From: Wall, Michael E (mewall_at_lanl.gov)
Date: Tue Nov 16 2021 - 15:39:25 CST
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 mewall_at_lanl.gov https://urldefense.com/v3/__http://public.lanl.gov/mewall__;!!DZ3fjg!sF2-qGbr94sZuQylawLrZXrTe3zqvOL5SUo1Po3pBtX5gf_92TKt2iTMDeyDZi9pJQ$
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