Rootn.exe startup crashes on Ubuntu 14.04.4

tjohnson53 · March 18, 2016, 1:48pm

Hi guys,

I’ve installed root on Ubuntu 14.04…4 (uname results are 3.13.0-79-generic x86_64 GNU/Linux). The gcc version is: 4.8.4. The root versions I’ve tried are 6.06/02 and 6.04/16, and building using appropriate architecture and --prefix=/usr/local (and /usr/local/root), and of course setting the appropriate path in libc.conf in /etc/ld.so.conf and running ldconfig. I’ve also tried downloading the binary distribution, setting LD_LIBRARY_PATH and running from within my home directory. In all cases, root works fine. However, rootn.exe (which is what we need) always fails on startup. A piece of the stack trace from one of the tests is:
/usr/local/root/bin/rootn.exe
Fatal in : storage area overwritten
aborting
#0 0x00007fe8f3aebb4c in __libc_waitpid (pid=17203, stat_loc=stat_loc
entry=0x7ffe00f9cb40, options=options

#15 0x00007fe8f0a7643e in CreateInterpreter () from /usr/local/root/lib/root/libCling.so
#16 0x00007fe8f494cf9b in TROOT::InitInterpreter() () from /usr/local/root/lib/root/libCore.so
#17 0x00007fe8f494d316 in ROOT::GetROOT2() () from /usr/local/root/lib/root/libCore.so
#18 0x00007fe8f4d3cff5 in operator delete(void*) () from /usr/local/root/lib/root/libNew.so
#19 0x00007fe8f498ca5e in TClassTable::Add(char const*, short, std::type_info const&, TClass* ()(), int) () from /usr/local/root/lib/root/libCore.so
#20 0x00007fe8f49bd0e6 in ROOT::TGenericClassInfo::TGenericClassInfo(char const, int, char const*, int, ROOT::TInitBehavior const*, TClass* (*)(), int) () from /usr/local/root/lib/root/libCore.so
#21 0x00007fe8f48ff218 in TMath::ROOT::GenerateInitInstance() () from /usr/local/root/lib/root/libCore.so
#22 0x00007fe8f489639c in _GLOBAL__sub_I_G__Core.cxx () from /usr/local/root/lib/root/libCore.so
#23 0x00007fe8f4f4f13a in call_init (l=, argc=argc
entry=1, argv=argv
entry=0x7ffe00fa0cc8, env=env

I’m attaching the whole thing for convenience, but maybe the above is enough to give somebody a clue.problem.txt (3.57 KB)

Does anybody have any ideas on this, or is there some other information I need to provide to shed on it? Should I backtrack down to one of the root 5 versions?

Thanks,
Tim

Danilo · March 18, 2016, 3:11pm

Hi Tim,

did you configure with cmake and, f not, may you try this out?

Danilo

Pepe_Le_Pew · March 21, 2016, 10:58pm

I confirm this problem (ROOT v6-06-02 built with cmake).

Danilo · March 22, 2016, 12:29am

Hi,

did you proceed with a vanilla “cmake path/to/root” or did you specify some flags for the configuration?

Cheers,
Danilo

Pepe_Le_Pew · March 22, 2016, 1:30am

cd /full/path/to/build unset ROOTSYS cmake -DCMAKE_INSTALL_PREFIX="/full/path/to/install" -Dall="ON" -Dgeocad="ON" -DOCC_INCLUDE_DIR="/usr/include/oce" -Dbuiltin_ftgl="OFF" -Dbuiltin_glew="OFF" -Dsoversion="ON" /full/path/to/source cmake --build . cmake --build . --target install [...]$ . /full/path/to/install/bin/thisroot.sh [...]$ root-config --features asimage astiff bonjour builtin_afterimage builtin_llvm cxx11 cling davix exceptions explicitlink fftw3 fitsio fortran gviz gdml geocad genvector http krb5 ldap mathmore memstat minuit2 mysql odbc opengl pch pgsql pythia8 python qt qtgsi roofit r shadowpw shared soversion sqlite ssl table thread tmva unuran vc vdt xft xml x11

