Repository: MDAnalysis/mdanalysis

Issue:
issue with large dcd seeking


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




Discussion:
forgot to mention the dcd file is 4GB. same file was run before with the same script.
If you run
```python
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? 

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!


@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.


How are you executing the RDF analysis? Can you show the minimal code example (from setting up the `Universe`) that displays the failure, together with the exception traceback?


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




Can you enable the Python debugger (`%pdb` in ipython/jupyter) and then find out at which frame `i` the error occurs?
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>


Yes,
```
p i
```
or possibly
```
u
p i
```
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" `u` and "down" `d` the last function calls and you can print `p` the values of variables.
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>


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.,
```python
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

```python
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 EOF
```

```python
u.trajectory[2182]
print(u.trajectory.ts.frame)
u.trajectory[-1]
print(u.trajectory.ts.frame)
```
gives same error message as 2181

This looks as if there's a real bug related to DCD `seek`.

- Which version of Windows are you using?
- Which version of Python?
- How did you install MDAnalysis?

Which version of Windows are you using? Windows 10.0.19045
Which version of Python? 3.12.3
How did you install MDAnalysis? Installed with anaconda prompt, using "conda install mdanalysis"
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.)
I was also having this issue on 2.8, updating to 2.9 did seem to resolve it however.
Thanks! Glad yours is working! Just update my version. No luck on my end though. Have been working on a server with older version.
Same problem. Works with MDAnalysis 2.7.0 but not 2.9.0
Thanks for the error report @fhh2626 . Could you please provide more details: What code were you running? What operating system? What was the error you received?

What is the output for your DCD file
```python
import MDAnalysis as mda
import os

u = mda.Universe(DCD)

print("size:", os.stat(DCD).st_size, "B")
print("length:", u.trajectory.n_frames)
print("n_atoms:", u.atoms.n_atoms)

print("Iterate over all frames")
for ts in u.trajectory:
   print(ts.frame, end=" ")
print("\nComplete")

ts = u.trajectory[-2]
print("Seek near end: trajectory[-2]", ts)
```

(sorry, clicked wrong button ... didn't want to close issue)
In order to address this issue we will need to have a reliable failure case. Then we can use `git bisect` to find out which commit between 2.7.0 (which reportedly worked) and 2.9.0 (or 2.8.0?) introduced the reported failure.

Hi, @orbeckst ,

for instance, the following script can raise the error (Windows 11, Python 3.13.3):
```
u = mda.Universe("crystal.psf", "output/wtm-eabf-01.dcd")
y33_chi1 = u.select_atoms("resid 33 and segid GB1A and name N CA CB CG")
chi1_analysis = Dihedral([y33_chi1.atoms])
chi1_analysis.run()
chi1_angles = chi1_analysis.angles[:, 0]
```

the output of your script:
```
size: 2744627012 B
length: 13687
n_atoms: 16704
Iterate over all frames
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
Traceback (most recent call last):
  File "e:\xxxxxxx\test.py", line 15, in <module>
    ts = u.trajectory[-2]
         ~~~~~~~~~~~~^^^^
  File "d:\miniconda3\envs\mlearn\Lib\site-packages\MDAnalysis\coordinates\base.py", line 836, in __getitem__
    return self._read_frame_with_aux(frame)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
  File "d:\miniconda3\envs\mlearn\Lib\site-packages\MDAnalysis\coordinates\base.py", line 868, in _read_frame_with_aux
    ts = self._read_frame(frame)  # pylint: disable=assignment-from-no-return
  File "d:\miniconda3\envs\mlearn\Lib\site-packages\MDAnalysis\coordinates\DCD.py", line 198, in _read_frame
    self._file.seek(i)
    ~~~~~~~~~~~~~~~^^^
  File "MDAnalysis/lib/formats/libdcd.pyx", line 400, in MDAnalysis.lib.formats.libdcd.DCDFile.seek
OSError: DCD seek failed with DCD error=Normal EOF
```

Thanks,
Haohao
In order to narrow down this error with `git bisect` we need a way to easily trigger the error so I started writing scripts. So far with MDA 2.10.0-dev0 `check_dcd_access.py` SUCCEEDS ✅  on macOS and Linux; I assume it will fail ❌ on Windows but I don't have access to a windows machine:
- ✅ macOS x86_64 (macOS-13.7.2-x86_64-i386-64bit)
- ✅ macOS arm64 (macOS-14.2.1-arm64-arm-64bit)
- ✅ Linux x86_64 (Linux-5.15.0-139-generic-x86_64-with-glibc2.35)
- ❓ Windows NOT TESTED

## Testing procedure
Install MDAnalysis and MDAnalysisData
```bash
mamba create -n mdatest python=3.12 mdanalysis mdanalysistests mdanalysisdata
mamba activate mdatest
```

Create a testing directory `issue_4879`, copy the scripts `make_test_dcd.py` and `check_dcd_access.py` from below into this directory,  and then create the test trajectory *1ake_007-nowater-core-dt240psx17.dcd* (use script below)
```bash
mkdir issue_4879 && cd issue_4879
python make_test_dcd.py
```

Run tests (script below)
```bash
python check_dcd_access.py 1ake_007-nowater-core-dt240psx17.dcd
```

If all goes well you get output like
```
INFO: MDAnalysis version 2.10.0-dev0
INFO: platform Linux-5.15.0-139-generic-x86_64-with-glibc2.35
INFO: Python 3.12.11
INFO: Testing DCD trajectory 1ake_007-nowater-core-dt240psx17.dcd
INFO:    size: 2859403144 B
INFO:    length: 71179 frames
INFO:    n_atoms: 3341
TEST 1: Iterate over all frames... PASSED
TEST 2: seek to second but last frame... PASSED
```
with shell exit status 0.

If there's a failure, it will say FAILED and the shell exit status will be different.


## Scripts
### Generate test trajectory `make_test_dcd.py`

Generate a DCD of size that's at least as large as the smallest reported size that triggers the issue (probably the limit is 2 GiB but https://github.com/MDAnalysis/mdanalysis/issues/4879#issuecomment-2811571755 reports 2.556 GiB so we go with that).

I am using a public DCD from MDAnalysisData but one can also just use the DCD from the tests (MDAnalysisTests.datafiles.dcd).

```python
# create test DCD for
# https://github.com/MDAnalysis/mdanalysis/issues/4879

import pathlib
import numpy as np

import MDAnalysis as mda
from MDAnalysisTests import datafiles as data

# https://github.com/MDAnalysis/mdanalysis/issues/4879#issuecomment-2811571755 shows failure with a DCD of size
MINSIZE_B = 2744627012

# bigger base trajectory
import MDAnalysisData
adk = MDAnalysisData.adk_equilibrium.fetch_adk_equilibrium()

psf = pathlib.Path(adk.topology)
dcd = pathlib.Path(adk.trajectory)

# concatenate n copies
trjsize = dcd.stat().st_size
n = int(np.ceil(MINSIZE_B / trjsize))

filename = pathlib.Path(dcd.stem + f"x{n}.dcd")

print(f"Building test trajectory {filename} = {n} x {dcd}")

u = mda.Universe(adk.topology, n * [adk.trajectory])
u.atoms.write(filename, frames="all")

newsize = filename.stat().st_size

GB = 1024**3
print(f"Target size: {MINSIZE_B / GB} GiB")
print(f"DCD size:    {newsize / GB} GiB")
```

### Test for failure `check_dcd_access.py`
The following script should be run on the test trajectory. It **should** complete without issue but fail if the problem diagnosed here is present.

