Issue when reading TTree containing short

ROOT
, ,
1

I am filling a TTree using pyROOT that contains several branches. One of the branches, the “data” branch, is the one causing the issue:

def fillSpectrums(spectrumFiles):
    spectrumsTree = ROOT.TTree("spectrums", "RAW spectrums from I4G")
    packetSize = np.array([0.0], dtype=np.int32)
    timeStamp = array.array('L', [0])
    validityFlag = np.array([0.0], dtype=np.int32)
    channelN = np.array([0.0], dtype=np.int32)
    fibreN = np.array([0.0], dtype=np.int32)
    startWL = array.array('f', [0])
    finalWL = array.array('f', [0])
    nPoints = np.array([0.0], dtype=np.int32)
    data = array.array('h', [0] * 39200)
    spectrumsTree.Branch("packetSize", packetSize, f"packetSize/I")
    spectrumsTree.Branch("timeStamp", timeStamp, f"timeStamp/l")
    spectrumsTree.Branch("validityFlag", validityFlag, f"validitFlag/I")
    spectrumsTree.Branch("channelN", channelN, f"channelN/I")
    spectrumsTree.Branch("fibreN", fibreN, f"fibreN/I")
    spectrumsTree.Branch("startWL", startWL, f"startWL/F")
    spectrumsTree.Branch("finalWL", finalWL, f"finalWL/F")
    spectrumsTree.Branch("nPoints", nPoints, f"nPoints/I")
    spectrumsTree.Branch("data", data, f"data[39200]/S")
    for spectrumFile in spectrumFiles:
        persistentRead = True
        nEvent = 0
        fileId=open(f"{spectrumFile}",'rb')
        while persistentRead == True:
            if nEvent > 1:
                persistentRead = False
            packetSize[0] = (np.fromfile(fileId, dtype='<i4', count=1))
            timeStamp[0]  = (np.fromfile(fileId, dtype='<u8', count=1))
            validityFlag[0] = (np.fromfile(fileId, dtype='<i4', count=1))
            channelN[0] = (np.fromfile(fileId, dtype='<i4', count=1))
            fibreN[0] = (np.fromfile(fileId, dtype='<i4', count=1))
            startWL[0] = (np.fromfile(fileId, dtype='<d', count=1))
            finalWL[0] = (np.fromfile(fileId, dtype='<d', count=1))
            nPoints[0] = (np.fromfile(fileId, dtype='<i4', count=1))
            dataIni = (np.fromfile(fileId, dtype='<i2', count=nPoints[0]))
            for index, element in enumerate(dataIni):
                data[index] = element
            spectrumsTree.Fill()
            nEvent += 1
    return spectrumsTree

The issue is that when trying to read the entries of the TTree using the normal procedure, the code violently breaks:

def fillRootFile(self):
        for deviceType in self.runDevices.keys():
            if deviceType != "fibres":
                continue
            foundTrees = setters.fillDeviceType(
                 runInfo=self.runInfo,
                 deviceType=deviceType
                )
            for rootTree in foundTrees:
                if rootTree.GetName() == "peaks":
                    continue
                for entry in rootTree:
                    print(entry.data)
                rootTree.Write()
        self.rootFile.Close()

Does anyone know what may be causing the issue? It is strange because when filling the tree it does not report any error, but when reading the entry yes. By exploring them with the TBrowser they appear to be fine.

The very long error log:

