PyROOT TMVA BookMethod gives segfault

WilliamK · February 26, 2020, 4:12pm

Hi all,
I’m trying to load several signal and background trees from a loop using python with pyROOT, but I am having some strange error with BookMethod.

This is the message I get:

Factory                  : Booking method: BDT
                         : 

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
    gdb.printing.register_pretty_printer(gdb.current_objfile(),
    gdb.printing.register_pretty_printer(gdb.current_objfile(),

Thread 2 (Thread 0x7f7e4fe55700 (LWP 2337572)):
#0  0x00007f7e6556bafb in do_futex_wait.constprop.1 () from /lib64/libpthread.so.0
#1  0x00007f7e6556bb8f in __new_sem_wait_slow.constprop.0 () from /lib64/libpthread.so.0
#2  0x00007f7e6556bc2b in sem_wait

GLIBC_2.2.5 () from /lib64/libpthread.so.0
#3  0x00007f7e6588f795 in PyThread_acquire_lock () from /lib64/libpython2.7.so.1.0
#4  0x00007f7e6585b2e6 in PyEval_RestoreThread () from /lib64/libpython2.7.so.1.0
#5  0x00007f7e4fe98016 in time_sleep () from /usr/lib64/python2.7/lib-dynload/timemodule.so
#6  0x00007f7e65862d40 in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#7  0x00007f7e6586508d in PyEval_EvalCodeEx () from /lib64/libpython2.7.so.1.0
#8  0x00007f7e657eeabd in function_call () from /lib64/libpython2.7.so.1.0
#9  0x00007f7e657c9ab3 in PyObject_Call () from /lib64/libpython2.7.so.1.0
#10 0x00007f7e6585d74d in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#11 0x00007f7e6586270d in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#12 0x00007f7e6586270d in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0
#13 0x00007f7e6586508d in PyEval_EvalCodeEx () from /lib64/libpython2.7.so.1.0
#14 0x00007f7e657ee9c8 in function_call () from /lib64/libpython2.7.so.1.0
#15 0x00007f7e657c9ab3 in PyObject_Call () from /lib64/libpython2.7.so.1.0
#16 0x00007f7e657d8aa5 in instancemethod_call () from /lib64/libpython2.7.so.1.0
#17 0x00007f7e657c9ab3 in PyObject_Call () from /lib64/libpython2.7.so.1.0
#18 0x00007f7e6585b947 in PyEval_CallObjectWithKeywords () from /lib64/libpython2.7.so.1.0
#19 0x00007f7e65893882 in t_bootstrap () from /lib64/libpython2.7.so.1.0
#20 0x00007f7e65565e65 in start_thread () from /lib64/libpthread.so.0
#21 0x00007f7e64b7488d in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7f7e65d6d740 (LWP 2337546)):
#0  0x00007f7e64b3b469 in waitpid () from /lib64/libc.so.6
#1  0x00007f7e64ab8f12 in do_system () from /lib64/libc.so.6
#2  0x00007f7e64ab92c1 in system () from /lib64/libc.so.6
#3  0x00007f7e5d420644 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so.6.18
#4  0x00007f7e5d42248c in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so.6.18
#5  <signal handler called>
#6  0x00007f7e4e825f56 in TMVA::DataInputHandler::GetEntries(std::vector<TMVA::TreeInfo, std::allocator<TMVA::TreeInfo> > const&) const () from /usr/lib64/root/libTMVA.so.6.18
#7  0x00007f7e4e825fac in TMVA::DataInputHandler::GetEntries() const () from /usr/lib64/root/libTMVA.so.6.18
#8  0x00007f7e4e840145 in TMVA::DataSetFactory::BuildInitialDataSet(TMVA::DataSetInfo&, TMVA::DataInputHandler&) () from /usr/lib64/root/libTMVA.so.6.18
#9  0x00007f7e4e8404c7 in TMVA::DataSetFactory::CreateDataSet(TMVA::DataSetInfo&, TMVA::DataInputHandler&) () from /usr/lib64/root/libTMVA.so.6.18
