VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Dec 18 2020 - 08:45:13 CST

Hi John,

I wonder if I missed something with the previous alpha builds. With build V5, the contents of
plugins\noarch\tcl\cv_dashboard1.3\templates

are outdated. The current contents of that directory should be 3 subdirectories, as of this commit:
https://github.com/Colvars/colvars/commit/4382319c9a676596ec57c07aa32f7946b559c069

Best,
Jerome

----- On 18 Déc 20, at 3:11, Jason Smith jason_smith_18_at_sfu.ca 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/