Danilo · March 22, 2016, 8:51pm

Hi,

I could not reproduce the issue on my kubuntu box.
I propose to simplify the configuration command in order to converge more rapidly on a solution:

cmake -DCMAKE_INSTALL_PREFIX="/full/path/to/install" /full/path/to/source
cmake --build .
cmake --build . --target install

Cheers,
Danilo

Pepe_Le_Pew · March 22, 2016, 11:16pm

[...]$ cat /etc/issue Ubuntu 14.04.4 LTS \n \l [...]$ uname -a Linux h111 3.13.0-83-generic #127-Ubuntu SMP Fri Mar 11 00:25:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux [...]$ . /opt/ROOT/debug/install/bin/thisroot.sh [...]$ root-config --features asimage astiff bonjour builtin_afterimage builtin_ftgl builtin_glew builtin_llvm cxx11 cling davix exceptions explicitlink fftw3 fitsio fortran gviz genvector krb5 ldap mathmore memstat mysql odbc opengl pch pgsql pythia8 python shadowpw shared sqlite ssl thread tmva vdt xft xml x11 [code][…]$ gdb /opt/ROOT/debug/install/bin/rootn.exe
GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.2) 7.7.1
Copyright © 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and “show warranty” for details.
This GDB was configured as “x86_64-linux-gnu”.
Type “show configuration” for configuration details.
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/.
Find the GDB manual and other documentation resources online at:
http://www.gnu.org/software/gdb/documentation/.
For help, type “help”.
Type “apropos word” to search for commands related to “word”…
Reading symbols from /opt/ROOT/debug/install/bin/rootn.exe…done.
(gdb) run
Starting program: /opt/ROOT/debug/install/bin/rootn.exe
[Thread debugging using libthread_db enabled]
Using host libthread_db library “/lib/x86_64-linux-gnu/libthread_db.so.1”.
Fatal in : storage area overwritten
aborting