* all tests pass: return 0
* trajectory iteration fails: return 1
* seeking to end fails: return 2

```python
# https://github.com/MDAnalysis/mdanalysis/issues/4879
# test seeking in large DCD
# https://github.com/MDAnalysis/mdanalysis/issues/4879#issuecomment-2806836898


import MDAnalysis as mda
import os
import sys
import platform
import argparse

if __name__ == "__main__":

    parser = argparse.ArgumentParser(description="Test that DCD can be seeked to the end")
    parser.add_argument("DCD", type=str, help="DCD filename")
    args = parser.parse_args()

    DCD = args.DCD

    u = mda.Universe(DCD)

    print(f"INFO: MDAnalysis version {mda.__version__}")
    print(f"INFO: platform {platform.platform()}")
    print(f"INFO: Python {platform.python_version()}")
    print(f"INFO: Testing DCD trajectory {DCD}")
    print(f"INFO:    size: {os.stat(DCD).st_size} B")
    print(f"INFO:    length: {u.trajectory.n_frames} frames")
    print(f"INFO:    n_atoms: {u.atoms.n_atoms}")

    print("TEST 1: Iterate over all frames... ", end="")
    frames = []
    try:
        for ts in u.trajectory:
            frames.append(ts.frame)
    except Exception as err:
        print("FAILED")
        print("FAILURE DETAIL: last frame was {frames[-1]} / {u.trajectory.n_frames - 1}")
        print(err)
        sys.exit(1)
    else:
        print("PASSED")

    print("TEST 2: seek to second but last frame... ", end="")
    try:
        ts = u.trajectory[-2]
    except Exception as err:
        print("FAILED")
        print("FAILURE DETAIL: failed to seek u.trajectory[-2]")
        print(err)
        sys.exit(2)
    else:
        print("PASSED")

    sys.exit(0)
```

Good output looks like
```
$ python check_dcd_access.py 1ake_007-nowater-core-dt240psx17.dcd
...
INFO: MDAnalysis version 2.10.0-dev0
INFO: platform macOS-13.7.2-x86_64-i386-64bit
INFO: Python 3.12.11
INFO: Testing DCD trajectory 1ake_007-nowater-core-dt240psx17.dcd
INFO:    size: 2859403144 B
INFO:    length: 71179 frames
INFO:    n_atoms: 3341
TEST 1: Iterate over all frames... PASSED
TEST 2: seek to second but last frame... PASSED
```

Assuming we can reproduce a failure, the following script `build_and_test.sh` should be useable with `git bisect`:

Put the script into the root dir of the MDAnalysis git repo and put the test file and `check_dcd_access.py` into another dir (TESTDIR). 

~~Work in a **python=3.10** environment (to work around #5061 and to be compatible across versions).~~ (EDIT: any supported python env should work again)

Then the following should reveal the commit that introduced the regression (assuming that 2.7.0 is working, as the original report https://github.com/MDAnalysis/mdanalysis/issues/4879#issue-2766742342 implies)
```bash
cd mdanalysis
git bisect start HEAD package-2.7.0 --
git bisect run build_and_test.sh PATH/TO/TESTDIR
git bisect reset
```


## `build_and_test.sh`

```bash
#!/bin/bash

# for `git bisect run`: run from the root dir of the MDAnalysis git repo:
# 
#    cd mdanalysis
#    git bisect start HEAD package-2.7.0 --
#    git bisect run build_and_test.sh PATH/TO/TESTDIR`
#    git bisect reset

# Assumes that check_dcd_access.py and trajectory are located in TEST_DIR.

# rc    event
# ----- ---------------
#    0   success
#    1   test 1 failed
#    2   test 2 failed
#  125   build error

TEST_DIR="${1}"

die () {
    local msg="$1" err=${2:-125}
    echo "ERROR: ${msg}" 1>&2
    exit $err
}

test -n "${TEST_DIR}" || die "usage: $0 TESTDIR"
test -d "${TEST_DIR}" || die "TESTDIR ${TEST_DIR} not found"

# run a top level of mda tree

# build current checked out version
pip uninstall --yes mdanalysis
pip uninstall --yes mdanalysistests

pip install package/     || die "pip install failed"
pip install testsuite/   || die "pip install failed"


cd ${TEST_DIR} || die "cd ${TEST_DIR} failed"

# run test and ensure that its return value is our exit code
# (assumes that check_dcd_access.py and trajectory are located in TEST_DIR)
python check_dcd_access.py 1ake_007-nowater-core-dt240psx17.dcd
exit $?
```
@qlearn-code or @fhh2626 would you be able to use your windows machines to
1. run the scripts from https://github.com/MDAnalysis/mdanalysis/issues/4879#issuecomment-2968227743 and report your results (confirm failure on windows)
2. if possible, attempt the `git bisect` in https://github.com/MDAnalysis/mdanalysis/issues/4879#issuecomment-2968324593 to find the commit that introduced the regression?
Note: We should enable the `LARGEDCD` test in CI

https://github.com/MDAnalysis/mdanalysis/blob/0dc5a1bb5b4fab5ad53a5ace82075ecf3b4915ce/testsuite/MDAnalysisTests/coordinates/test_dcd.py#L544-L547

