Re: Memory leak in espresso

[Jean-Noël Grad]

Hi,

I ran a polymer simulation with a hat potential and tabulated bonds to 
reproduce your system, and was able to measure a memory leak when the 
OpenGL visualizer was active. This is reproducible with other types of 
simulation. The leak rate is 12 megabyte/minute, which is substantial. 
Depending on the polymer parameters, I measured between 10 MB/min to 14 
MB/min, which is of the same order of magnitude as the 8 MB/min you 
measured on your machine.

Thanks for reporting this issue. I've opened a ticket on GitHub:
https://github.com/espressomd/espresso/issues/3530

Best regards,
JN

On 2/20/20 12:06 PM, David Power wrote:
> Hi Jean,
>
> Sorry for the late reply. I figured out that I was only seeing the 
> memory leak on my machine when the visualizer
> was enabled. I turned visualization off and the leak went away.
>
> Thanks,
> David
>
> On Sun, 16 Feb 2020 at 16:35, Jean-Noël Grad <address@hidden 
> <mailto:address@hidden>> wrote:
>
>     Hi,
>
>     system.set_random_state_PRNG() sets and warms up the global Mersenne
>     Twister random number generator. It is used to make espresso
>     simulations
>     deterministic. Since espresso 4.0, a lot of effort went into replacing
>     the global Mersenne Twister generator by local Philox generators. In
>     espresso 4.1, very few features still use the global Mersenne Twister,
>     for example the NPT thermostat and diamond polymer. In the upcoming
>     espresso 4.2.0 release, the global Mersenne Twister has been completely
>     removed (https://github.com/espressomd/espresso/pull/3482).
>
>     Thanks for the files you attached. Unfortunately, the espresso script
>     seems to be missing a custom Python module called Molecule. I was not
>     able to run your example. Could you please generate a minimal working
>     example (MWE), where non-relevant parts of the script are removed? For
>     instance, the numpy data analysis in the main_thread() function is
>     unlikely to be part of the problem, and the exclusion-list logic has no
>     associated data field in file 1n5u.struct. The Molecule package also
>     seems unnecessary in that MWE, since it is only a convenience
>     wrapper to
>     read 3D coordinates from a file and set up espresso bonded interaction
>     objects. In general, the shorter the MWE, the quicker it is for us to
>     figure out which part of the C++ code needs to be investigated.
>
>     With best regards,
>     JN
>
>     On 1/16/20 2:58 PM, David Power wrote:
>      > I'm on the latest 4.1 branch from git. Espresso runs along fine,
>     but the
>      > amount of available ram that's free on my system slowly starts to
>      > decrease. When it gets to 0 espresso crashes and all the ram
>     become free
>      > again. I've attached the script I used to capture the amount of
>      > available memory on my machine and a sample output showing the
>     memory
>      > decreasing.
>      >
>      > This is an issue as some of my simulations take quite a while to
>      > generate the data I need.
>      >
>      > I've attached my python script and associated data files if want
>     to try
>      > and reproduce the issue. Please let me know if there is anything
>     else
>      > you need from me.
>      >
>      > Thanks,
>      > David