issue with large dcd seeking #4879
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forgot to mention the dcd file is 4GB. same file was run before with the same script. |
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If you run import MDAnalysis as mda
import os
u = mda.Universe(DCD)
print("size:", os.stat(DCD).st_size, "B")
print("length:", u.trajectory.n_frames)
for ts in u.trajectory:
print(ts.frame, end=" ")
print("\nComplete")with MDA 2.8.0 and a previous version (2.7.0, ... whichever is the last one working) then what do you get? |
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Hi,
Below are the return results (2.8.0):
size: 4255373076 B
length: 4320
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 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Complete
Thanks!
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@qlearn-code thanks for checking. This output indicates that your DCD is read fully (with MDA 2.8.0), so at least the basic DCD reading code does not seem to be at fault. |
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How are you executing the RDF analysis? Can you show the minimal code example (from setting up the |
orbeckst
added
the
more information needed
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Sure. I was running this cell by cell.
import MDAnalysis as mda
from MDAnalysis.analysis import rdf
import time
from IPython.display import Image
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
u = mda.Universe("psf","dcd")
print(u)
print(len(u.trajectory))
<Universe with 82080 atoms>
4320
PF6 = u.select_atoms('resname PF6')
Na = u.select_atoms('resname SOD')
irdf = rdf.InterRDF(Na, PF6,
nbins=75, # default
range=(0.0, 7.45), # distance in angstroms
)
irdf.run()
OSError Traceback (most recent call last)
Cell In[7], line 5
1 irdf = rdf.InterRDF(Na, PF6,
2 nbins=75, # default
3 range=(0.0, 7.45), # distance in angstroms
4 )
----> 5 irdf.run()
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\analysis\base.py:822, in AnalysisBase.run(self, start, stop, step, frames, verbose, n_workers, n_parts, backend, unsupported_backend, progressbar_kwargs)
815 computation_groups = self._setup_computation_groups(
816 start=start, stop=stop, step=step, frames=frames, n_parts=n_parts
817 )
819 # get all results from workers in other processes.
820 # we need `AnalysisBase` classes
821 # since they hold `frames`, `times` and `results` attributes
--> 822 remote_objects: list["AnalysisBase"] = executor.apply(
823 worker_func, computation_groups)
824 self.frames = np.hstack([obj.frames for obj in remote_objects])
825 self.times = np.hstack([obj.times for obj in remote_objects])
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\analysis\backends.py:206, in BackendSerial.apply(self, func, computations)
190 def apply(self, func: Callable, computations: list) -> list:
191 """
192 Serially applies `func` to each task object in ``computations``.
193
(...)
204 list of results of the function
205 """
--> 206 return [func(task) for task in computations]
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\analysis\base.py:515, in AnalysisBase._compute(self, indexed_frames, verbose, progressbar_kwargs)
512 if len(frames) == 0: # if `frames` were empty in `run` or `stop=0`
513 return self
--> 515 for idx, ts in enumerate(ProgressBar(
516 self._sliced_trajectory,
517 verbose=verbose,
518 **progressbar_kwargs)):
519 self._frame_index = idx # accessed later by subclasses
520 self._ts = ts
File C:\ProgramData\anaconda3\Lib\site-packages\tqdm\notebook.py:250, in tqdm_notebook.__iter__(self)
248 try:
249 it = super().__iter__()
--> 250 for obj in it:
251 # return super(tqdm...) will not catch exception
252 yield obj
253 # NB: except ... [ as ...] breaks IPython async KeyboardInterrupt
File C:\ProgramData\anaconda3\Lib\site-packages\tqdm\std.py:1169, in tqdm.__iter__(self)
1166 # If the bar is disabled, then just walk the iterable
1167 # (note: keep this check outside the loop for performance)
1168 if self.disable:
-> 1169 for obj in iterable:
1170 yield obj
1171 return
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\base.py:331, in FrameIteratorIndices.__iter__(self)
329 def __iter__(self):
330 for frame in self.frames:
--> 331 yield self.trajectory._read_frame_with_aux(frame)
332 self.trajectory.rewind()
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\base.py:868, in ProtoReader._read_frame_with_aux(self, frame)
866 def _read_frame_with_aux(self, frame):
867 """Move to *frame*, updating ts with trajectory, transformations and auxiliary data."""
