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choderalab / yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
http://getyank.org
MIT License
175 stars 70 forks source link

mpi4py should be a dependency of conda installer #1215

Open daveminh opened 4 years ago

daveminh commented 4 years ago

I got this error from a fresh install from miniconda3 when running on XSEDE Bridges.

Traceback (most recent call last): File "/home/dminh/.conda/envs/yank/bin/yank", line 11, in load_entry_point('yank==0.25.2', 'console_scripts', 'yank')() File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/cli.py", line 73, in main dispatched = getattr(commands, command).dispatch(command_args) File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/commands/script.py", line 147, in dispatch yaml_builder = ExperimentBuilder(script=yaml_path, job_id=job_id, n_jobs=n_jobs) File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 591, in init self.parse(script) File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 684, in parse utils.config_root_logger(self._options['verbose'], log_file_path=None) File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/yank/utils.py", line 132, in config_root_logger mpicomm = mpiplus.get_mpicomm() File "/home/dminh/.conda/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 122, in get_mpicomm from mpi4py import MPI ModuleNotFoundError: No module named 'mpi4py'

jchodera commented 4 years ago

The yank recipe requires mpiplus. We migrated the recipe to conda-forge, but it appears we neglected to include that dependency. Could you refile the issue that mpiplus should require mpi4py here?

cc @andrrizzi

andrrizzi commented 4 years ago

Hmm. This shouldn't happen. mpiplus should be a requirement of openmmtools so there should be no need to include it in yank's recipe.

andrrizzi commented 4 years ago

Oh, I see, it's the mpiplus recipe that needs to include the python mpi4py package. Yes, I agree (cc @hannahbrucemacdonald).