Hello, I notice that when the simulation has many events and the nohup file, or the ROOT file are higher than 3GB, the simulation crash. For example this is the log of a crash due to a big ROOT file.
Hi @php1ic [quote=“php1ic, post:2, topic:3029, full:true”]
Do you get this error with smaller ROOT files?[/quote]
No…just if the Root file or the nohup file is higher than 3GB!
[/quote]
I don’t know it because I’m not running on my computer…I’m running on the computer hosted in the laboratory (ssh connection)
The -m flag sets the output to MB so looks like you have 128GB. I was wondering if you only had 4GB so were running out reading a 3GB file. I’m going to assume this is not the case if you have 128GB
I don’t use ROOT, but google suggests something is being free’d twice. Can you run the code with gdb or valgrind?
Basic usage is as below (output is from I system I have access to)
$ gdb ./exampleB1
GNU gdb (Debian 8.2.1-2+b3) 8.2.1
Copyright (C) 2018 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 ./exampleB1...done.
(gdb)
Then type run to actually execute the simulation. Once it crashes, type where to get details about what was happening when the crash occured. Hopefully this will give you the line number causing the issue.
I don’t know why python is getting involved in this process on your system. I think if you give a second argument to gdb it tries to read it as a core dump file which may be causing the issue.
Can you please running as below
$ gdb ./exampleB1
GNU gdb (Debian 8.2.1-2+b3) 8.2.1
Copyright (C) 2018 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 ./exampleB1...done.
(gdb) run ./run1.mac
Starting program: /home/php1ic/tmp/B1/build/exampleB1 ./run1.mac
This will likely make your simulation run a lot slower.
If I compile the file and I give the command gdb ./exampleB1
I get the error that you can see in my previous printscreen
If I close the terminal, I open it again and I give the command gdb ./exampleB1
without compile the file again I get this (similiar to what you get too)
As suggested by @anna in this topi Errors during compilation using old Geant4 versions - #12 by faca87
I’m using this gcc source /cvmfs/sft.cern.ch/lcg/contrib/gcc/8.3.0/x86_64-centos7-gcc8-opt/setup.sh
because on the machine hosted in the laboratory there wasn’t a cmake compatible with geant4 10.6.1
Hi @faca87, I don’t know anything about the system you are working on, looking at the post you referenced /cvmfs/sft.cern.ch/lcg/contrib appears to be the place for newer packages. Is there a gdb in there?
Otherwise from the stackoverflow post, via google, you could try running your code via valgrind
I agree, you should consult your supervisor to get information on how to access the necessary software (I also have no clue where do you work).
I pointed you to the gcc version you could use since you said you have access to cvmfs. For more software on cvmfs, if you cannot find it yourself following what Ian suggests, you can have a look at the LCG releases that provide a large stack of different software packages: http://lcgdocs.web.cern.ch/lcgdocs/lcgreleases/introduction/