Merging TChain object with Merge method results in "* Break * segmentation fault"

Galdiano · April 21, 2020, 4:55pm

Hello there! I’m trying to merge two TTrees located in two root files. Through some research, I figure the following should work:

  TChain chain("reco");
  chain.Add("runs/run_1520.root");
  chain.Add("runs/run_1519.root");
  chain.Merge("test.root");

However, when running the code I obtain the following output:

*** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f0b52d42687 in __GI___waitpid (pid=3088, stat_loc=stat_loc
entry=0x7fffdd5b68e8, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007f0b52cad067 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x00007f0b53951823 in TUnixSystem::Exec (shellcmd=<optimized out>, this=0x556c17205b80) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/core/unix/src/TUnixSystem.cxx:2106
#3  TUnixSystem::StackTrace (this=0x556c17205b80) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/core/unix/src/TUnixSystem.cxx:2400
#4  0x00007f0b53954214 in TUnixSystem::DispatchSignals (this=0x556c17205b80, sig=kSigSegmentationViolation) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/core/unix/src/TUnixSystem.cxx:3631
#5  <signal handler called>
#6  0x00007f0b538ee0aa in TClass::StreamerTObject (pThis=0x556c17b42890, object=<optimized out>, b=...) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/core/meta/src/TClass.cxx:6534
#7  0x00007f0b512ec0ac in TClass::Streamer (onfile_class=0x0, b=..., obj=0x556c189cbb41, this=0x556c17b42890) at /home/mdbg/Desktop/CERN-Root/my_build/include/TClass.h:570
#8  TBufferFile::WriteObjectClass (this=0x556c18b75e40, actualObjectStart=0x556c189cbb41, actualClass=0x556c17b42890, cacheReuse=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:2552
#9  0x00007f0b512f3335 in TBufferIO::WriteObjectAny (this=0x556c18b75e40, obj=0x556c189cbb40, ptrClass=0x556c18438110, cacheReuse=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferIO.cxx:519
#10 0x00007f0b512e67b9 in TBufferFile::WriteFastArray (this=0x556c18b75e40, start=<optimized out>, cl=0x556c18438110, n=<optimized out>, isPreAlloc=<optimized out>, streamer=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:2296
#11 0x00007f0b5154e61f in TStreamerInfo::WriteBufferAux<char**> (this=0x556c183e7740, b=..., arr=
0x7fffdd5b9580: 0x7fffdd5b9578, compinfo=0x556c18a06328, first=first
entry=0, last=last
entry=1, narr=1, eoffset=0, arrayMode=0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TStreamerInfoWriteBuffer.cxx:441
#12 0x00007f0b513aae30 in TStreamerInfoActions::GenericWriteAction (buf=..., addr=<optimized out>, config=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TStreamerInfoActions.cxx:192
#13 0x00007f0b512e5fa4 in TStreamerInfoActions::TConfiguredAction::operator() (this=<optimized out>, this=<optimized out>, object=0x556c18a049a0, buffer=...) at /home/mdbg/Desktop/CERN-Root/my_build/include/TStreamerInfoActions.h:124
#14 TBufferFile::ApplySequence (this=0x556c18b75e40, sequence=..., obj=0x556c18a049a0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:3564
#15 0x00007f0b45ffb187 in TBranch::FillImpl (this=this
entry=0x556c18a08d90, imtHelper=imtHelper
entry=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranch.cxx:871
#16 0x00007f0b46008c3d in TBranchElement::FillImpl (this=0x556c18a08d90, imtHelper=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranchElement.cxx:1243
#17 0x00007f0b4600896f in TBranchElement::FillImpl (this=0x556c18a07450, imtHelper=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranchElement.cxx:1268
#18 0x00007f0b46072c18 in TTree::Fill (this=0x556c17e676b0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TTree.cxx:4448
#19 0x00007f0b460724bd in TTree::CopyEntries (this=0x556c17e676b0, tree=0x7fffdd5b9ad8, nentries=9223372036854775807, option=0x7f0b540f94f0 "") at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TTree.cxx:3517
#20 0x00007f0b46028afa in TChain::Merge (this=0x7fffdd5b9ad8, file=<optimized out>, basketsize=0, option=0x7f0b540f94f0 "") at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TChain.cxx:2050
#21 0x00007f0b540f84b1 in ?? ()
#22 0x000000635f32535f in ?? ()
#23 0x0000000000000041 in ?? ()
#24 0x2d746f6f725f646c in ?? ()
#25 0x0000000100000001 in ?? ()
#26 0x00007fffdd5b9ad8 in ?? ()
#27 0x6975622f746f6f52 in ?? ()
#28 0x646d2f656d6f682f in ?? ()
#29 0x00007f0b462b95f8 in vtable for TChain () from /home/mdbg/Desktop/CERN-Root/build_root-6.18.04/lib/libTree.so
#30 0x0200000000000000 in ?? ()
#31 0x00007f0b53c6c518 in vtable for TString () from /home/mdbg/Desktop/CERN-Root/build_root-6.18.04/lib/libCore.so
#32 0x0000006f63657208 in ?? ()
#33 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  0x00007f0b538ee0aa in TClass::StreamerTObject (pThis=0x556c17b42890, object=<optimized out>, b=...) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/core/meta/src/TClass.cxx:6534
