name)
os.system(cmd)
os.chmod(new_name, 0644)
else:
hadd(new_name, files, chunk_size)
return new_name
def cs_hadd(working_dir, new_name=None, new_dir=None, raise_on_empty=False, chunk_size=900, pattern=None):
if working_dir.endswith('/'):
working_dir = working_dir[:-1]
if new_name is None:
new_name = '_'.join(os.path.basename(working_dir).split('_')[1:])
if not new_name.endswith('.root'):
new_name += '.root'
if new_dir is not None:
new_name = os.path.join(new_dir, new_name)
expected = cs_njobs(working_dir)
print '%s: expecting %i files if all jobs succeeded' % (working_dir, expected)
files = glob(os.path.join(working_dir, '*.root'))
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
jobs = [int(f.split('_')[-1].split('.root')[0]) for f in files]
jobs.sort()
expected = range(expected)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (len(jobs), jobs)
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(str(j) for j in missing))
l = len(files)
if l == 0:
msg = 'cs_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CSHelpersException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
cmd = 'cp %s %s' % (files[0], new_name)
os.system(cmd)
os.chmod(new_name, 0644)
else:
hadd(new_name, files, chunk_size)
return new_name
def cs_hadd(working_dir,
new_name=None,
new_dir=None,
raise_on_empty=False,
chunk_size=900,
pattern=None,
range_filter=None):
working_dir, new_name, new_dir = cs_hadd_args(working_dir, new_name,
new_dir)
expected, files = cs_hadd_files(working_dir, range_filter=range_filter)
result = HaddBatchResult('condor', working_dir, new_name, new_dir,
expected, files)
print '%s: expecting %i files if all jobs succeeded' % (working_dir,
expected)
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
jobs = [int(f.split('_')[-1].split('.root')[0]) for f in files]
jobs.sort()
expected = range(expected)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (
len(jobs), jobs)
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(
str(j) for j in missing))
l = len(files)
if l == 0:
result.success = False
msg = 'cs_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CSHelpersException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
if files[0].startswith('root://'):
cmd = 'xrdcp -s %s %s' % (files[0], new_name)
else:
cmd = 'cp %s %s' % (files[0], new_name)
result.success = os.system(cmd) == 0
if result.success and not new_name.startswith('root://'):
os.chmod(new_name, 0644)
else:
result.success = hadd(new_name, files)
return result
def cs_hadd(working_dir, new_name=None, new_dir=None, raise_on_empty=False, chunk_size=900, pattern=None, range_filter=None):
working_dir, new_name, new_dir = cs_hadd_args(working_dir, new_name, new_dir)
expected, files = cs_hadd_files(working_dir, range_filter=range_filter)
print '%s: expecting %i files if all jobs succeeded' % (working_dir, expected)
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
jobs = [int(f.split('_')[-1].split('.root')[0]) for f in files]
jobs.sort()
expected = range(expected)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (len(jobs), jobs)
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(str(j) for j in missing))
l = len(files)
if l == 0:
msg = 'cs_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CSHelpersException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
if files[0].startswith('root://'):
cmd = 'xrdcp -s %s %s' % (files[0], new_name)
else:
cmd = 'cp %s %s' % (files[0], new_name)
os.system(cmd)
os.chmod(new_name, 0644)
else:
hadd(new_name, files)
return new_name
def doit(path, out_fn):
x = fromtree(os.path.join(path, 'observed.root'))
if len(x) != 1:
print 'using observed_byhand for this!'
x = fromtree(os.path.join(path, 'observed_byhand.root'))
obs = x[0]
exp_fn = os.path.join(path, 'expected.root')
if not os.path.isfile(exp_fn):
exp_fns = glob(exp_fn.replace('.root', '_*.root'))
if len(exp_fns) != njobs:
raise ValueError('only found %i files, expected %i' %
(len(exp_fns), njobs))
if not hadd(exp_fn, exp_fns):
raise ValueError('problem hadding %s from %s files' %
(exp_fn, len(exp_fns)))
exp = fromtree(exp_fn)
if len(exp) != njobs * ntoysperjob:
raise ValueError(
'unexpected number of points in %s' %
exp_fn) # this can't be given the asserts in fromtree right now
stats(out_fn, obs, exp)
def crab_hadd(working_dir,
new_name=None,
new_dir=None,
raise_on_empty=False,
chunk_size=900,
pattern=None,
lpc_shortcut=False,
range_filter=None):
working_dir, new_name, new_dir = crab_hadd_args(working_dir, new_name,
new_dir)
expected, files = crab_hadd_files(working_dir,
lpc_shortcut,
range_filter=range_filter)
result = HaddBatchResult('crab', working_dir, new_name, new_dir, expected,
files)
print '%s: expecting %i files if all jobs succeeded' % (working_dir,
expected)
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
automatic_splitting = False
pprinted = False
jobs = []
for f in files:
jobnum = f.split('_')[-1].split('.root')[0]
if crab_global_options.support_automatic_splitting and '-' in jobnum:
automatic_splitting = True
if not pprinted:
pprint(files)
pprinted = True
it, jobnum = jobnum.split('-')
it, jobnum = int(it), int(jobnum)
assert it >= 1 # probe jobs "0-*" should not show up
jobnum = it * 10000 + jobnum
else:
jobnum = int(jobnum)
jobs.append(jobnum)
jobs.sort()
expected = range(1, expected + 1)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (
len(jobs), crabify_list(jobs))
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(
str(j) for j in missing))
l = len(files)
if l == 0:
result.success = False
msg = 'crab_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CRABToolsException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
cmd = 'xrdcp -s %s %s' % (files[0], new_name)
result.success = os.system(cmd) == 0
if result.success and not new_name.startswith('root://'):
os.chmod(new_name, 0644)
else:
result.success = hadd(new_name, files)
if automatic_splitting:
n = norm_from_file(new_name)
sn, s = fn_to_sample(Samples, new_name)
if not s:
print colors.yellow(
"\tnorm_from_file returns %r, couldn't get sample %s" %
(n, sn))
else:
no1, no2 = s.datasets['main'].nevents_orig, s.datasets[
'miniaod'].nevents_orig
if n == no1 or n == no2:
print '\tnorm_from_file returns nevents_orig = %i' % n
else:
print colors.yellow(
'\tnorm_from_file returns %r while %s.nevents_orig is %i (main) %i (miniaod'
% (n, sn, no1, no2))
return result
parser.add_argument('positional', nargs='*')
parser.add_argument('-l',
'--list',
help='File containing list of filenames for input.')
options = parser.parse_args()
output_fn = None
input_files = []
if options.list:
if len(options.positional) != 1:
raise ValueError(
'when doing --list, only one positional argument allowed (the output filename)'
)
output_fn = options.positional[0]
for line in file(options.list):
line = line.strip()
if line:
input_files.append(line)
else:
if len(options.positional) < 2:
parser.print_usage()
sys.exit(1)
output_fn = options.positional[0]
input_files = options.positional[1:]
hadd(output_fn, input_files)
%(prog)s output.root file1.root file2.root [file3.root ... fileN.root]
-or-
%(prog)s -l input_file_list.txt output.root''')
parser.add_argument('positional', nargs='*')
parser.add_argument('-l', '--list',
help='File containing list of filenames for input.')
options = parser.parse_args()
output_fn = None
input_files = []
if options.list:
if len(options.positional) != 1:
raise ValueError('when doing --list, only one positional argument allowed (the output filename)')
output_fn = options.positional[0]
for line in file(options.list):
line = line.strip()
if line:
input_files.append(line)
else:
if len(options.positional) < 2:
parser.print_usage()
sys.exit(1)
output_fn = options.positional[0]
input_files = options.positional[1:]
hadd(output_fn, input_files)
new_vh_paths[path_mo.group(1)] += 1
vh_fn = os.path.join(dn, 'vertex_histos_%s.root' % jobnum)
if verbosity >= 3:
print dn, bn, jobnum, vh_fn
if not eos.exists(vh_fn):
raise IOError('no %r for %r' % vh_fn, fn)
vh_fns.append(eos.canon(vh_fn))
new_vh_path = new_vh_paths.most_common(1)[0][0]
new_vh_fn = eos.canon(os.path.join(new_vh_path, 'vertex_histos.root'))
if verbosity >= 3:
print new_vh_fn
if eos.exists(new_vh_fn):
raise ValueError('exists already: %r' % new_vh_fn)
hadds.append((new_vh_fn, vh_fns))
if rm:
print 'hadd and rm these:'
else:
print 'hadd these:'
pprint(hadds)
if rm and raw_input('ok? ').strip().lower() != 'y':
sys.exit('giving up')
for new_fn, fns in hadds:
if hadd(new_fn, fns) and rm:
for fn in fns:
eos.rm(fn)
#!/usr/bin/env python import sys from JMTucker.Tools.hadd import hadd hadd(sys.argv[1], sys.argv[2:])
def crab_hadd(working_dir, new_name=None, new_dir=None, raise_on_empty=False, chunk_size=900):
if working_dir.endswith('/'):
working_dir = working_dir[:-1]
if new_name is None:
new_name = os.path.basename(working_dir).replace('crab_','')
if not new_name.endswith('.root'):
new_name += '.root'
if new_dir is not None:
new_name = os.path.join(new_dir, new_name)
expected = crab_get_njobs(working_dir)
print '%s: expecting %i files if all jobs succeeded' % (working_dir, expected)
on_resilient = False
on_store = False
cfg = crab_cfg_parser(working_dir)
try:
storage_path = cfg.get('USER', 'storage_path')
on_resilient = 'resilient' in storage_path
except NoOptionError:
pass
try:
storage_element = cfg.get('USER', 'storage_element')
on_store = storage_element == 'T3_US_FNALLPC'
except NoOptionError:
pass
files = []
if on_resilient:
pfns = [crab_analysis_file_pfn(path) for path in glob.glob(os.path.join(working_dir, 'res/crab_fjr*xml'))]
files = ['dcap://cmsdca3.fnal.gov:24145/pnfs/fnal.gov/usr/cms/WAX/resilient/' + pfn.split('/resilient/')[1] for pfn in pfns] # JMTBAD
elif on_store:
pfns = [crab_analysis_file_pfn(path) for path in glob.glob(os.path.join(working_dir, 'res/crab_fjr*xml'))]
files = ['dcap://cmsdca3.fnal.gov:24145/pnfs/fnal.gov/usr/cms/WAX/11/' + pfn.split('/11/')[1] for pfn in pfns] # JMTBAD
else:
files = glob.glob(os.path.join(working_dir, 'res/*root'))
job_nums = defaultdict(lambda: defaultdict(list))
for f in files:
f_ = f.split('_')
job, num = int(f_[-3]), int(f_[-2])
job_nums[job][num].append(f)
sexpected = set(xrange(1,expected+1))
sjobs = set(job_nums)
if sjobs != sexpected:
print '\033[36;7m files found %r not what expected \033[m' % sorted(sjobs)
missing = sorted(sexpected - sjobs)
print '\033[36;7m missing: %r \033[m' % missing
to_drop = []
for job, nums_and_fs in job_nums.iteritems():
for num, fs in nums_and_fs.iteritems():
if len(fs) > 1:
print '\033[36;7m for job %i, more than one file with resub num %i *** will keep latest by mtime *** \033[m' % (job, num)
fs.sort(key=lambda f: os.stat(f).st_mtime)
good_f = fs[-1]
while len(fs) > 1:
bad_f = fs.pop(0)
to_drop.append((bad_f, good_f))
if len(nums_and_fs) > 1:
good_num = max(nums_and_fs)
assert len(nums_and_fs[good_num]) == 1
good_f = nums_and_fs[good_num][0]
for num, fs in nums_and_fs.iteritems():
if num != good_num:
assert len(fs) == 1
to_drop.append((fs[0], good_f))
for f, good_f in to_drop:
print '\033[36;7m dropping %s in favor of %s \033[m' % (f, good_f)
files.remove(f)
l = len(files)
if l == 0:
msg = 'crab_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CrabError(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
cmd = '%scp %s %s' % ('dc' if 'dcap' in files[0] else '', files[0], new_name)
os.system(cmd)
os.chmod(new_name, 0644)
else:
hadd(new_name, files, chunk_size)
return new_name
def crab_hadd(working_dir, new_name=None, new_dir=None, raise_on_empty=False, chunk_size=900, pattern=None, lpc_shortcut=False, range_filter=None):
working_dir, new_name, new_dir = crab_hadd_args(working_dir, new_name, new_dir)
expected, files = crab_hadd_files(working_dir, lpc_shortcut, range_filter=range_filter)
print '%s: expecting %i files if all jobs succeeded' % (working_dir, expected)
if pattern:
if '/' not in pattern:
pattern = '*/' + pattern
files = fnmatch.filter(files, pattern)
automatic_splitting = False
pprinted = False
jobs = []
for f in files:
jobnum = f.split('_')[-1].split('.root')[0]
if crab_global_options.support_automatic_splitting and '-' in jobnum:
automatic_splitting = True
if not pprinted:
pprint(files)
pprinted = True
it, jobnum = jobnum.split('-')
it, jobnum = int(it), int(jobnum)
assert it >= 1 # probe jobs "0-*" should not show up
jobnum = it*10000 + jobnum
else:
jobnum = int(jobnum)
jobs.append(jobnum)
jobs.sort()
expected = range(1, expected+1)
if jobs != expected:
print '\033[36;7m %i files found %s not what expected \033[m' % (len(jobs), crabify_list(jobs))
missing = sorted(set(expected) - set(jobs))
print '\033[36;7m %i missing: %r \033[m' % (len(missing), ' '.join(str(j) for j in missing))
l = len(files)
if l == 0:
msg = 'crab_hadd: no files found in %s' % working_dir
if raise_on_empty:
raise CRABToolsException(msg)
else:
print '\033[36;7m', msg, '\033[m'
elif l == 1:
print working_dir, ': just one file found, copying'
cmd = 'xrdcp -s %s %s' % (files[0], new_name)
os.system(cmd)
os.chmod(new_name, 0644)
else:
hadd(new_name, files)
if automatic_splitting:
n = norm_from_file(new_name)
sn, s = fn_to_sample(Samples, new_name)
if not s:
print colors.yellow("\tnorm_from_file returns %r, couldn't get sample %s" % (n, sn))
else:
no1, no2 = s.datasets['main'].nevents_orig, s.datasets['miniaod'].nevents_orig
if n == no1 or n == no2:
print '\tnorm_from_file returns nevents_orig = %i' % n
else:
print colors.yellow('\tnorm_from_file returns %r while %s.nevents_orig is %i (main) %i (miniaod' % (n, sn, no1, no2))
return new_name
