Segmentation fault with GetEntries

I have been running scripts on the LSF batch system at CERN and have been getting segmentation fault errors like the one posted below. I am very sure it is a problem in the GetEntries(configString) function, where my configString looks like the following:

“(Dplus_IPCHI2<”+str(inTuple[0])+") && (Dplus_ENDVERTEX_CHI2<"+str(inTuple[1])+") && (Dplus_FDCHI2>"+str(inTuple[2])+") && (Kplus_P>"+str(inTuple[3])+") && (Kminus_P>"+str(inTuple[3])+") && (Kplus_PT>"+str(inTuple[4])+") && (Kminus_PT>"+str(inTuple[4])+") && (piplus_P>"+str(inTuple[5])+") && (Kplus_PIDK>"+str(inTuple[6])+") && (Kminus_PIDK>"+str(inTuple[6])+") && (piplus_PIDK<"+str(inTuple[7])+") && (piplus_PIDe<"+str(inTuple[8])+") && (piplus_PIDp<"+str(inTuple[9])+")"

where each entry in inTuple is a 3-5 digit decimal number.

I have not been able to reproduce this error in interactive mode. The “creating generation” messages in the program output below are from print statements in the script and indicate that the GetEntries(configString) function has been called several hundred times before giving this error. I thought it may be a problem with the string length, as I had problems with this a couple of weeks ago, but that wouldn’t explain why the error only occurs once every several hundred times. The tuple being processed using get entries is ~230MB - could the filesize be causing the problem?

The CERN nodes use python 2.5.4 and Root 5.22/00c.

R__unzip: error in header
Error in TBasket::ReadBasketBuffers: fNbytes = -252257756, fKeylen = 0, fObjlen = 17574, noutot = 0, nout=0, nin=12845, nbuf=4456448
Error in TBranch::GetBasket: File: rfio:///castor/cern.ch/user/p/pawatson/D2KKpi_bkgrd_minbias_cut5_masswin100_B.root at byte:3359450026530045952, branch:piplus_PIDe, entry:75376, badread=1, nerrors=1, basketnumber=15

*** Break *** segmentation violation
Creating generation 0
Creating generation 1
Creating generation 2
Using host libthread_db library “/lib64/tls/libthread_db.so.1”.
Attaching to program: /proc/18704/exe, process 18704
[Thread debugging using libthread_db enabled]
[New Thread 182894220320 (LWP 18704)]
[New Thread 1075841376 (LWP 18964)]
0x000000322368fdaa in waitpid () from /lib64/tls/libc.so.6
Thread 2 (Thread 1075841376 (LWP 18964)):
#0 0x0000003223d0a7ef in sem_wait () from /lib64/tls/libpthread.so.0
#1 0x00000000004ab328 in PyThread_acquire_lock (lock=0x942ce0, waitflag=1)
at Python/thread_pthread.h:334
#2 0x0000000000478d78 in PyEval_RestoreThread (tstate=0x1c549e0)
at Python/ceval.c:332
#3 0x0000002a9e528c1c in time_sleep (self=Variable “self” is not available.
)
at /build/LCG/work/Python-2.5.4/Modules/timemodule.c:921
#4 0x000000000047f704 in PyEval_EvalFrameEx (f=0x16e2e80, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3612
#5 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a98477b70, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#6 0x00000000004cd8d4 in function_call (func=0x2a9853e500, arg=0x2a9c257410,
kw=0x1c58f10) at Objects/funcobject.c:517
#7 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#8 0x000000000047d9bb in PyEval_EvalFrameEx (f=0x16e9500, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3892
#9 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x16e40c0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#10 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x1c0e900, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#11 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a9c2433f0, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#12 0x00000000004cd8d4 in function_call (func=0x2a9c259500, arg=0x2a9c248550,
kw=0x0) at Objects/funcobject.c:517
#13 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#14 0x000000000042477d in instancemethod_call (func=0x2a9c259500,
arg=0x2a9c248550, kw=0x0) at Objects/classobject.c:2519
#15 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#16 0x0000000000479169 in PyEval_CallObjectWithKeywords (func=0x2a9c254320,
arg=0x2a95587050, kw=0x0) at Python/ceval.c:3481
#17 0x00000000004af34d in t_bootstrap (boot_raw=0x173c430)
at ./Modules/threadmodule.c:427
#18 0x0000003223d06137 in start_thread () from /lib64/tls/libpthread.so.0
#19 0x00000032236c9a43 in clone () from /lib64/tls/libc.so.6