Program received signal SIGABRT, Aborted.
0x00007ffff6b37cc9 in __GI_raise (sig=sig@entry=6) at …/nptl/sysdeps/unix/sysv/linux/raise.c:56
56 …/nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) where
#0 0x00007ffff6b37cc9 in __GI_raise (sig=sig@entry=6) at …/nptl/sysdeps/unix/sysv/linux/raise.c:56
#1 0x00007ffff6b3b0d8 in __GI_abort () at abort.c:89
#2 0x00007ffff78c0c49 in TUnixSystem::Abort (this=) at /opt/ROOT/debug/source/core/unix/src/TUnixSystem.cxx:2124
#3 0x00007ffff77e977f in DefaultErrorHandler (level=, abort_bool=, location=0x7ffff7bd8374 “operator delete”, msg=0x7fffffffbb50 “storage area overwritten”)
at /opt/ROOT/debug/source/core/base/src/TError.cxx:193
#4 0x00007ffff77e91ba in ErrorHandler(Int_t, const char , const char , typedef __va_list_tag __va_list_tag ) (level=level@entry=6000, location=location@entry=0x7ffff7bd8374 “operator delete”, fmt=fmt@entry=0x7ffff7bd8253 “%s”,
ap=ap@entry=0x7fffffffbca8) at /opt/ROOT/debug/source/core/base/src/TError.cxx:251
#5 0x00007ffff77e9612 in Fatal (location=location@entry=0x7ffff7bd8374 “operator delete”, fmt=fmt@entry=0x7ffff7bd8253 “%s”) at /opt/ROOT/debug/source/core/base/src/TError.cxx:347
#6 0x00007ffff7bd7fe0 in operator delete (ptr=0x675580) at /opt/ROOT/debug/source/core/newdelete/src/NewDelete.cxx:271
#7 0x00007ffff41ae8fc in clang::driver::toolchains::Linux::Linux(clang::driver::Driver const&, llvm::Triple const&, llvm::opt::ArgList const&) () from /opt/ROOT/debug/install/lib/libCling.so
#8 0x00007ffff41862fb in clang::driver::Driver::getToolChain(llvm::opt::ArgList const&, llvm::StringRef) const () from /opt/ROOT/debug/install/lib/libCling.so
#9 0x00007ffff418ddd3 in clang::driver::Driver::BuildCompilation(llvm::ArrayRef<char const>) () from /opt/ROOT/debug/install/lib/libCling.so
#10 0x00007ffff38b0e21 in (anonymous namespace)::createCIImpl(std::unique_ptr<llvm::MemoryBuffer, std::default_deletellvm::MemoryBuffer >, int, char const const, char const*, bool) () from /opt/ROOT/debug/install/lib/libCling.so
#11 0x00007ffff38b37db in cling::CIFactory::createCI(llvm::StringRef, int, char const* const*, char const*) () from /opt/ROOT/debug/install/lib/libCling.so
#12 0x00007ffff388a105 in cling::IncrementalParser::IncrementalParser(cling::Interpreter*, int, char const* const*, char const*) () from /opt/ROOT/debug/install/lib/libCling.so
#13 0x00007ffff3839e28 in cling::Interpreter::Interpreter(int, char const* const*, char const*, bool) () from /opt/ROOT/debug/install/lib/libCling.so
#14 0x00007ffff37d0985 in TCling::TCling (this=0x667b28, name=, title=) at /opt/ROOT/debug/source/core/meta/src/TCling.cxx:1097
#15 0x00007ffff37d1bfe in CreateInterpreter (interpLibHandle=) at /opt/ROOT/debug/source/core/meta/src/TCling.cxx:577
#16 0x00007ffff775131b in TROOT::InitInterpreter (this=0x7ffff7b9e820 ROOT::Internal::GetROOT1()::alloc) at /opt/ROOT/debug/source/core/base/src/TROOT.cxx:1766
#17 0x00007ffff77516c6 in ROOT::Internal::GetROOT2 () at /opt/ROOT/debug/source/core/base/src/TROOT.cxx:362
#18 0x00007ffff7bd8006 in WhichMapFile (addr=0x655460) at /opt/ROOT/debug/build/include/TMapFile.h:176
#19 operator delete (ptr=0x655468) at /opt/ROOT/debug/source/core/newdelete/src/NewDelete.cxx:274
#20 0x00007ffff784a1be in _M_dispose (__a=…, this=0x655468) at /usr/include/c++/4.8/bits/basic_string.h:249
#21 ~basic_string (this=0x7fffffffd9e0, __in_chrg=) at /usr/include/c++/4.8/bits/basic_string.h:539
#22 TClassTable::Add (cname=, id=, info=…, dict=, pragmabits=) at /opt/ROOT/debug/source/core/cont/src/TClassTable.cxx:350
#23 0x00007ffff788b016 in ROOT::TGenericClassInfo::TGenericClassInfo (this=0x7ffff7bb6d80 TMath::ROOT::GenerateInitInstance()::instance, fullClassname=, version=, declFileName=,
declFileLine=, action=, dictionary=0x7ffff77956c0 TMath::ROOT::TMath_Dictionary(), pragmabits=0) at /opt/ROOT/debug/source/core/meta/src/TGenericClassInfo.cxx:102
#24 0x00007ffff77ba668 in TMath::ROOT::GenerateInitInstance () at /opt/ROOT/debug/build/core/base/G__Core.cxx:260
#25 0x00007ffff7749b3c in __static_initialization_and_destruction_0 (__initialize_p=1, __priority=65535) at /opt/ROOT/debug/build/core/base/G__Core.cxx:266
#26 _GLOBAL__sub_I_G__Core.cxx(void) () at /opt/ROOT/debug/build/core/base/G__Core.cxx:27690
#27 0x00007ffff7dea13a in call_init (l=, argc=argc@entry=1, argv=argv@entry=0x7fffffffdb18, env=env@entry=0x7fffffffdb28) at dl-init.c:78
#28 0x00007ffff7dea223 in call_init (env=, argv=, argc=, l=) at dl-init.c:36
#29 _dl_init (main_map=0x7ffff7ffe1c8, argc=1, argv=0x7fffffffdb18, env=0x7fffffffdb28) at dl-init.c:126
#30 0x00007ffff7ddb30a in _dl_start_user () from /lib64/ld-linux-x86-64.so.2
#31 0x0000000000000001 in ?? ()
#32 0x00007fffffffdf32 in ?? ()
#33 0x0000000000000000 in ?? ()
(gdb) [/code]

