VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Thu Dec 17 2020 - 21:11:57 CST

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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/