Thread 1 (Thread 182894220320 (LWP 18704)):
#0 0x000000322368fdaa in waitpid () from /lib64/tls/libc.so.6
#1 0x0000003223639b7f in do_system () from /lib64/tls/libc.so.6
#2 0x0000003223639df6 in system () from /lib64/tls/libc.so.6
#3 0x0000002a98fdc1d1 in TUnixSystem::StackTrace ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#4 0x0000002a98fd8cea in TUnixSystem::DispatchSignals ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#5
#6 0x0000003223672810 in memcpy () from /lib64/tls/libc.so.6
#7 0x0000002a9b2b110a in TBasket::ReadBasketBuffers ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#8 0x0000002a9b2ba309 in TBranch::GetBasket ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#9 0x0000002a9b2be752 in TBranch::GetEntry ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#10 0x0000002a9f5ac562 in TTreeFormula::EvalInstance ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#11 0x0000002a9f5a7a1e in TSelectorEntries::Process ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#12 0x0000002a9f5c55ea in TTreePlayer::Process ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#13 0x0000002a9f5bfda3 in TTreePlayer::GetEntries ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#14 0x0000002a9b332ab6 in G__G__Tree_109_0_62 ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#15 0x0000002a996b2f2a in Cint::G__CallFunc::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCint.so
#16 0x0000002a98c109e1 in PyROOT::TLongLongExecutor::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#17 0x0000002a98c16bf5 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::CallSafe ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#18 0x0000002a98c16de3 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#19 0x0000002a98c1a389 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::operator() ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#20 0x0000002a98c1eb00 in PyROOT::(anonymous namespace)::mp_call ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#21 0x000000000041a033 in PyObject_Call (func=0x2aa3933f70, arg=0x2aa35ff000,
kw=0xffffffffffffffff) at Objects/abstract.c:1861
#22 0x000000000047de61 in PyEval_EvalFrameEx (f=0x221ee10, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3823
#23 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x2218af0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#24 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x6d3ca0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#25 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a98461828, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#26 0x0000000000480c12 in PyEval_EvalCode (co=0x2aa3933f70,
globals=0x2aa35ff000, locals=0xffffffffffffffff) at Python/ceval.c:514
#27 0x00000000004a287c in PyRun_FileExFlags (fp=0x64b010,
filename=0x7fbfff3fa1 “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, start=Variable “start” is not available.
) at Python/pythonrun.c:1273
#28 0x00000000004a3503 in PyRun_SimpleFileExFlags (fp=0x64b010,
filename=0x7fbfff3fa1 “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, closeit=1, flags=0x7fbfff2a0c) at Python/pythonrun.c:879
#29 0x0000000000413098 in Py_Main (argc=Variable “argc” is not available.
) at Modules/main.c:532
#30 0x000000322361c40b in __libc_start_main () from /lib64/tls/libc.so.6
#31 0x00000000004126da in _start ()
#32 0x0000007fbfff2b98 in ?? ()
#33 0x000000000000001c in ?? ()
#34 0x0000000000000010 in ?? ()
#35 0x0000007fbfff3f9a in ?? ()
#36 0x0000007fbfff3fa1 in ?? ()
#37 0x0000007fbfff3fe6 in ?? ()
#38 0x0000007fbfff3fed in ?? ()
#39 0x0000007fbfff3ff1 in ?? ()
#40 0x0000007fbfff3ff8 in ?? ()
#41 0x0000007fbfff3ffc in ?? ()
#42 0x0000007fbfff4003 in ?? ()
#43 0x0000007fbfff4007 in ?? ()
#44 0x0000007fbfff400e in ?? ()
#45 0x0000007fbfff4011 in ?? ()
#46 0x0000007fbfff4018 in ?? ()
#47 0x0000007fbfff401c in ?? ()
#48 0x0000007fbfff4024 in ?? ()
#49 0x0000007fbfff4026 in ?? ()
#50 0x0000007fbfff402f in ?? ()
#51 0x0000000000000000 in ?? ()

