VMD-L Mailing List

From: Tom Bartl (tom.helmut.bartl_at_gmail.com)
Date: Thu Mar 28 2019 - 12:11:05 CDT

Hi, sorry for the unnecesary message, but any news?

Thanks a lot! Tom

> On 18 Mar 2019, at 15:50, Tom Bartl <tom.helmut.bartl_at_gmail.com> wrote:
>
> 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/
>