#10 0x00007f7e4e846c6d in TMVA::DataSetManager::CreateDataSet(TString const&) () from /usr/lib64/root/libTMVA.so.6.18
#11 0x00007f7e4e8454ec in TMVA::DataSetInfo::GetDataSet() const () from /usr/lib64/root/libTMVA.so.6.18
#12 0x00007f7e4e8b780a in TMVA::MethodBDT::ProcessOptions() () from /usr/lib64/root/libTMVA.so.6.18
#13 0x00007f7e4e85ac4c in TMVA::Factory::BookMethod(TMVA::DataLoader*, TString, TString, TString) () from /usr/lib64/root/libTMVA.so.6.18
#14 0x00007f7e4e85b864 in TMVA::Factory::BookMethod(TMVA::DataLoader*, TMVA::Types::EMVA, TString, TString) () from /usr/lib64/root/libTMVA.so.6.18
#15 0x00007f7e65bac381 in ?? ()
#16 0x000000000542adf8 in ?? ()
#17 0x00007f7e5942c63c in clang::DiagnosticsEngine::setSeverity(unsigned int, clang::diag::Severity, clang::SourceLocation) () from /usr/lib64/root/libCling.so
#18 0x00000000052be330 in ?? ()
#19 0x00000009053d5608 in ?? ()
#20 0x00007f7e5d3358b0 in ?? () from /usr/lib64/root/libCore.so.6.18
#21 0x00007fffd4fc97a0 in ?? ()
#22 0x0000000004ed9a10 in ?? ()
#23 0x00000000053d0950 in ?? ()
#24 0x00007f7e64e3d760 in ?? () from /lib64/libc.so.6
#25 0x0000000000000030 in ?? ()
#26 0x00007f7e5a29d420 in __bss_start () from /usr/lib64/root/libCling.so
#27 0x00007fffd4fc9590 in ?? ()
#28 0x0000000004f25b30 in ?? ()
#29 0x0000000000000000 in ?? ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at http://root.cern.ch/bugs Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#6  0x00007f7e4e825f56 in TMVA::DataInputHandler::GetEntries(std::vector<TMVA::TreeInfo, std::allocator<TMVA::TreeInfo> > const&) const () from /usr/lib64/root/libTMVA.so.6.18
#7  0x00007f7e4e825fac in TMVA::DataInputHandler::GetEntries() const () from /usr/lib64/root/libTMVA.so.6.18
#8  0x00007f7e4e840145 in TMVA::DataSetFactory::BuildInitialDataSet(TMVA::DataSetInfo&, TMVA::DataInputHandler&) () from /usr/lib64/root/libTMVA.so.6.18
#9  0x00007f7e4e8404c7 in TMVA::DataSetFactory::CreateDataSet(TMVA::DataSetInfo&, TMVA::DataInputHandler&) () from /usr/lib64/root/libTMVA.so.6.18
#10 0x00007f7e4e846c6d in TMVA::DataSetManager::CreateDataSet(TString const&) () from /usr/lib64/root/libTMVA.so.6.18
#11 0x00007f7e4e8454ec in TMVA::DataSetInfo::GetDataSet() const () from /usr/lib64/root/libTMVA.so.6.18
#12 0x00007f7e4e8b780a in TMVA::MethodBDT::ProcessOptions() () from /usr/lib64/root/libTMVA.so.6.18
#13 0x00007f7e4e85ac4c in TMVA::Factory::BookMethod(TMVA::DataLoader*, TString, TString, TString) () from /usr/lib64/root/libTMVA.so.6.18
#14 0x00007f7e4e85b864 in TMVA::Factory::BookMethod(TMVA::DataLoader*, TMVA::Types::EMVA, TString, TString) () from /usr/lib64/root/libTMVA.so.6.18
#15 0x00007f7e65bac381 in ?? ()
#16 0x000000000542adf8 in ?? ()
#17 0x00007f7e5942c63c in clang::DiagnosticsEngine::setSeverity(unsigned int, clang::diag::Severity, clang::SourceLocation) () from /usr/lib64/root/libCling.so
#18 0x00000000052be330 in ?? ()
#19 0x00000009053d5608 in ?? ()
#20 0x00007f7e5d3358b0 in ?? () from /usr/lib64/root/libCore.so.6.18
#21 0x00007fffd4fc97a0 in ?? ()
#22 0x0000000004ed9a10 in ?? ()
#23 0x00000000053d0950 in ?? ()
#24 0x00007f7e64e3d760 in ?? () from /lib64/libc.so.6
#25 0x0000000000000030 in ?? ()
#26 0x00007f7e5a29d420 in __bss_start () from /usr/lib64/root/libCling.so
#27 0x00007fffd4fc9590 in ?? ()
#28 0x0000000004f25b30 in ?? ()
#29 0x0000000000000000 in ?? ()
===========================================================