--> 868 ts = self._read_frame(frame) # pylint: disable=assignment-from-no-return
869 for aux in self.aux_list:
870 ts = self._auxs[aux].update_ts(ts)
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\DCD.py:198, in DCDReader._read_frame(self, i)
196 """read frame i"""
197 self._frame = i - 1
--> 198 self._file.seek(i)
199 return self._read_next_timestep()
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\lib\formats\libdcd.pyx:400, in MDAnalysis.lib.formats.libdcd.DCDFile.seek()
OSError: DCD seek failed with DCD error=Normal EOF
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orbeckst
removed
the
more information needed
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Can you enable the Python debugger ( |
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This is the line after enabling pdb. Do I need to type in something after ipdb?
c:\users\downloads\md analysis\mdanalysis\lib\formats\libdcd.pyx(400)MDAnalysis.lib.formats.libdcd.DCDFile.seek()
ipdb>
|
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Yes, or possibly You might have to learn how to use the debugger https://docs.python.org/3/library/pdb.html to be able to navigate the call stack. You can move "up" |
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Got it! Thanks, I will look into the pdb functions.
Here is the output:
ipdb> u
c:\programdata\anaconda3\lib\site-packages\mdanalysis\coordinates\dcd.py(198)_read_frame()
196 """read frame i"""
197 self._frame = i - 1
--> 198 self._file.seek(i)
199 return self._read_next_timestep()
200
ipdb> p i
2181
ipdb>
|
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This looks indeed as if the DCD reading stopped in the middle of the trajectory. I am not sure what's happening. Can you check if you can trigger the error by manually seeking to these frames, i.e., u = mda.Universe("psf","dcd")
u.trajectory[0]
print(u.trajectory.ts.frame)
u.trajectory[2180]
print(u.trajectory.ts.frame)
u.trajectory[2181]
print(u.trajectory.ts.frame)
u.trajectory[2182]
print(u.trajectory.ts.frame)
u.trajectory[-1]
print(u.trajectory.ts.frame) |
|
The dcd reading seems to stop right at frame2181 u.trajectory[0]
print(u.trajectory.ts.frame)
0
u.trajectory[2180]
print(u.trajectory.ts.frame)
2180
u.trajectory[2181]
print(u.trajectory.ts.frame)
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
Cell In[35], line 1
----> 1 u.trajectory[2181]
2 print(u.trajectory.ts.frame)
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\base.py:836, in ProtoReader.__getitem__(self, frame)
834 if isinstance(frame, numbers.Integral):
835 frame = self._apply_limits(frame)
--> 836 return self._read_frame_with_aux(frame)
837 elif isinstance(frame, (list, np.ndarray)):
838 if len(frame) != 0 and isinstance(frame[0], (bool, np.bool_)):
839 # Avoid having list of bools
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\base.py:868, in ProtoReader._read_frame_with_aux(self, frame)
866 def _read_frame_with_aux(self, frame):
867 """Move to *frame*, updating ts with trajectory, transformations and auxiliary data."""
--> 868 ts = self._read_frame(frame) # pylint: disable=assignment-from-no-return
869 for aux in self.aux_list:
870 ts = self._auxs[aux].update_ts(ts)
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\coordinates\DCD.py:198, in DCDReader._read_frame(self, i)
196 """read frame i"""
197 self._frame = i - 1
--> 198 self._file.seek(i)
199 return self._read_next_timestep()
File C:\ProgramData\anaconda3\Lib\site-packages\MDAnalysis\lib\formats\libdcd.pyx:400, in MDAnalysis.lib.formats.libdcd.DCDFile.seek()
OSError: DCD seek failed with DCD error=Normal EOFu.trajectory[2182]
print(u.trajectory.ts.frame)
u.trajectory[-1]
print(u.trajectory.ts.frame)gives same error message as 2181 |
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This looks as if there's a real bug related to DCD
|
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Which version of Windows are you using? Windows 10.0.19045 |
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I don't have an immediate solution (and I don't have a Windows machine to reproduce) so for right now, we are keeping this issue up as a bug. (We do need to check that the issue does not also happens on Linux/macOS.) |
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Reinstalled the MDanalysis today and run rdf calculation. Got this error message "OSError: DCD seek failed with DCD error=Normal EOF"
Exact same script was successfully run before with previous version of mdanalysis.
Shouldn't be memory issue, cause that gives a different error message.
mdanalysis 2.8.0
on Windows using Jupyter notebook
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