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Trajectory load memory error #23

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rsexton2 opened this issue Mar 11, 2022 · 0 comments
Open

Trajectory load memory error #23

rsexton2 opened this issue Mar 11, 2022 · 0 comments

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@rsexton2
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When loading a large trajectory I receive the error

---------------------------------------------------------------------------
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

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