Levi Naden

The new PyYaml does this. Here was the snippet I came up with to suppress that safely: ```python try: yaml_load = partial(yaml.load, Loader=yaml.FullLoader) except AttributeError: yaml_load= yaml.load ``` since `yaml.FullLoader`...

PyYaml emits the warning in the most recent version (5.1), I don't think its functionally doing anything different. The site it links to has some shortcut methods to chose the...

I recall going through the code and replacing all the `yaml.load`'s with safe versions that I could find. Are you seeing an error being thrown now somewhere and/or did I...

I'm pretty sure those are pickle files. Not YAML

Ah. The serialization line is used by the Jupyter Notebooks to dump their data to file. The problem is the Numpy arrays are bing dumped as arrays, instead of as...

YANK itself has no way to actively assign GPUs. However, you can mask GPU's from the CUDA side by setting the `CUDA_VISIBLE_DEVICES` environment variable. [This link](https://devblogs.nvidia.com/cuda-pro-tip-control-gpu-visibility-cuda_visible_devices/) has some helpful info...

OpenMM does expose that option, but YANK, and the main sampler suite `MultistateSampler` in OpenMMTools does not because its possible to have multiple OpenMM contexts in YANK which may be...

> can you please let me know if i can distribute the load on the 6 gpus? Can you elaborate on this a bit? Based on your initial post... >...

> can you please let me know if i can distribute the load on the 6 gpus? Can you elaborate on this a bit? Based on your initial post... >...

> i mean when i run yank it only use one gpu, so i wonder if the load can be on more than one gpu to make it faster. That...