Traceback (most recent call last):
  File "TMVA/BDTClassification.py", line 180, in <module>
    classifier()
  File "TMVA/BDTClassification.py", line 160, in classifier
    "!H:!V:NTrees=1000:MinNodeSize=2.5%:MaxDepth=6:BoostType=AdaBoost:AdaBoostBeta=0.3:UseBaggedBoost:BaggedSampleFraction=0.3:SeparationType=GiniIndex:nCuts=20" );
TypeError: none of the 3 overloaded methods succeeded. Full details:
  TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader* loader, TString theMethodName, TString methodTitle, TString theOption = "") =>
    could not convert argument 2
  TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader* loader, TMVA::Types::EMVA theMethod, TString methodTitle, TString theOption = "") =>
    problem in C++; program state has been reset
  TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader*, TMVA::Types::EMVA, TString, TString, TMVA::Types::EMVA, TString) =>
    takes at least 6 arguments (4 given)

And here is the code that produces this error:

#!/usr/bin/env python
from ROOT import TMVA, TFile, TTree, TCut
from subprocess import call
from os import listdir



def is_signal(infile):
	"""
	Method checks if input string is a signal by looking for 'MA' chars in it.
	"""
	if 'MA' in infile:
		return True
	else:
		return False


def tree_name(infile, path= '/path/to/trees/'):
	"""
	Method takes a string as input and returns the name of associated tree.
	"""
	f = infile

	if is_signal(f):
		out = f.replace(path + 'Out_', 'signal_tree')
		out = out.replace('.root', '')
		return out
	else:
		out = f.replace(path + 'Out_', 'background_tree')
		out = out.replace('.root', '')
		return out
		


def n_entries(infile):
	"""
	Method takes a string as an input corresponding to dataset name and returns number of events in dataset.
	"""

	file = TFile.Open(infile)
	
	tree_name_ = tree_name(infile)

	tree = file.Get(tree_name_)
	print("Stored {} tree..\n".format(tree_name_))
	n = tree.GetEntries()
	
	return n

def total_entries(infiles = []):
	"""
	Method takes list of string corresponding to dataset names and returns the summation over all the file of the entries.
	"""
	tot_entries = 0
	for file in infiles:
		tot_entries += n_entries(file)
	return tot_entries


def weight(n_entries, tot_entries):
	"""
	return weight for classification
	"""
	w = float((tot_entries*0.5/n_entries))
	return w

def background_data(list_file):
	"""
	Method filters background names from input list and returns them in form of a list
	"""
	bkg = []
	for file in list_file:
		if not is_signal(file) and "MSSM" not in file:
			bkg.append(file)
	return bkg

def signal_data(list_file): 
	"""
	Method filters ALL signal names from input list and returns them in form of a list
	"""
	sgn = []
	for file in list_file:
		if is_signal(file):
			sgn.append(file)
	return sgn

def custom_signal_data(list_file):												#MODIFY THIS TO SELECT SUBSETS OF SIGNAL
	"""
	Method filters desired signal names from input list and returns them in form of a list
	"""
	sgn = []
	for file in list_file:
		if 'MA400' in file:
			sgn.append(file)
	return sgn


def classifier(path = '/path/to/trees/', tmva_output_file_name = 'TMVA_Output.root'):

	tmva_output_file =TFile.Open(tmva_output_file_name, 'RECREATE') 			#Opens TMVA output file. Ovverrides if tmva_output_file_name is not changed.
	
	TMVA.Tools.Instance()
	TMVA.PyMethodBase.PyInitialize()
	factory = TMVA.Factory('TMVAClassification', tmva_output_file,
		                   '!V:!Silent:Color:DrawProgressBar:Transformations=D,G:AnalysisType=Classification')	


	all_files = listdir(path)											#array containing all the file names in path
	bkg_data = [path+b for b in background_data(all_files)]								#load background dataset
	sgn_data = [path+s for s in custom_signal_data(all_files)]							#load signal dataset
	#TOT_ENTRIES = total_entries(all_files)										#uncomment when using all the data.
	TOT_ENTRIES = total_entries(bkg_data)										#comment this when using all data.
	TOT_ENTRIES += total_entries(sgn_data)										#comment this when using all data.
	print("TOTAL ENTRIES ======> ")
	print(TOT_ENTRIES)

	variables = ["dimuon_deltar",												#Define discrimination variables
			     "dimuon_deltaphi",			
			     "dimuon_deltaeta",
			     "met_pt",
			     "bjet_n",
			     #"no_btag_jet",
			     "bjet_1.Pt()",
			     "bjet_1.Eta()",
			     #"btag_jet_over2.4",
			     "deltar_bjet1_dimuon",
			     "deltapt_bjet1_dimuon",
			     "deltaeta_bjet1_dimuon"
			    ]
		