[jcapotor@lxplus7130 FTMS]$ /usr/bin/python3 /afs/cern.ch/user/j/jcapotor/FTMS/ROOTconversion/main.py
Filling spectrums
*** Error in `/usr/bin/python3': free(): invalid pointer: 0x00007f4244c40666 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f427dc27329]
/lib64/libpython3.6m.so.1.0(+0xfe89b)[0x7f427e99789b]
/lib64/libpython3.6m.so.1.0(_PyCFunction_FastCallDict+0x27a)[0x7f427e97f26a]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x146)[0x7f427e941ae6]
/lib64/libpython3.6m.so.1.0(+0xfedde)[0x7f427e997dde]
/lib64/libpython3.6m.so.1.0(PyType_Ready+0x188)[0x7f427e9913d8]
/lib64/libpython3.6m.so.1.0(+0xfd5ee)[0x7f427e9965ee]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy16CreateScopeProxyERKSsP7_object+0xc91)[0x7f427434cec1]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy16CreateScopeProxyERKSsP7_object+0x1311)[0x7f427434d541]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy16CreateScopeProxyEm+0x5a)[0x7f427434e93a]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy19BindCppObjectNoCastEPvmj+0x24)[0x7f427434e9d4]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy9CPPMethod16ExecuteProtectedEPvlPNS_11CallContextE+0x149)[0x7f4274327bc9]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy9CPPMethod7ExecuteEPvlPNS_11CallContextE+0x41)[0x7f42743251f1]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(_ZN8CPyCppyy9CPPMethod4CallERPNS_11CPPInstanceEP7_objectS5_PNS_11CallContextE+0xe8)[0x7f4274325d18]
/usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so(+0x56789)[0x7f427432a789]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x7f427e941a30]
/lib64/libpython3.6m.so.1.0(+0x15160c)[0x7f427e9ea60c]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f427e9ded97]
/lib64/libpython3.6m.so.1.0(+0x15124a)[0x7f427e9ea24a]
/lib64/libpython3.6m.so.1.0(+0x151583)[0x7f427e9ea583]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f427e9ded97]
/lib64/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x24f)[0x7f427e9ea91f]
/lib64/libpython3.6m.so.1.0(PyEval_EvalCode+0x3b)[0x7f427e9eb42b]
/lib64/libpython3.6m.so.1.0(+0x1dad2e)[0x7f427ea73d2e]
/lib64/libpython3.6m.so.1.0(PyRun_FileExFlags+0xa4)[0x7f427e92080b]
/lib64/libpython3.6m.so.1.0(PyRun_SimpleFileExFlags+0x39c)[0x7f427e920bdd]
/lib64/libpython3.6m.so.1.0(Py_Main+0x652)[0x7f427ea7a232]
/usr/bin/python3(main+0x119)[0x400ab9]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f427dbc8555]
/usr/bin/python3[0x400c40]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fc:01 4901726                            /usr/bin/python3.6
00601000-00602000 r--p 00001000 fc:01 4901726                            /usr/bin/python3.6
00602000-00603000 rw-p 00002000 fc:01 4901726                            /usr/bin/python3.6
00755000-04d98000 rw-p 00000000 00:00 0                                  [heap]
7f41fc000000-7f41fc021000 rw-p 00000000 00:00 0 
7f41fc021000-7f4200000000 ---p 00000000 00:00 0 
7f4202363000-7f4204000000 rw-p 00000000 00:00 0 
7f4204000000-7f4204032000 rw-p 00000000 00:00 0 
7f4204032000-7f4208000000 ---p 00000000 00:00 0 
7f4208ed6000-7f4208f16000 rw-p 00000000 00:00 0 
7f4208f16000-7f4208f17000 ---p 00000000 00:00 0 
7f4208f17000-7f4209757000 rw-p 00000000 00:00 0 
7f4209757000-7f420976a000 r-xp 00000000 00:2b 254895584                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/testing.cpython-36m-x86_64-linux-gnu.so
7f420976a000-7f420996a000 ---p 00013000 00:2b 254895584                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/testing.cpython-36m-x86_64-linux-gnu.so
7f420996a000-7f420996c000 rw-p 00013000 00:2b 254895584                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/testing.cpython-36m-x86_64-linux-gnu.so
7f420996c000-7f4209aad000 rw-p 00000000 00:00 0 
7f4209aad000-7f4209ac1000 r-xp 00000000 00:2b 254895588                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/json.cpython-36m-x86_64-linux-gnu.so
7f4209ac1000-7f4209cc1000 ---p 00014000 00:2b 254895588                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/json.cpython-36m-x86_64-linux-gnu.so
7f4209cc1000-7f4209cc2000 rw-p 00014000 00:2b 254895588                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/json.cpython-36m-x86_64-linux-gnu.so
7f4209cc2000-7f4209d02000 rw-p 00000000 00:00 0 
7f4209d02000-7f4209d7d000 r-xp 00000000 00:2b 254895572                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/parsers.cpython-36m-x86_64-linux-gnu.so
7f4209d7d000-7f4209f7c000 ---p 0007b000 00:2b 254895572                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/parsers.cpython-36m-x86_64-linux-gnu.so
7f4209f7c000-7f4209f83000 rw-p 0007a000 00:2b 254895572                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/parsers.cpython-36m-x86_64-linux-gnu.so
7f4209f83000-7f420a046000 rw-p 00000000 00:00 0 
7f420a046000-7f420a08b000 r-xp 00000000 00:2b 254895580                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/reduction.cpython-36m-x86_64-linux-gnu.so
7f420a08b000-7f420a28b000 ---p 00045000 00:2b 254895580                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/reduction.cpython-36m-x86_64-linux-gnu.so
7f420a28b000-7f420a290000 rw-p 00045000 00:2b 254895580                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/reduction.cpython-36m-x86_64-linux-gnu.so
7f420a290000-7f420a291000 rw-p 00000000 00:00 0 
7f420a291000-7f420a388000 r-xp 00000000 00:2b 254895596                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/groupby.cpython-36m-x86_64-linux-gnu.so
7f420a388000-7f420a587000 ---p 000f7000 00:2b 254895596                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/groupby.cpython-36m-x86_64-linux-gnu.so
7f420a587000-7f420a590000 rw-p 000f6000 00:2b 254895596                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/groupby.cpython-36m-x86_64-linux-gnu.so
7f420a590000-7f420a654000 rw-p 00000000 00:00 0 
7f420a654000-7f420a67a000 r-xp 00000000 00:2b 254895612                  /afs/cern.ch/user/j/jcapotor/.local/lib/python3.6/site-packages/pandas/_libs/window/indexers.cpython-36m-x86_64-linux-gnu.so *** Break *** abort



