VMD-L Mailing List

From: Vermaas, Joshua V (vermaas2_at_illinois.edu)
Date: Tue Jun 14 2016 - 18:35:32 CDT

Hi Peter,

Yup. 32 bits means only 4GB is addressable, and generally means that once you load in ~2GB of data, VMD segfaults. Recompilation on a mac is not straightforward, and I've never done it personally, but Jay Bardhan has his own experience documented on his own website: https://boundaries-in-biophysics.org/2013/01/17/installing-vmd-with-python-options-on-a-mac/

-Josh Vermaas

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Peter Schmidtke [peter.schmidtke_at_discngine.com]
Sent: Tuesday, June 14, 2016 3:00 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: segmentation fault on OSX El capitan

Dear VMD users/developers,

I recently installed VMD 1.9.2 on my OSX El Capitan. It works ok for a few tasks. However, if I load a full trajectory (2Gb only though) I get the following segmentation fault :
vmd(827,0xa3137000) malloc: *** mach_vm_map(size=339968) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Segmentation fault: 11

I have 48Gb of RAM, but from what I got there is only a 32bit version of VMD for OSX. Might this be the reason when I load lots of data? Is there any 64 bit version available, or do I have to compile this one by hand?

Thanks in advance.

Peter Schmidtke