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When loading a large trajectory I receive the error
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MemoryError Traceback (most recent call last)
/tmp/ipykernel_1511828/2176272352.py in <module>
----> 1 li.collect_residue_contacts()
~/Library/miniconda3/envs/BALMP/lib/python3.9/site-packages/pylipid/api/api.py in collect_residue_contacts(self)
331 for traj_idx in trange(len(self._trajfile_list), desc="COLLECT INTERACTIONS FROM TRAJECTORIES",
332 total=len(self._trajfile_list)):
--> 333 traj = md.load(self._trajfile_list[traj_idx], top=self._topfile_list[traj_idx], stride=self._stride)
334 traj_info, self._protein_ref, self._lipid_ref = get_traj_info(traj, lipid=self._lipid,
335 lipid_atoms=self._lipid_atoms,
~/Library/miniconda3/envs/BALMP/lib/python3.9/site-packages/mdtraj/core/trajectory.py in load(filename_or_filenames, discard_overlapping_frames, **kwargs)
427 #TODO make all the loaders accept a pre parsed topology (top) in order to avoid
428 #this part and have a more consistent interface and a faster load function
--> 429 t = loader(tmp_file, **kwargs)
430
431 except TypeError as e:
mdtraj/formats/xtc/xtc.pyx in mdtraj.formats.xtc.load_xtc()
mdtraj/formats/xtc/xtc.pyx in mdtraj.formats.xtc.load_xtc()
mdtraj/formats/xtc/xtc.pyx in mdtraj.formats.xtc.XTCTrajectoryFile.read_as_traj()
mdtraj/formats/xtc/xtc.pyx in mdtraj.formats.xtc.XTCTrajectoryFile.read()
mdtraj/formats/xtc/xtc.pyx in mdtraj.formats.xtc.XTCTrajectoryFile._read()
MemoryError: Unable to allocate 195. GiB for an array with shape (1881562, 9260, 3) and data type float32
Using stride is not an option for my system
The text was updated successfully, but these errors were encountered:
When loading a large trajectory I receive the error
Using stride is not an option for my system
The text was updated successfully, but these errors were encountered: