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Trajectory load memory error

Open rsexton2 opened this issue 3 years ago • 0 comments

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

rsexton2 avatar Mar 11 '22 18:03 rsexton2