*** Break *** segmentation violation
Using host libthread_db library “/lib64/tls/libthread_db.so.1”.
Attaching to program: /proc/18704/exe, process 18704
[Thread debugging using libthread_db enabled]
[New Thread 182894220320 (LWP 18704)]
[New Thread 1075841376 (LWP 18964)]
0x000000322368fdaa in waitpid () from /lib64/tls/libc.so.6
Thread 2 (Thread 1075841376 (LWP 18964)):
#0 0x0000003223d0a7ef in sem_wait () from /lib64/tls/libpthread.so.0
#1 0x00000000004ab33c in PyThread_acquire_lock (lock=0x942ce0, waitflag=1)
at Python/thread_pthread.h:334
#2 0x0000000000478d78 in PyEval_RestoreThread (tstate=0x1c549e0)
at Python/ceval.c:332
#3 0x0000002a9e528c1c in time_sleep (self=Variable “self” is not available.
)
at /build/LCG/work/Python-2.5.4/Modules/timemodule.c:921
#4 0x000000000047f704 in PyEval_EvalFrameEx (f=0x16e2e80, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3612
#5 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a98477b70, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#6 0x00000000004cd8d4 in function_call (func=0x2a9853e500, arg=0x2a9c257410,
kw=0x1c58f10) at Objects/funcobject.c:517
#7 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#8 0x000000000047d9bb in PyEval_EvalFrameEx (f=0x16e9500, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3892
#9 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x16e40c0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#10 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x1c0e900, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#11 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a9c2433f0, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#12 0x00000000004cd8d4 in function_call (func=0x2a9c259500, arg=0x2a9c248550,
kw=0x0) at Objects/funcobject.c:517
#13 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#14 0x000000000042477d in instancemethod_call (func=0x2a9c259500,
arg=0x2a9c248550, kw=0x0) at Objects/classobject.c:2519
#15 0x000000000041a033 in PyObject_Call (func=0x942ce0, arg=0x0, kw=0x0)
at Objects/abstract.c:1861
#16 0x0000000000479169 in PyEval_CallObjectWithKeywords (func=0x2a9c254320,
arg=0x2a95587050, kw=0x0) at Python/ceval.c:3481
#17 0x00000000004af34d in t_bootstrap (boot_raw=0x173c430)
at ./Modules/threadmodule.c:427
#18 0x0000003223d06137 in start_thread () from /lib64/tls/libpthread.so.0
#19 0x00000032236c9a43 in clone () from /lib64/tls/libc.so.6

