VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 18 2020 - 10:22:58 CST

Jason,
  I'm aware of the the installer directory override issue.

It is tricky to resolve because this has to do with the NSIS installer
originally having been designed for 32-bit apps and not having a native
x64 installation generation scheme. Windows auto-rewrites
64-bit installer target directories by treating the path prefix as a
sort of macro, and I'll have to see if I can get the installer to honor
user-specified installation paths despite the way 64-bit installers
auto-rewrite the path. It will likely require more custom written
installer code on my side.

Best,
  John Stone

On Fri, Dec 18, 2020 at 03:11:57AM +0000, Jason Smith wrote:
> John,
>
> thanks. I have tested DCD opening in V4 and was able to open a 168 GB
> file. I did not test larger.
>
> FYI with the installer for that one though, it seems to ignore the
> installation path without giving any errors. It always installed to the
> default C:\Porgam Files\VMD. I tried a few times to get it to other
> folders or other drives. When I tried to install while using the VMD.exe
> in that folder, it gave every indication of doing it's extraction job, but
> did not actually overwrite any of the files nor give any errors. I don't
> know if V3 did that as I didn't try to change the install path for that.
>
> Cheers,
>
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Thursday, 17 December 2020 7:43:05 AM
> To: Jason Smith
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: 1.9.4a50 - unable to open DCDs win64
>
> Jason,
> I tested this carefully last night and it seems that the issue is
> caused by differences in how different versions of the Microsoft compilers
> handle the state() system call on large files. With the new compilers
> operating in 64-bit mode, stat() returns a failure on large files.
>
> The DCD plugin previously used stat() to ascertain the size of the
> DCD file (for both Unix and Windows platforms). Since this is now
> failing on Windows with the new compilers in 64-bit mode, I've rewritten
> the associated code to use different system calls to determine file
> size, and that seems to have cured the problem.
>
> I expect to build a new V4 installer later this morning after I
> complete some further tests on other trajectory reader/writer plugins.
>
> Best regards,
> John Stone
>
> On Thu, Dec 17, 2020 at 01:35:18AM +0000, Jason Smith wrote:
> > Hi,
> >
> > just installed this today (vmd194a50win64-SetupV3) and have been
> unable to
> > open large trajectories :(. BTW I am very very excited to be able to
> > address larger amounts of memory on a 64-bit version. Thank You!
> >
> > Through some trial and error it seems like the problem lies in the
> file
> > size, not whether the file fits in memory. For e.g.
> >
> > 977 MB file in a50 opens, a 2.9 GB does not (28 GB free memory, 32
> > installed). For 1.9.3 in the past I always found it would crash when
> > trying to use more than around 1.1 - 1.3 GB of memory.
> >
> > What's more is that I can't use frame striding to get around it. In
> 1.9.3
> > and 4a48 I can open up my 100 GB files using striding, but I can't
> open
> > the 2.9 GB in a50 using striding.
> >
> > I also repeatedly opened a 750 MB DCD in a50 until task manager
> indicated
> > 4.5 GB usage by VMD, so not a 32-bit memory limit. I also tried to
> open
> > the files from HDD vs NVME in case it was a hardware issue.
> >
> > The error given is:
> >
> > dcdplugin) Could not access file 'E:/temp/6yb7_NPT_Production-2.dcd'.
> > ERROR) Could not read file E:/temp/6yb7_NPT_Production-2.dcd
> >
> > Cheers,
> >
> > -
> > Jason Smith
> > Post-Doctoral Fellow
> > Robert N. Young Lab, Simon Fraser University
> > 8888 University Drive, Burnaby, BC, V5A-1S6
> > Canada
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [2]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/~johns/
> 2. 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/