===========================================================
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 0x7f4209716700 (LWP 8996)):
#0  0x00007f427e688de2 in pthread_cond_timedwait

GLIBC_2.3.2 () from /lib64/libpthread.so.0
#1  0x00007f427e9de5f8 in take_gil () from /lib64/libpython3.6m.so.1.0
#2  0x00007f427e9de739 in PyEval_RestoreThread () from /lib64/libpython3.6m.so.1.0
#3  0x00007f427ea34e35 in time_sleep () from /lib64/libpython3.6m.so.1.0
#4  0x00007f427e97f0fe in _PyCFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#5  0x00007f427e9ea45f in call_function () from /lib64/libpython3.6m.so.1.0
#6  0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#7  0x00007f427e9ea91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#8  0x00007f427e959a92 in function_call () from /lib64/libpython3.6m.so.1.0
#9  0x00007f427e941833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#10 0x00007f427e9e0a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f427e9ea24a in fast_function () from /lib64/libpython3.6m.so.1.0
#12 0x00007f427e9ea583 in call_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#14 0x00007f427e9ea24a in fast_function () from /lib64/libpython3.6m.so.1.0
#15 0x00007f427e9ea583 in call_function () from /lib64/libpython3.6m.so.1.0
#16 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#17 0x00007f427e9eb58a in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#18 0x00007f427e941aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#19 0x00007f427e941bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#20 0x00007f427e941833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#21 0x00007f427ea7b2b2 in t_bootstrap () from /lib64/libpython3.6m.so.1.0
#22 0x00007f427ea78764 in pythread_wrapper () from /lib64/libpython3.6m.so.1.0
#23 0x00007f427e684ea5 in start_thread () from /lib64/libpthread.so.0
#24 0x00007f427dca4b0d in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7f427efa9740 (LWP 8962)):
#0  0x00007f427dc6b659 in waitpid () from /lib64/libc.so.6
#1  0x00007f427dbe8f62 in do_system () from /lib64/libc.so.6
#2  0x00007f427dbe9311 in system () from /lib64/libc.so.6
#3  0x00007f427676a3fc in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#4  0x00007f42740bb5ef in (anonymous namespace)::TExceptionHandlerImp::HandleException(int) () from /usr/lib64/root/libcppyy_backend3_6.so.6.24
#5  0x00007f427676c24b in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#6  <signal handler called>
#7  0x00007f427dbdc387 in raise () from /lib64/libc.so.6
#8  0x00007f427dbdda78 in abort () from /lib64/libc.so.6
#9  0x00007f427dc1ef67 in __libc_message () from /lib64/libc.so.6
#10 0x00007f427dc27329 in _int_free () from /lib64/libc.so.6
#11 0x00007f427e99789b in mro_implementation () from /lib64/libpython3.6m.so.1.0
#12 0x00007f427e97f26a in _PyCFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#13 0x00007f427e941ae6 in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#14 0x00007f427e997dde in mro_internal () from /lib64/libpython3.6m.so.1.0
#15 0x00007f427e9913d8 in PyType_Ready () from /lib64/libpython3.6m.so.1.0
#16 0x00007f427e9965ee in type_new () from /lib64/libpython3.6m.so.1.0
#17 0x00007f427434cec1 in CPyCppyy::CreateScopeProxy(std::string const&, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#18 0x00007f427434d541 in CPyCppyy::CreateScopeProxy(std::string const&, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#19 0x00007f427434e93a in CPyCppyy::CreateScopeProxy(unsigned long) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#20 0x00007f427434e9d4 in CPyCppyy::BindCppObjectNoCast(void*, unsigned long, unsigned int) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#21 0x00007f4274327bc9 in CPyCppyy::CPPMethod::ExecuteProtected(void*, long, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#22 0x00007f42743251f1 in CPyCppyy::CPPMethod::Execute(void*, long, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#23 0x00007f4274325d18 in CPyCppyy::CPPMethod::Call(CPyCppyy::CPPInstance*&, _object*, _object*, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#24 0x00007f427432a789 in CPyCppyy::(anonymous namespace)::mp_call(CPyCppyy::CPPOverload*, _object*, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#25 0x00007f427e941a30 in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#26 0x00007f427e9ea60c in call_function () from /lib64/libpython3.6m.so.1.0