Thread 1 (Thread 182894220320 (LWP 18704)):
#0 0x000000322368fdaa in waitpid () from /lib64/tls/libc.so.6
#1 0x0000003223639b7f in do_system () from /lib64/tls/libc.so.6
#2 0x0000003223639df6 in system () from /lib64/tls/libc.so.6
#3 0x0000002a98fdc1d1 in TUnixSystem::StackTrace ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#4 0x0000002a98fd8cea in TUnixSystem::DispatchSignals ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#5
#6 0x0000003223672810 in memcpy () from /lib64/tls/libc.so.6
#7 0x0000002a9b2b110a in TBasket::ReadBasketBuffers ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#8 0x0000002a9b2ba309 in TBranch::GetBasket ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#9 0x0000002a9b2be752 in TBranch::GetEntry ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#10 0x0000002a9f5ac562 in TTreeFormula::EvalInstance ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#11 0x0000002a9f5a7a1e in TSelectorEntries::Process ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#12 0x0000002a9f5c55ea in TTreePlayer::Process ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#13 0x0000002a9f5bfda3 in TTreePlayer::GetEntries ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTreePlayer.so
#14 0x0000002a9b332ab6 in G__G__Tree_109_0_62 ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libTree.so
#15 0x0000002a996b2f2a in Cint::G__CallFunc::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCint.so
#16 0x0000002a98c109e1 in PyROOT::TLongLongExecutor::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#17 0x0000002a98c16bf5 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::CallSafe ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#18 0x0000002a98c16de3 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::Execute ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#19 0x0000002a98c1a389 in PyROOT::TMethodHolder<PyROOT::TScopeAdapter, PyROOT::TMemberAdapter>::operator() ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#20 0x0000002a98c1ea2b in PyROOT::(anonymous namespace)::mp_call ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libPyROOT.so
#21 0x000000000041a033 in PyObject_Call (func=0x2acd921220, arg=0x2aa25fb000,
kw=0xffffffffffffffff) at Objects/abstract.c:1861
#22 0x000000000047de61 in PyEval_EvalFrameEx (f=0x221ee10, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3823
#23 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x2218af0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#24 0x000000000047ff94 in PyEval_EvalFrameEx (f=0x6d3ca0, throwflag=Variable “throwflag” is not available.
)
at Python/ceval.c:3698
#25 0x0000000000480a95 in PyEval_EvalCodeEx (co=0x2a98461828, globals=Variable “globals” is not available.
)
at Python/ceval.c:2875
#26 0x0000000000480c12 in PyEval_EvalCode (co=0x2acd921220,
globals=0x2aa25fb000, locals=0xffffffffffffffff) at Python/ceval.c:514
#27 0x00000000004a287c in PyRun_FileExFlags (fp=0x64b010,
filename=0x7fbfff3fa1 “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, start=Variable “start” is not available.
) at Python/pythonrun.c:1273
#28 0x00000000004a3503 in PyRun_SimpleFileExFlags (fp=0x64b010,
filename=0x7fbfff3fa1 “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, closeit=1, flags=0x7fbfff2a0c) at Python/pythonrun.c:879
#29 0x0000000000413098 in Py_Main (argc=Variable “argc” is not available.
) at Modules/main.c:532
#30 0x000000322361c40b in __libc_start_main () from /lib64/tls/libc.so.6
#31 0x00000000004126da in _start ()
#32 0x0000007fbfff2b98 in ?? ()
#33 0x000000000000001c in ?? ()
#34 0x0000000000000010 in ?? ()
#35 0x0000007fbfff3f9a in ?? ()
#36 0x0000007fbfff3fa1 in ?? ()
#37 0x0000007fbfff3fe6 in ?? ()
#38 0x0000007fbfff3fed in ?? ()
#39 0x0000007fbfff3ff1 in ?? ()
#40 0x0000007fbfff3ff8 in ?? ()
#41 0x0000007fbfff3ffc in ?? ()
#42 0x0000007fbfff4003 in ?? ()
#43 0x0000007fbfff4007 in ?? ()
#44 0x0000007fbfff400e in ?? ()
#45 0x0000007fbfff4011 in ?? ()
#46 0x0000007fbfff4018 in ?? ()
#47 0x0000007fbfff401c in ?? ()
#48 0x0000007fbfff4024 in ?? ()
#49 0x0000007fbfff4026 in ?? ()
#50 0x0000007fbfff402f in ?? ()
#51 0x0000000000000000 in ?? ()
Traceback (most recent call last):
File “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, line 373, in
genAndScoreRandom(newscoreDict, tt_optiS, tt_optiB, tt_optiAll, minbiasS, minbiasB, nNewRnd, nback)
File “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, line 176, in genAndScoreRandom
score = scoreSignificance(rndIdx, tt_inS, tt_inB, tt_inAll, minbiasS, minbiasB, nback)
File “/afs/cern.ch/user/p/pawatson/cmtuser/Dtokkpi/selectionMC_batch_17.py”, line 111, in scoreSignificance
nbkg_minbias = minbiasB.GetEntries(configString)
TypeError: none of the 2 overloaded methods succeeded. Full details:
Long64_t TTree::GetEntries() =>
takes at most 0 arguments (1 given)
problem in C++; program state has been reset

