[Gate-users] Large voxelised source images causing segfaults

Christopher Oldfield christopher.oldfield at manchester.ac.uk
Tue Aug 2 17:47:01 CEST 2016 

Dear all,

I've been doing some work in Gate v7.0 recently using voxelised sources for large images 750x75x750 voxels, these all work fine.  I've switched to trying something with a 2350x2350x2350 source image (24 GB of short integers) and I get the following error.  I've also run the simulation in GATE v7.1 and it works for the smaller images but not the larger ones.  The machine I'm using has more than enough available RAM and I'm at a loss as to how to begin to tackle this problem.

I've included the crash information for both GATE versions.  Does anyone know why it would fail for this or have any suggestions for how I'd go about fixing this?

Thanks
Chris


This is the crash information for GATE 7.0


 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000003bf90ac7be in waitpid () from /lib64/libc.so.6
#1  0x0000003bf903e5c9 in do_system () from /lib64/libc.so.6
#2  0x00007f1ee1e92928 in TUnixSystem::StackTrace() () from /opt/root/lib/root/libCore.so
#3  0x00007f1ee1e91db3 in TUnixSystem::DispatchSignals(ESignals) () from /opt/root/lib/root/libCore.so
#4  <signal handler called>
#5  0x000000000079d794 in GateSourceVoxelInterfileReader::ReadFile(G4String) ()
#6  0x000000000079f2e5 in GateSourceVoxelInterfileReaderMessenger::SetNewValue(G4UIcommand*, G4String) ()
#7  0x00007f1ee2cddc1a in G4UIcommand::DoIt(G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#8  0x00007f1ee2ce9a53 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#9  0x00007f1ee2ccfab7 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#10 0x00007f1ee2cd0a3b in G4UIbatch::SessionStart() () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#11 0x00007f1ee2ce7ca3 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#12 0x00007f1ee2ce437f in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#13 0x00007f1ee2cddc1a in G4UIcommand::DoIt(G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#14 0x00007f1ee2ce9a53 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#15 0x00000000004f1698 in main ()
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug 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.
===========================================================
#5  0x000000000079d794 in GateSourceVoxelInterfileReader::ReadFile(G4String) ()
#6  0x000000000079f2e5 in GateSourceVoxelInterfileReaderMessenger::SetNewValue(G4UIcommand*, G4String) ()
#7  0x00007f1ee2cddc1a in G4UIcommand::DoIt(G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#8  0x00007f1ee2ce9a53 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#9  0x00007f1ee2ccfab7 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#10 0x00007f1ee2cd0a3b in G4UIbatch::SessionStart() () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#11 0x00007f1ee2ce7ca3 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#12 0x00007f1ee2ce437f in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#13 0x00007f1ee2cddc1a in G4UIcommand::DoIt(G4String) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#14 0x00007f1ee2ce9a53 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.9.6.p02/lib64/libG4intercoms.so
#15 0x00000000004f1698 in main ()
===========================================================


Segmentation fault






Below is the crash information for GATE 7.1







 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000003bf90ac7be in waitpid () from /lib64/libc.so.6
#1  0x0000003bf903e5c9 in do_system () from /lib64/libc.so.6
#2  0x00007ffa9abe1928 in TUnixSystem::StackTrace() () from /opt/root/lib/root/libCore.so
#3  0x00007ffa9abe0db3 in TUnixSystem::DispatchSignals(ESignals) () from /opt/root/lib/root/libCore.so
#4  <signal handler called>
#5  0x000000000081630e in GateSourceVoxelImageReader::ReadFile(G4String) ()
#6  0x00000000007f97b1 in GateSourceVoxelImageReaderMessenger::SetNewValue(G4UIcommand*, G4String) ()
#7  0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#8  0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#9  0x00007ffa9bcea857 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#10 0x00007ffa9bceb81b in G4UIbatch::SessionStart() () from /opt/geant4.10.01/lib64/libG4intercoms.so
#11 0x00007ffa9bd03223 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#12 0x00007ffa9bcfe568 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#13 0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#14 0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#15 0x00007ffa9bcea857 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#16 0x00007ffa9bceb81b in G4UIbatch::SessionStart() () from /opt/geant4.10.01/lib64/libG4intercoms.so
#17 0x00007ffa9bd03223 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#18 0x00007ffa9bcfe568 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#19 0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#20 0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#21 0x00000000004f860d in main ()
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug 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.
===========================================================
#5  0x000000000081630e in GateSourceVoxelImageReader::ReadFile(G4String) ()
#6  0x00000000007f97b1 in GateSourceVoxelImageReaderMessenger::SetNewValue(G4UIcommand*, G4String) ()
#7  0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#8  0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#9  0x00007ffa9bcea857 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#10 0x00007ffa9bceb81b in G4UIbatch::SessionStart() () from /opt/geant4.10.01/lib64/libG4intercoms.so
#11 0x00007ffa9bd03223 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#12 0x00007ffa9bcfe568 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#13 0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#14 0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#15 0x00007ffa9bcea857 in G4UIbatch::ExecCommand(G4String const&) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#16 0x00007ffa9bceb81b in G4UIbatch::SessionStart() () from /opt/geant4.10.01/lib64/libG4intercoms.so
#17 0x00007ffa9bd03223 in G4UImanager::ExecuteMacroFile(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#18 0x00007ffa9bcfe568 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#19 0x00007ffa9bcf814b in G4UIcommand::DoIt(G4String) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#20 0x00007ffa9bd055e7 in G4UImanager::ApplyCommand(char const*) () from /opt/geant4.10.01/lib64/libG4intercoms.so
#21 0x00000000004f860d in main ()
===========================================================









---------------------------------------------------------------
-  Chris Oldfield <christopher.oldfield at manchester.ac.uk>
-  School of Physics and Astronomy,        Tel. 0161 275 4167
-  University of Manchester,
-  Manchester, M13 9PL.
---------------------------------------------------------------
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