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Re: Memory leak in espresso

From: Jean-Noël Grad
Subject: Re: Memory leak in espresso
Date: Sun, 16 Feb 2020 17:35:09 +0100
User-agent: Mozilla/5.0 (X11; Linux i686; rv:68.0) Gecko/20100101 Thunderbird/68.4.1


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 (

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,

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.


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