openmmtools: incompatible with the netCDF4 stack

I think there might be some incompatibility issue with the most recent netCDF4 stack. I have pulled in the latest openmmtools conda package and run it on a script that used to run. However, I’m getting some netCDF4 related issues. Please find the conda list, and input files attached.

Traceback (most recent call last):
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatereporter.py", line 1800, in _write_dict
    nc_variable = self._resolve_nc_path(path, storage_name)
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatereporter.py", line 1465, in _resolve_nc_path
    return nc_group.variables[path_split[-1]]
KeyError: 'options'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/sharedfs-home/zwu/C/vac/prod/lambda_0/OpenMMTools_script.py", line 56, in <module>
    simulation.create(
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 606, in create
    self._initialize_reporter()
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/mpiplus/mpiplus.py", line 271, in _wrapper
    return run_single_node(rank, task, *args, **kwargs)
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/mpiplus/mpiplus.py", line 220, in run_single_node
    result = task(*args, **kwargs)
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 1182, in _initialize_reporter
    self._store_options()
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 1256, in _store_options
    self._reporter.write_dict('options', self.options)
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatereporter.py", line 1104, in write_dict
    self._write_dict(path, data, storage_name=storage_name)
  File "/sharedfs-home/zwu/.conda/envs/openmmtools/lib/python3.10/site-packages/openmmtools/multistate/multistatereporter.py", line 1812, in _write_dict
    nc_variable = storage_nc.createVariable(path, variable_type,
  File "src/netCDF4/_netCDF4.pyx", line 2945, in netCDF4._netCDF4.Dataset.createVariable
  File "src/netCDF4/_netCDF4.pyx", line 4184, in netCDF4._netCDF4.Variable.__init__
  File "src/netCDF4/_netCDF4.pyx", line 2014, in netCDF4._netCDF4._ensure_nc_success
RuntimeError: NetCDF: Filter error: bad id or parameters or duplicate filter

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About this issue

  • Original URL
  • State: closed
  • Created a year ago
  • Comments: 15 (7 by maintainers)

Most upvoted comments

@ijpulidos Thank you very much. I only use mamba as otherwise, it is just too slow.

@ijpulidos Thank you very much for the help.