#7  0x00007f0b512ec0ac in TClass::Streamer (onfile_class=0x0, b=..., obj=0x556c189cbb41, this=0x556c17b42890) at /home/mdbg/Desktop/CERN-Root/my_build/include/TClass.h:570
#8  TBufferFile::WriteObjectClass (this=0x556c18b75e40, actualObjectStart=0x556c189cbb41, actualClass=0x556c17b42890, cacheReuse=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:2552
#9  0x00007f0b512f3335 in TBufferIO::WriteObjectAny (this=0x556c18b75e40, obj=0x556c189cbb40, ptrClass=0x556c18438110, cacheReuse=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferIO.cxx:519
#10 0x00007f0b512e67b9 in TBufferFile::WriteFastArray (this=0x556c18b75e40, start=<optimized out>, cl=0x556c18438110, n=<optimized out>, isPreAlloc=<optimized out>, streamer=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:2296
#11 0x00007f0b5154e61f in TStreamerInfo::WriteBufferAux<char**> (this=0x556c183e7740, b=..., arr=
0x7fffdd5b9580: 0x7fffdd5b9578, compinfo=0x556c18a06328, first=first
entry=0, last=last
entry=1, narr=1, eoffset=0, arrayMode=0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TStreamerInfoWriteBuffer.cxx:441
#12 0x00007f0b513aae30 in TStreamerInfoActions::GenericWriteAction (buf=..., addr=<optimized out>, config=<optimized out>) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TStreamerInfoActions.cxx:192
#13 0x00007f0b512e5fa4 in TStreamerInfoActions::TConfiguredAction::operator() (this=<optimized out>, this=<optimized out>, object=0x556c18a049a0, buffer=...) at /home/mdbg/Desktop/CERN-Root/my_build/include/TStreamerInfoActions.h:124
#14 TBufferFile::ApplySequence (this=0x556c18b75e40, sequence=..., obj=0x556c18a049a0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/io/io/src/TBufferFile.cxx:3564
#15 0x00007f0b45ffb187 in TBranch::FillImpl (this=this
entry=0x556c18a08d90, imtHelper=imtHelper
entry=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranch.cxx:871
#16 0x00007f0b46008c3d in TBranchElement::FillImpl (this=0x556c18a08d90, imtHelper=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranchElement.cxx:1243
#17 0x00007f0b4600896f in TBranchElement::FillImpl (this=0x556c18a07450, imtHelper=0x0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TBranchElement.cxx:1268
#18 0x00007f0b46072c18 in TTree::Fill (this=0x556c17e676b0) at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TTree.cxx:4448
#19 0x00007f0b460724bd in TTree::CopyEntries (this=0x556c17e676b0, tree=0x7fffdd5b9ad8, nentries=9223372036854775807, option=0x7f0b540f94f0 "") at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TTree.cxx:3517
#20 0x00007f0b46028afa in TChain::Merge (this=0x7fffdd5b9ad8, file=<optimized out>, basketsize=0, option=0x7f0b540f94f0 "") at /home/mdbg/Desktop/CERN-Root/root-6.18.04/tree/tree/src/TChain.cxx:2050
#21 0x00007f0b540f84b1 in ?? ()
#22 0x000000635f32535f in ?? ()
#23 0x0000000000000041 in ?? ()
#24 0x2d746f6f725f646c in ?? ()
#25 0x0000000100000001 in ?? ()
#26 0x00007fffdd5b9ad8 in ?? ()
#27 0x6975622f746f6f52 in ?? ()
#28 0x646d2f656d6f682f in ?? ()
#29 0x00007f0b462b95f8 in vtable for TChain () from /home/mdbg/Desktop/CERN-Root/build_root-6.18.04/lib/libTree.so
#30 0x0200000000000000 in ?? ()
#31 0x00007f0b53c6c518 in vtable for TString () from /home/mdbg/Desktop/CERN-Root/build_root-6.18.04/lib/libCore.so
#32 0x0000006f63657208 in ?? ()
#33 0x0000000000000000 in ?? ()
===========================================================

I really don’t know what’s going on here, as the code seems quite simple. When I commented out the chain.Merge("test.root"); portion the code runs smoothly. Interacting with the TChain object through

chain.Draw("clusters[0].f90", "clusters[0].f90 > 0. && clusters[0].f90 < 1.");

returns the expected output. I’m quite lost and any help would be greatly appreciated.

Miguel.

Here’s a link with the root files in question, in case anyone wishes to reproduce the error:

ROOT Version: 6.18/04
Platform: Ubuntu 18.04.4 LTS
Compiler: Not Provided

pcanal · April 21, 2020, 6:23pm

Because the class EvHeader inherits from TObject, a pointer to instances of that class can only be written when the its library is loaded.

So to solve the problem either load the library that implements EvHeader or even better use the fast mode for Merging (which copies the data without creating the object, just copying the on-disk bytes):

ch.Merge("test.root","fast");

Cheers,
Philippe.

Galdiano · April 21, 2020, 6:28pm

Wow, it was that simple huh? Thank you very much, this might have just made my day!

Cheers,
Miguel.

Merging TChain object with Merge method results in "*** Break *** segmentation fault"

Merging TChain object with Merge method results in "* Break * segmentation fault"