	dataloader = TMVA.DataLoader('dataset')
	for v in variables:
		dataloader.AddVariable(v)

	
	for b in bkg_data:
		f =  TFile.Open(b)
		bkg_tree = f.Get(tree_name(b))
		n = bkg_tree.GetEntries()
		bkg_weight = weight(n, TOT_ENTRIES)
		dataloader.AddBackgroundTree(bkg_tree, bkg_weight)

	for s in sgn_data:
		f =TFile.Open(s)
		sgn_tree = f.Get(tree_name(s))
		n = sgn_tree.GetEntries()
		sgn_weight = weight(n, TOT_ENTRIES)
		dataloader.AddSignalTree(sgn_tree, sgn_weight)
		

	dataloader.PrepareTrainingAndTestTree(TCut(''), "nTrain_Signal=10000:nTrain_Background=100000:nTest_Signal=0:nTest_Background=0:SplitMode=Random:NormMode=None:!V")

###################################################################### Book methods ########################################################################

	# Generate model
	#factory.BookMethod(dataloader, TMVA.Types.kBDT, "BDTG",
			                   # "!H:!V:NTrees=1000:MinNodeSize=2.5%:BoostType=Grad:Shrinkage=0.20:UseBaggedBoost:BaggedSampleFraction=0.5:nCuts=20:MaxDepth=6" );

	factory.BookMethod(dataloader, TMVA.Types.kBDT, "BDT",
			   "!H:!V:NTrees=1000:MinNodeSize=2.5%:MaxDepth=6:BoostType=AdaBoost:AdaBoostBeta=0.3:UseBaggedBoost:BaggedSampleFraction=0.3:SeparationType=GiniIndex:nCuts=20" );

	#factory.BookMethod(dataloader, TMVA.Types.kBDT, "BDTB",
			                  #  "!H:!V:NTrees=1000:BoostType=Bagging:SeparationType=GiniIndex:nCuts=20" );

	#factory.BookMethod(dataloader, TMVA.Types.kBDT, "BDTD",
			                   # "!H:!V:NTrees=1000:MinNodeSize=2.5%:MaxDepth=6:BoostType=AdaBoost:AdaBoostBeta=0.7:SeparationType=GiniIndex:nCuts=20:VarTransform=Decorrelate" );

	# Run training, test and evaluation
	factory.TrainAllMethods()
	factory.TestAllMethods()
	factory.EvaluateAllMethods()

	tmva_output_file.close()

	print("""
			==> Wrote root file: {} \n
			==> TMVAClassification is done!\n
		  """).format(tmva_output_file.GetName())

classifier()

I hope somebody can help me with this.
Many thanks,

William.

moneta · February 28, 2020, 3:04pm

Hi,

I cannot understand the error just from your code I would need to debug it. Maybe an issue with the input data .Can you please add a link to your data so one can runs your code ?

Thank you

Lorenzo

Tommaso_Diotalevi · February 28, 2020, 4:35pm

Dear Lorenzo,

I work with William and I’m interested as well. You can find a sample of a few dataset here: https://cernbox.cern.ch/index.php/s/5USXsNnstA8lz8c
The path has to be filled only in two code lines (‘path/to/trees’).

Best,
Tommaso

WilliamK · February 28, 2020, 5:15pm

Hi Lorenzo,

I see Tommaso already sent you everything, hope it helps. Thank for answering,

William.

WilliamK · March 4, 2020, 12:22pm

I resolved the issue opening all the files in a separated tree and appending them in a list so that their pointed value doesn’t get lost at each iteration of the for loop.

Then with another loop i loaded the trees in the dataloader.

Cheers,

William.

marisk · May 18, 2020, 8:04am

Hi William,

I have a similar issue as well, but I try to apply your fix and it doesn’t seem to work. Do you maybe have the code of your fix that I can take a look at?

WilliamK · May 18, 2020, 8:49am

Hi,
Yes I see I missworded what I did. The fact is that the file must be kept open during the all process so what I did is something like:

s_files = [0 for s in range(len(sgn_data))]
s_trees = [0 for s in range(len(sgn_data))]

for i, s in enumerate(sgn_data):
		s_files[i] = TFile.Open(s)
		s_trees[i] = s_files[i].Get('tree_name')
		dataloader.AddSignalTree(s_trees[i], 1)

There are probably more elegant ways to do so, but that worked for me.

Hope that helps,

William

marisk · May 18, 2020, 9:33am

Yes, this works like a charm! Thank you so much!