Danilo · March 23, 2016, 2:15pm

Ok,

cat /etc/issue
Ubuntu 14.04.1 LTS \n \l

All what you have but

bonjour fftw3 fitsio odbc pythia8

Cannot reproduce. Looking inside the issue deeper.

Pepe_Le_Pew · March 23, 2016, 2:21pm

Run: sync && sudo apt-get clean && sudo apt-get update && sudo apt-get check && sudo apt-get dist-upgrade && sudo apt-get upgrade && sudo apt-get clean && sync and then reboot.

Danilo · March 24, 2016, 12:30pm

Hi,

I can now reproduce the issue. More information to come.

Danilo

tjohnson53 · March 24, 2016, 8:13pm

Hi all,

Thanks for looking into, which, after a short break while diverted to other projects, I am looking at again. We didn’t have cmake installed (?!) on our system, so after taking take care of that, as per the first suggestion, I tried using cmake, after a make uninstall/clean, etc. Just trying:
cmake -DCMAKE_INSTALL_PREFIX="/usr/local" /home/johnsont/rootsrc/root-6.06.02
cmake --build .
sudo cmake --build . --target install

This somehow resulted in different errors when starting rootn.exe, which unfortunately I don’t remember (this was a couple of days ago) as I then tried to go back, after cleaning and redoing the make procedure from the README to see if anything changed (since I had installed cmake and did other general system updates). Now this resulted in “Fatal in TROOT::InitInterpreter: cannot load symbol /usr/local/root/bin/root.exe: undefined symbol: CreateInterpreter”. I suspect something in the cmake cache went awry with all the trials I’ve been doing, since certainly all the library paths are o.k. So, I’m going to try to clean everything up and start from scratch, using cmake again, and see what happens.

Of course, as Pepe Le Pew says he’s confirmed the problem cmake on 6-06-2, I’m not too hopeful. It may be as I thought, I might have to back down to one of the 5 versions.

Thanks for all your help and I’ll let you know what else I find out…

cheers,
Tim

Danilo · March 25, 2016, 8:01am

Hi Tim,

thanks for the helpful post.
I could also verify that the crash is not due to the installing procedure: it’s there also if rootn is ran after building.
I’ll debug this during or immediately after the break.

Danilo

Otto_Schaile · March 29, 2016, 7:42am

Hi,

as far as I remember libNew and hence rootn does not work with root 6 (yet):
pcanal:
"If you need the TMapFile functionality … indeed you will need libNew and we would need to get it to work properly in v6."
We use 6.06.00 on Ubuntu 14.04.4 and the same happens with rootn.exe or any
application linked with libNew:
“Fatal in : storage area overwritten”

Cheers
Otto

tjohnson53 · April 6, 2016, 3:15pm

Hi all,

So after a break to do an experiment elsewhere, I’m back to this problem. Looks like what Otto said is correct. So, I backed off version 6 and put on 5.34/6 and this seems to work fine. Thanks for all the responses…

cheers,
Tim

pcanal · January 18, 2017, 10:10pm

Hi,

This problem is finally resolved in the master and the v6.08 patch branch (so in v6.10/00 and v6.08/06.

Our apologies for the long delay and thanks for your patience.

Cheers,
Philippe.