*** Break *** segmentation violation
Using host libthread_db library “/lib64/tls/libthread_db.so.1”.
Attaching to program: /proc/18704/exe, process 18704
[Thread debugging using libthread_db enabled]
[New Thread 182894220320 (LWP 18704)]
0x000000322368fdaa in waitpid () from /lib64/tls/libc.so.6
#1 0x0000003223639b7f in do_system () from /lib64/tls/libc.so.6
#2 0x0000003223639df6 in system () from /lib64/tls/libc.so.6
#3 0x0000002a98fdc1d1 in TUnixSystem::StackTrace ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#4 0x0000002a98fd8cea in TUnixSystem::DispatchSignals ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#5
#6 0x0000002a98f0ecd3 in TDirectory::RegisterContext ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#7 0x0000002a9a192058 in TDirectoryFile::Save ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libRIO.so
#8 0x0000002a9a18ea69 in TDirectoryFile::Close ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libRIO.so
#9 0x0000002a9a19c69b in TFile::Close ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libRIO.so
#10 0x0000002a9a19ca55 in TFile::~TFile$delete ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libRIO.so
#11 0x0000002a98f81b9d in TCollection::GarbageCollect ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#12 0x0000002a98f86135 in TList::Delete ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#13 0x0000002a98f3c702 in TROOT::~TROOT ()
from /afs/cern.ch/sw/lcg/app/releases/ROOT/5.22.00c/slc4_amd64_gcc34/root/lib/libCore.so
#14 0x0000003223630c95 in exit () from /lib64/tls/libc.so.6
#15 0x000000322361c412 in __libc_start_main () from /lib64/tls/libc.so.6
#16 0x00000000004126da in _start ()
#17 0x0000007fbfff2b98 in ?? ()
#18 0x000000000000001c in ?? ()
#19 0x0000000000000010 in ?? ()
#20 0x0000007fbfff3f9a in ?? ()
#21 0x0000007fbfff3fa1 in ?? ()
#22 0x0000007fbfff3fe6 in ?? ()
#23 0x0000007fbfff3fed in ?? ()
#24 0x0000007fbfff3ff1 in ?? ()
#25 0x0000007fbfff3ff8 in ?? ()
#26 0x0000007fbfff3ffc in ?? ()
#27 0x0000007fbfff4003 in ?? ()
#28 0x0000007fbfff4007 in ?? ()
#29 0x0000007fbfff400e in ?? ()
#30 0x0000007fbfff4011 in ?? ()
#31 0x0000007fbfff4018 in ?? ()
#32 0x0000007fbfff401c in ?? ()
#33 0x0000007fbfff4024 in ?? ()
#34 0x0000007fbfff4026 in ?? ()
#35 0x0000007fbfff402f in ?? ()
#36 0x0000000000000000 in ?? ()

Hi,

can’t make much more of it then that the file it corrupt? Is it only with this file or does it happen on other files as well? If the file is okay, but reading is a problem, can you assess from the return statistics of LSF what the total memory usage of the job was?

Cheers,
Wim

Thanks for the reply. It does happen on other files as well. I couldn’t find the memory usage stats for the job I posted above but for another that failed for a similar reasoning these were:

Max Memory : 95 MB
Max Swap : 622 MB

These numbers are comparable to those for jobs that have succeeded. So sorry this probably doesn’t help much…

Hi.,

quoting Philippe on this:[quote]Usually this ("R__unzip: error in header … File:rfio:///) comes from a bug in the castor/rfio library that has been fixed a while back.[/quote]
Any chance you can use a more recent version of the castor libs?

Cheers,
Wim

Hi,

A priori the problem is fixed by using the rfio/castor client library version 2.1.8-4 or higher.

Cheers,
Philippe.