QMMM latency in PME correction

From: Wall, Michael E (mewall_at_lanl.gov)
Date: Tue Nov 16 2021 - 15:39:25 CST

Hello NAMD-L,

I'm using NAMD to perform QMMM using a large QM region, using LATTE as a QM solver (https://urldefense.com/v3/__https://github.com/lanl/latte__;!!DZ3fjg!sF2-qGbr94sZuQylawLrZXrTe3zqvOL5SUo1Po3pBtX5gf_92TKt2iTMDez8dOCyhg$ ). I'm seeing some latency on the NAMD side that I'm trying to address.

I've done some profiling and found that most of the latency is associated with a PME correction in src/ComputeQM.C (line 5033 in the NAMD_2.14b2_Source version, about 6-9 seconds required for the system I'm currently looking at).

I had a conversation with Marcelo Melo about strategies for addressing this issue by parallelizing the PME correction (along with a couple of other calculations). He shared his thoughts and also suggested I post to this mailing list to share the observation more broadly and to see whether one of the other developers might have any insights.

Thank you for considering this issue.


Michael Wall

Michael Wall

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