#27 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#28 0x00007f427e9ea24a in fast_function () from /lib64/libpython3.6m.so.1.0
#29 0x00007f427e9ea583 in call_function () from /lib64/libpython3.6m.so.1.0
#30 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f427e9ea91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#32 0x00007f427e9eb42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#33 0x00007f427ea73d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#34 0x00007f427e92080b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#35 0x00007f427e920bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#36 0x00007f427ea7a232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#37 0x0000000000400ab9 in main ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum https://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at https://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.
===========================================================
#7  0x00007f427dbdc387 in raise () from /lib64/libc.so.6
#8  0x00007f427dbdda78 in abort () from /lib64/libc.so.6
#9  0x00007f427dc1ef67 in __libc_message () from /lib64/libc.so.6
#10 0x00007f427dc27329 in _int_free () from /lib64/libc.so.6
#11 0x00007f427e99789b in mro_implementation () from /lib64/libpython3.6m.so.1.0
#12 0x00007f427e97f26a in _PyCFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#13 0x00007f427e941ae6 in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#14 0x00007f427e997dde in mro_internal () from /lib64/libpython3.6m.so.1.0
#15 0x00007f427e9913d8 in PyType_Ready () from /lib64/libpython3.6m.so.1.0
#16 0x00007f427e9965ee in type_new () from /lib64/libpython3.6m.so.1.0
#17 0x00007f427434cec1 in CPyCppyy::CreateScopeProxy(std::string const&, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#18 0x00007f427434d541 in CPyCppyy::CreateScopeProxy(std::string const&, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#19 0x00007f427434e93a in CPyCppyy::CreateScopeProxy(unsigned long) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#20 0x00007f427434e9d4 in CPyCppyy::BindCppObjectNoCast(void*, unsigned long, unsigned int) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#21 0x00007f4274327bc9 in CPyCppyy::CPPMethod::ExecuteProtected(void*, long, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#22 0x00007f42743251f1 in CPyCppyy::CPPMethod::Execute(void*, long, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#23 0x00007f4274325d18 in CPyCppyy::CPPMethod::Call(CPyCppyy::CPPInstance*&, _object*, _object*, CPyCppyy::CallContext*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#24 0x00007f427432a789 in CPyCppyy::(anonymous namespace)::mp_call(CPyCppyy::CPPOverload*, _object*, _object*) () from /usr/lib64/python3.6/site-packages/libcppyy3_6.cpython-36m-x86_64-linux-gnu.so
#25 0x00007f427e941a30 in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#26 0x00007f427e9ea60c in call_function () from /lib64/libpython3.6m.so.1.0
#27 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#28 0x00007f427e9ea24a in fast_function () from /lib64/libpython3.6m.so.1.0
#29 0x00007f427e9ea583 in call_function () from /lib64/libpython3.6m.so.1.0
#30 0x00007f427e9ded97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f427e9ea91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#32 0x00007f427e9eb42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#33 0x00007f427ea73d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#34 0x00007f427e92080b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#35 0x00007f427e920bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#36 0x00007f427ea7a232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#37 0x0000000000400ab9 in main ()
===========================================================


