Re: Memory leak in espresso

[Jean-Noël Grad]

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