(which was added as part of PR #4048 that fixed a similar issue; note that the previous issue affected all OS, this one only seems to affect Windows.)
I get the same error when reading a DCD file. The five simulation trajectories I repeated in the same system all stopped reading at the same frame. When I'm free in a couple of days, I will run the file you provided on the windows system.
It would be great if someone here with access to a development environment on windows could dig into this issue. It looks as if the core developers are busy (and few use windows as far as I know) so anyone with an interest in getting this fixed is **more than welcome to contribute** — MDAnalysis is **open source**, maintained largely by volunteers, so this is an instance where we are relying on the broader user/developer community to help. Thanks.



Patch:
diff --git a/package/CHANGELOG b/package/CHANGELOG
index ff3c1bc349..d6a76a1265 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -16,12 +16,14 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
          yuxuanzhuang, yuyuan871111, tanishy7777, tulga-rdn, Gareth-elliott,
-         hmacdope
+         hmacdope, tylerjereddy
 
 
  * 2.10.0
 
 Fixes
+ * Fixed an integer overflow in large DCD file seeks on Windows
+   (Issue #4879, PR #5086)
  * Fix compile failure due to numpy issues in transformations.c (Issue #5061, PR #5068)
  * Fix incorrect `self.atom` assignment in SingleFrameReaderBase (Issue #5052, PR #5055)
  * Fixes bug in `analysis/hydrogenbonds.py`: `_donors` and `_hydrogens`
diff --git a/package/MDAnalysis/lib/formats/libdcd.pyx b/package/MDAnalysis/lib/formats/libdcd.pyx
index 08ba4f120f..3400fd4ae8 100644
--- a/package/MDAnalysis/lib/formats/libdcd.pyx
+++ b/package/MDAnalysis/lib/formats/libdcd.pyx
@@ -387,13 +387,13 @@ cdef class DCDFile:
             raise EOFError('Trying to seek over max number of frames')
         self.reached_eof = False
 
-        cdef fio_size_t offset
+        cdef long long offset
         if frame == 0:
             offset = self._header_size
         else:
             offset = self._header_size
             offset += self._firstframesize
-            offset += self._framesize * (frame - 1)
+            offset += self._framesize * (<long long>frame - 1)
 
         cdef int ok = fio_fseek(self.fp, offset, _whence_vals['FIO_SEEK_SET'])
         if ok != 0:


Test patch:
diff --git a/testsuite/MDAnalysisTests/formats/test_libdcd.py b/testsuite/MDAnalysisTests/formats/test_libdcd.py
index 8f2dd31094..63a9d83622 100644
--- a/testsuite/MDAnalysisTests/formats/test_libdcd.py
+++ b/testsuite/MDAnalysisTests/formats/test_libdcd.py
@@ -34,6 +34,7 @@
     assert_almost_equal,
 )
 
+import MDAnalysis as mda
 from MDAnalysis.lib.formats.libdcd import (
     DCDFile,
     DCD_IS_CHARMM,
@@ -41,6 +42,7 @@
 )
 
 from MDAnalysisTests.datafiles import (
+    PSF,
     DCD,
     DCD_NAMD_TRICLINIC,
     legacy_DCD_ADK_coords,
@@ -671,3 +673,19 @@ def test_write_random_unitcell(tmpdir):
     with DCDFile(testname) as test:
         for index, frame in enumerate(test):
             assert_array_almost_equal(frame.unitcell, random_unitcells[index])
+
+
+@pytest.mark.skipif(
+    not os.environ.get("LARGEDCD", False), reason="Skipping large file test"
+)
+def test_gh_4879(tmpdir):
+    # NOTE: we really only need a trajectory with a frame
+    # count that is large enough to overflow a 32-bit signed
+    # integer in the DCD frame seeking arithmetic to reproduce
+    # the original issue
+    u = mda.Universe(PSF, 800 * [DCD])
+    with tmpdir.as_cwd():
+        f = "large.dcd"
+        u.atoms.write(f, frames="all")
+        u = mda.Universe(f)
+        u.trajectory[-2]