Traceback (most recent call last):
  File "/afs/cern.ch/user/j/jcapotor/FTMS/ROOTconversion/main.py", line 5, in <module>
    conversion = RAWconverter(date=date).fillRootFile()
  File "/afs/cern.ch/user/j/jcapotor/FTMS/ROOTconversion/convertRAWdata.py", line 23, in fillRootFile
    print(data_branch.GetLeaf("data").GetValue())
cppyy.ll.AbortSignal: TLeaf* TBranch::GetLeaf(const char* name) =>
    AbortSignal: abort from C++; program state was reset

ROOT Version: 6.24/08
Platform: linuxx8664gcc
Compiler: c++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

2

It actually gets even weirder… If I run the following script the run is clean:

    def fillRootFile(self):
        for deviceType in self.runDevices.keys():
            if deviceType != "fibres":
                continue
            foundTrees = setters.fillDeviceType(
                 runInfo=self.runInfo,
                 deviceType=deviceType
                )
            for rootTree in foundTrees:
                if rootTree.GetName() == "peaks":
                    continue
                for entry in rootTree:
                    points = list(entry.data)
                    print(len(points))
                    print(type(points))
                    # plt.plot(points)
                rootTree.Write()
        self.rootFile.Close()

But if I run the script uncommenting the plotting line, it crashes:

===========================================================
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 0x7f9ea61c6700 (LWP 21771)):
#0  0x00007f9eef51ade2 in pthread_cond_timedwait

