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我提一句，不要一味地追求速度而过度使用2020和2021版本的gromacs，特别是gpu这一块。-update gpu严格意义上来说是不稳定和有bug的，据我所知，2021.6之前的所有使用-update gpu这个选项都会带来某些问题，特别含有水的体系，帖一句开发者讨论的东西:
When using GPU update with SETTLE or LINCS constraints, virial calculations
could have been incorrect on Volta and newer NVIDIA GPUs, which in turn
would lead to incorrect pressure. The GPU update is not enabled by default,
so the error can only appear in simulations where it was manually selected,
and even in this case the error might be rare since we have not observed it
in practice in the testing we have performed.
To check whether your runs could have been affected, please examine your mdrun log file:
- Look for the line "GPU support: CUDA";
- Look for the line "PP task will update and constrain coordinates on the GPU";
- Check whether any GPU the value of "compute cap." 7.0 or higher in the "GPU Info:" section.
If all three are present, than the bug could have perturbed the virial calculation and,
in turn, led to incorrect pressure coupling. All |Gromacs| version prior to 2021.6 and 2022.0
that allow offloading of the update and constraint calculations to GPUs are affected.
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发表于 Post on 2022-6-9 10:41:31
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