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[Giulia Macaro <question215877@xxxxxxxxxxxxxxxxxxxxx>]

New question #215877 on Yade:
https://answers.launchpad.net/yade/+question/215877

Hello,

I am running a very long simulation, in which a big sphere is loaded on a packing of 50,000 smaller spheres settled under gravity force.
After 4 days of running, the simulation ends without any particular reason. In the terminal it is only written "killed".
I have rerun the same test in the debug mode, compiling Yade with debug=1, and then

$ gdb /usr/bin/python

GNU gdb (GDB) 7.1-ubuntu
Copyright (C) 2010 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".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/bin/python...(no debugging symbols found)...done.

(gdb) run /home/giulia/YetAnotherDynamicEngine/12.07.09_yade/YADE/bin/yade-bzr3040 -j4 --debug 2012.11.28_1_realSph.py

Starting program: /usr/bin/python /home/giulia/YetAnotherDynamicEngine/12.07.09_yade/YADE/bin/yade-bzr3040 -j4 --debug 2012.11.28_1_realSph.py
[Thread debugging using libthread_db enabled]
Welcome to Yade bzr3040 (debug build)
TCP python prompt on localhost:9000, auth cookie `cesaud'
[New Thread 0x7fffd6f2c700 (LWP 7675)]
[New Thread 0x7fffd672b700 (LWP 7676)]

I did not get any information apart from [New Thread ... (LWP ... )] and  [Thread ... (LWP ...) exited]
and then at the end I got

Program terminated with signal SIGKILL, Killed.
The program no longer exists.

I also tried
(gdb) thread apply bt full
But I did not get anything.

And then
(gdb) bt full
which gave me
No stack.

I was recording the CPU and memory usage during the simulation.  The machine has 8 cores and 12GB of memory. The CPU was constant around 40% (using 4 over 8 cores) but the total memory went from 31% to 99% in 24 hours, then constant to 99% for the following 3 days, and then the test ended.
I am not erasing any body. I am creating the spheres, apply gravity, wait that the deposition ends, create the big sphere, and push the big sphere in the packing very slowly.
I was expecting to use a lot of memory since I have a lot of particles, but not that much... is that possible? I am wondering if the ending of the simulation is related to the memory.


At this point I am also rerunning some periodic triaxial tests, with only 5,000 particles. The memory usage has increased from 22 to 32% in 3 hours of simulation, and it is still increasing... Has anybody encountered the same increasing of memory? Is it expected in Yade?

Thank you
Giulia

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