GLIBC_2.3.2 () from /lib64/libpthread.so.0
#1  0x00007f9eef8705f8 in take_gil () from /lib64/libpython3.6m.so.1.0
#2  0x00007f9eef870739 in PyEval_RestoreThread () from /lib64/libpython3.6m.so.1.0
#3  0x00007f9eef8c6e35 in time_sleep () from /lib64/libpython3.6m.so.1.0
#4  0x00007f9eef8110fe in _PyCFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#5  0x00007f9eef87c45f in call_function () from /lib64/libpython3.6m.so.1.0
#6  0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#7  0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7eba92 in function_call () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87d58a in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef90d2b2 in t_bootstrap () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef90a764 in pythread_wrapper () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef516ea5 in start_thread () from /lib64/libpthread.so.0
#24 0x00007f9eeeb36b0d in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7f9eefe3b740 (LWP 21490)):
#0  0x00007f9eeeafd659 in waitpid () from /lib64/libc.so.6
#1  0x00007f9eeea7af62 in do_system () from /lib64/libc.so.6
#2  0x00007f9eeea7b311 in system () from /lib64/libc.so.6
#3  0x00007f9ee75fc3fc in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#4  0x00007f9ee4f4d5ef in (anonymous namespace)::TExceptionHandlerImp::HandleException(int) () from /usr/lib64/root/libcppyy_backend3_6.so.6.24
#5  0x00007f9ee75fe24b in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#6  <signal handler called>
#7  0x00007f9eef81496f in PyMem_Calloc () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7efb6d in PyList_New () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7efc0a in list_repeat () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef87219a in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef872009 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#24 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#25 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#26 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#27 0x00007f9eef826705 in slot_tp_init () from /lib64/libpython3.6m.so.1.0
#28 0x00007f9eef8230c2 in type_call () from /lib64/libpython3.6m.so.1.0
#29 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#30 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#32 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#33 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#34 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#35 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#36 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#37 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#38 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#39 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#40 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#41 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#42 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#43 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#44 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#45 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#46 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#47 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#48 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#49 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#50 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#51 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#52 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#53 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#54 0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#55 0x00007f9eef87d42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#56 0x00007f9eef905d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#57 0x00007f9eef7b280b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#58 0x00007f9eef7b2bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#59 0x00007f9eef90c232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#60 0x0000000000400ab9 in main ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum https://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at https://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.
===========================================================
#7  0x00007f9eef81496f in PyMem_Calloc () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7efb6d in PyList_New () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7efc0a in list_repeat () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef87219a in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef872009 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#24 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#25 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#26 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#27 0x00007f9eef826705 in slot_tp_init () from /lib64/libpython3.6m.so.1.0
#28 0x00007f9eef8230c2 in type_call () from /lib64/libpython3.6m.so.1.0
#29 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#30 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#32 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#33 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#34 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#35 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#36 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#37 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#38 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#39 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#40 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#41 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#42 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#43 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#44 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#45 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#46 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#47 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#48 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#49 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#50 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#51 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#52 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#53 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#54 0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#55 0x00007f9eef87d42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#56 0x00007f9eef905d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#57 0x00007f9eef7b280b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#58 0x00007f9eef7b2bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#59 0x00007f9eef90c232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#60 0x0000000000400ab9 in main ()
===========================================================


 *** Break *** bus error



===========================================================
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 0x7f9ea61c6700 (LWP 21771)):
#0  0x00007f9eef51ade2 in pthread_cond_timedwait

