VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 28 2019 - 21:39:03 CDT

Hi Tom,
  I was traveling all last week, and I'm still catching up on a huge
pile of email. I saw you were running a VMD 1.9.4 test version, which
alpha is it? I've made changes to how VMD handles per-timestep memory
allocations that should be beneficial for small-sized structures, but
you might be running an earlier version. If you can tell me which precise
test build you're using, that would be helpful.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 28, 2019 at 06:11:05PM +0100, Tom Bartl wrote:
> 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/
> >
> 

-- 
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/