[Gate-users] merging errors

Lena Thomas lena.thomas at cumcui.de
Wed Mar 16 10:51:24 CET 2011

Dear Gateusers,

I used the Gate jobsplitter (gjs) to split my PET-simulation across 10 
cpus (on a ubuntu 64 bit machine). The simulation finished without any 
error message. To merge the root output files I used the Gate jobmerger 
(gjm), but I got warnings about overlapping singles  and finally a 
*** Break *** segmentation violation
 Generating stack trace...

I tried the segmentiaion violation with the gnu debugger and got this:

$ gdb gjm

GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
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".
For bug reporting instructions, please see:
Reading symbols from /opt/gate_v6.0_p01/bin/Linux-g++/gjm...(no 
debugging symbols found)...done.

(gdb) run -v 3 .Gate/Gemini_TF/Gemini_TF.split
Starting program: /opt/gate_v6.0_p01/bin/Linux-g++/gjm -v 3 
[Thread debugging using libthread_db enabled]
Root input file name: Y-90-100MBq1.root
Root input file name: Y-90-100MBq2.root
Root input file name: Y-90-100MBq3.root
Root input file name: Y-90-100MBq4.root
Root input file name: Y-90-100MBq5.root
Root input file name: Y-90-100MBq6.root
Root input file name: Y-90-100MBq7.root
Root input file name: Y-90-100MBq8.root
Root input file name: Y-90-100MBq9.root
Root input file name: Y-90-100MBq10.root
Root output file name: Y-90-100MBq.root
Combining: Y-90-100MBq1.root Y-90-100MBq2.root Y-90-100MBq3.root 
Y-90-100MBq4.root Y-90-100MBq5.root Y-90-100MBq6.root Y-90-100MBq7.root 
Y-90-100MBq8.root Y-90-100MBq9.root Y-90-100MBq10.root -> Y-90-100MBq.root
Warning - overlapping Singles time (206690) in file: Y-90-100MBq2.root
Warning - overlapping Singles time (314599) in file: Y-90-100MBq3.root
Warning - overlapping Singles time (289330) in file: Y-90-100MBq4.root
Warning - overlapping Singles time (218606) in file: Y-90-100MBq5.root
Fill: Switching to new file: Y-90-100MBq_1.root
Warning - overlapping Singles time (54921.6) in file: Y-90-100MBq6.root
Warning - overlapping Singles time (218545) in file: Y-90-100MBq7.root
Warning - overlapping Singles time (37645.9) in file: Y-90-100MBq8.root
Warning - overlapping Singles time (77194.9) in file: Y-90-100MBq9.root
Warning - overlapping Singles time (120316) in file: Y-90-100MBq10.root
Fill: Switching to new file: Y-90-100MBq_2.root

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff30d00d8 in ?? () from /lib/libc.so.6

(gdb) backtrace
#0  0x00007ffff30d00d8 in ?? () from /lib/libc.so.6
#1  0x00000000004055d9 in GateMergeManager::MergeSing(TChain*) ()
#2  0x0000000000407b47 in GateMergeManager::MergeTree(std::string) ()
#3  0x0000000000408304 in GateMergeManager::MergeRoot() ()
#4  0x0000000000408e13 in GateMergeManager::StartMerging(std::string) ()
#5  0x000000000040421a in main ()
(gdb) x 0x00007ffff30d00d8
0x7ffff30d00d8: 0xf30d00c8
(gdb) x 0xf30d00c8
0xf30d00c8:     Cannot access memory at address 0xf30d00c8

Does anybody has an idea what happend?

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