GLIBC_2.3.2 () from /lib64/libpthread.so.0
#1  0x00007f9eef8705f8 in take_gil () from /lib64/libpython3.6m.so.1.0
#2  0x00007f9eef870739 in PyEval_RestoreThread () from /lib64/libpython3.6m.so.1.0
#3  0x00007f9eef8c6e35 in time_sleep () from /lib64/libpython3.6m.so.1.0
#4  0x00007f9eef8110fe in _PyCFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#5  0x00007f9eef87c45f in call_function () from /lib64/libpython3.6m.so.1.0
#6  0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#7  0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7eba92 in function_call () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87d58a in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef90d2b2 in t_bootstrap () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef90a764 in pythread_wrapper () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef516ea5 in start_thread () from /lib64/libpthread.so.0
#24 0x00007f9eeeb36b0d in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7f9eefe3b740 (LWP 21490)):
#0  0x00007f9eeeafd659 in waitpid () from /lib64/libc.so.6
#1  0x00007f9eeea7af62 in do_system () from /lib64/libc.so.6
#2  0x00007f9eeea7b311 in system () from /lib64/libc.so.6
#3  0x00007f9ee75fc3fc in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#4  0x00007f9ee4f4d4b3 in (anonymous namespace)::TExceptionHandlerImp::HandleException(int) () from /usr/lib64/root/libcppyy_backend3_6.so.6.24
#5  0x00007f9ee75fe24b in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#6  <signal handler called>
#7  0x00007f9eef81496f in PyMem_Calloc () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7efb6d in PyList_New () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7efc0a in list_repeat () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef87219a in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef872009 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#24 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#25 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#26 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#27 0x00007f9eef826705 in slot_tp_init () from /lib64/libpython3.6m.so.1.0
#28 0x00007f9eef8230c2 in type_call () from /lib64/libpython3.6m.so.1.0
#29 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#30 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#32 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#33 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#34 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#35 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#36 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#37 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#38 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#39 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#40 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#41 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#42 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#43 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#44 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#45 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#46 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#47 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#48 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#49 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#50 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#51 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#52 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#53 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#54 0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#55 0x00007f9eef87d42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#56 0x00007f9eef905d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#57 0x00007f9eef7b280b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#58 0x00007f9eef7b2bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#59 0x00007f9eef90c232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#60 0x0000000000400ab9 in main ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum https://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at https://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.
===========================================================
#7  0x00007f9eef81496f in PyMem_Calloc () from /lib64/libpython3.6m.so.1.0
#8  0x00007f9eef7efb6d in PyList_New () from /lib64/libpython3.6m.so.1.0
#9  0x00007f9eef7efc0a in list_repeat () from /lib64/libpython3.6m.so.1.0
#10 0x00007f9eef87219a in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#11 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#12 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#13 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#14 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#15 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#16 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#17 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#18 0x00007f9eef872009 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#19 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#20 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#21 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#22 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#23 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#24 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#25 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#26 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#27 0x00007f9eef826705 in slot_tp_init () from /lib64/libpython3.6m.so.1.0
#28 0x00007f9eef8230c2 in type_call () from /lib64/libpython3.6m.so.1.0
#29 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#30 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#31 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#32 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#33 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#34 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#35 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#36 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#37 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#38 0x00007f9eef87d67f in _PyFunction_FastCallDict () from /lib64/libpython3.6m.so.1.0
#39 0x00007f9eef7d3aae in _PyObject_FastCallDict () from /lib64/libpython3.6m.so.1.0
#40 0x00007f9eef7d3bc1 in _PyObject_Call_Prepend () from /lib64/libpython3.6m.so.1.0
#41 0x00007f9eef7d3833 in PyObject_Call () from /lib64/libpython3.6m.so.1.0
#42 0x00007f9eef872a47 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#43 0x00007f9eef87b617 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#44 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#45 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#46 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#47 0x00007f9eef87ba12 in _PyEval_EvalCodeWithName () from /lib64/libpython3.6m.so.1.0
#48 0x00007f9eef87c2fa in fast_function () from /lib64/libpython3.6m.so.1.0
#49 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#50 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#51 0x00007f9eef87c24a in fast_function () from /lib64/libpython3.6m.so.1.0
#52 0x00007f9eef87c583 in call_function () from /lib64/libpython3.6m.so.1.0
#53 0x00007f9eef870d97 in _PyEval_EvalFrameDefault () from /lib64/libpython3.6m.so.1.0
#54 0x00007f9eef87c91f in PyEval_EvalCodeEx () from /lib64/libpython3.6m.so.1.0
#55 0x00007f9eef87d42b in PyEval_EvalCode () from /lib64/libpython3.6m.so.1.0
#56 0x00007f9eef905d2e in run_mod () from /lib64/libpython3.6m.so.1.0
#57 0x00007f9eef7b280b in PyRun_FileExFlags () from /lib64/libpython3.6m.so.1.0
#58 0x00007f9eef7b2bdd in PyRun_SimpleFileExFlags () from /lib64/libpython3.6m.so.1.0
#59 0x00007f9eef90c232 in Py_Main () from /lib64/libpython3.6m.so.1.0
#60 0x0000000000400ab9 in main ()
===========================================================
3

Dear Jordi,

Welcome to the Forum and thanks for posting.
To debug the issue further, we’ll need a reproducer if you can provide one.

I take this opportunity to signal the modern way to fill ROOT columnar datasets (TTrees) from Numpy array wih RDataFrame. You can find a very informative example here if you are interested.

Best,
Danilo

4

Dear Danilo,

Thank you for reaching me out. I am trying to provide the reproducer.

In the meantime, it looks that RDataFrame may solve the issue, but I have not found the way to write a RDataFrame into a ROOT TDirectory. It seems that the Snapshot() method only allows to create new TFiles instead. I need several RDataFRame under the same TDirectory, and several TDirectories at the same time. Are you aware of any way to do that?

Thank you,

Jordi

5

Hello Jordi,

You can save a particular tree in a directory, for example:

myDataFrame.Snapshot("foo/bar","baz.root")

and you can merge root files together via the hadd command.
Does this address your enquiry?

Best,
D

6

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