VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 17 2019 - 19:14:31 CDT

Hi,
  This is likely caused by some other problem, as the system size
you're working with (176,000 atoms) is "small" and only works out to
roughly 2.2MB per trajectory frame. Assuming normal behavior, I would
expect a MacOS system to be able to load more like 800 frames, certainly
far more than just 50 frames.

You didn't say anything about what file format the trajectory was
stored in, and that may play an important role here. Please share
more details if you still want assistance.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 16, 2019 at 08:10:48PM +0100, Tom Bartl wrote:
> Hi,
> Im having issues with crashing VMD on Mac on multiple ocasions, most often when i try to open quite large tajectory files (.dcd file, 176000 atoms, 50 frames).
> In terminal the folowing lines are writen after the last succesful line
>
> VMD(30559,0x600a40) malloc: can't allocate region
> *** mach_vm_map(size=2265628672) failed (error code=3)
> VMD(30559,0x600a40) malloc: *** set a breakpoint in malloc_error_break to debug
> /Applications/VMD 1.9.4.app/Contents/MacOS/startup.command: line 7: 30559 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> logout
> Saving session...
> ..copying shared history...
> ..saving history...truncating history files...
> ???completed.
>
> Mac than opens Problem report window stating the process that crashed is "vmd_MACOSXX86 [30559]???
>
> >From similar problems here reported here earlier (for example https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/26325.html) i understand it has something to do with memory allocation on 32 bit Macs. Is there any solution? 64bit version of VMD maybe?
>
> Thanks a lot, Tom
>
> running a macOS Mojave 10.14.3 on MacBook Air early 2015, 1,6 GHz Intel Core i5, 4 GB 1600 MHz DDR3, Intel HD Graphics 6000 1536 MB 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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