VMD-L Mailing List

From: Eiros Zamora, Juan (j.eiros-zamora14_at_imperial.ac.uk)
Date: Fri Nov 06 2015 - 09:32:57 CST

Dear John,

Thanks for the reply. Is there a way to specify the stride of frames when loading the MD trajectory through the command line? Been looking around on how to change this without success.

Best,

Juan

> On 2 Nov 2015, at 16:35, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> The current VMD builds for MacOS X are 32-bit (long story with
> cross-platform GUI toolkits not working well enough with the new Cocoa APIs).
> As such, the data size that you can load and work with is limited by 32-bit
> addressing even though you're running on a 64-bit machine with large physical
> memory. You will need to limit the size of the data you load to fit within
> the addressing limit, under 4GB. You can do this by having VMD load a subset
> of trajectory frames at a time, either by changing the first/last frames
> loaded, or by changing the stride it uses when loading the frames.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Nov 02, 2015 at 09:35:36AM +0000, Eiros Zamora, Juan wrote:
>> Dear VMD users,
>>
>> I recently installed VMD 1.9.2
>> ??? MacOS X OpenGL (32-bit Intel x86) (Apple MacOS-X (10.4.7 or later) with hardware OpenGL (native bundle))
>> on a new iMac with the following specs:
>>
>> OS X El Capitan
>> Version 10.11.1
>> Processor 4 GHz Intel Core i7
>> Memory 8 GB 1867 MHz DDR3
>> Graphics AMD Radeon R9 M395 2048 MB
>>
>> I tried loading a netcdf trajectory that I obtained with AMBER split in chunks, in total its around 6GB of data.
>>
>> I got the following error
>>
>>> VMD(63006,0xa344c000) malloc: *** mach_vm_map(size=8388608) failed (error code=3)
>>> *** error: can't allocate region
>>> *** set a breakpoint in malloc_error_break to debug
>>> putget.c:3593: failed assertion `value != NULL'
>>> Abort trap: 6
>>
>> I tried to attach a more complete error message on a 54 KB text file, but the message didn???t reach the mailing list, so I can email it off-list if need be.
>>
>> I googled the error and saw some similar problems on this mailing list, but they were from 2007 to 2011.
>> I understand that this is related to the 32-bit version of VMD for Mac, is there any solution to this now (as in, can I get a 64-bit version)? Also, would installing the CUDA version make any difference? I presume not, but just to be sure that I am installing the most appropriate version of VMD for this machine???
>>
>> Thanks for any suggestions,
>>
>> Juan Eiros
>
> --
> 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/