Out of memory converting Gromacs list of numpy coords to 2D numpy array

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10.gro

Summary of feedback from opening
C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10.gro  
---  
note | Singleton residues assigned chain ID B  
  
Chain information for Protein in water #1  
---  
Chain | Description  
A | No description available  
  

> select solvant

Expected an objects specifier or a keyword  

> select water

Expected an objects specifier or a keyword  

> select solvent

407538 atoms, 271684 bonds, 135854 residues, 1 model selected  

> delete sel

> show cartoons

> style sphere

Changed 7949 atom styles  

> hide cartoons

> hide atoms

> show atoms

> sphere hide

Unknown command: sphere hide  

> style stick

Changed 7949 atom styles  

> show cartoons

> select side chain

Expected an objects specifier or a keyword  

> select sidechain

5907 atoms, 5483 bonds, 498 residues, 1 model selected  

> delete sel

> open C:/Users/Jzhan/Desktop/Apple/JLab/PcUGT1/md_0_10_center.xtc

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 768, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2154, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\\__init__.py", line 118, in open  
num_coords = read_coords(session, data, structure_model, md_type,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 9.30 GiB for an
array with shape (1001, 415487, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 9.30 GiB for an
array with shape (1001, 415487, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\md_crds\read_coords.py", line 40, in read_coords  
coords = array(coords_list, dtype=float64)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 24.20.100.6293
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Book
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 8,503,255,040
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6300U CPU @ 2.40GHz
OSLanguage: zh-CN

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[Eric Pettersen]

This conversion uses 2x the memory it really needs. gromacs.cpp should directly create the 2D array.

[Eric Pettersen]

The xdrfile library does not offer a way to determine the number of frames in the file (and the frames are variable length, so you can't "cheat"), so can't really avoid doubling the memory use. Nonetheless, recoding so that the final numpy coordinate array is created in the C++ layer rather than the Python layer seems to have significantly reduced peak memory use at no cost in speed.