VMD-L Mailing List

From: Tom Bartl (tom.helmut.bartl_at_gmail.com)
Date: Mon Mar 18 2019 - 09:50:54 CDT

Hi John,
thanks for the reply, it was a .dcd file generated by namd.

Thanks, Tom

> On 18 Mar 2019, at 01:14, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> http://www.ks.uiuc.edu/Research/vmd/