VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 18 2020 - 10:10:27 CST

Hi,
  Yes, I'm keenly aware, but I only do updates when I'm in a position to
cope with the ramifications of new files being added to the distribution.

You don't know it, but whenever new files get added to the VMD distribution,
I have to completely remake the Windows installers, and this is currently a
time consuming (and error prone) manual operation at present.

I have to subsequently hand-patch the installer code in several places
to operate correctly for 64-bit Windows.
As such, I haven't been adding any new plugin files for several weeks.

I'll see about updating the distribution with the new cv_dashboard files
next week when I can afford the time to again hand-patch the installer
scripts after they're re-generated.

Best,
  John

On Fri, Dec 18, 2020 at 10:51:52AM -0500, Giacomo Fiorin wrote:
> Just to confirm, running the updater script from the Colvars repository
> should generate the correct file structure in the plugin repo:
> vmdcvs checkout vmd
> vmdcvs checkout pluginsÂ
> git clone git_at_github.com:Colvars/colvars
> cd colvars/
> ./update-colvars-code.sh ../vmd; # Update VMD tree
> ./update-colvars-code.sh ../plugins; # Update plugins tree
> The cv_dashboard Makefile will need rsync, though, to work.
> On Fri, Dec 18, 2020 at 10:04 AM Jérôme Hénin <[1]jerome.henin_at_ibpc.fr>
> wrote:
>
> 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 are outdated.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:
> [2]https://github.com/Colvars/colvars/commit/4382319c9a676596ec57c07aa32f7946b559c069
>
> Best,
> Jerome
>
> ----- On 18 Déc 20, at 3:11, Jason Smith [3]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 <[4]johns_at_ks.uiuc.edu>
> > Sent: Thursday, 17 December 2020 7:43:05 AM
> > To: Jason Smith
> > Cc: [5]vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: 1.9.4a50 - unable to open DCDs win64
> >
> > Jason,
> >Â 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,
> >Â John Stone
> >
> > On Thu, Dec 17, 2020 at 01:35:18AM +0000, Jason Smith wrote:
> >>Â Â Hi,
> >>
> >>Â Â just installed this today (vmd194a50win64-SetupV3) and have been
> unable to
> >>Â Â open large trajectories :(. BTW I am very very excited to be
> able to
> >>Â Â address larger amounts of memory on a 64-bit version. Thank You!
> >>
> >>Â Â Through some trial and error it seems like the problem lies in
> the file
> >>Â Â size, not whether the file fits in memory. For e.g.
> >>
> >>Â Â 977 MB file in a50 opens, a 2.9 GB does not (28 GB free memory,
> 32
> >>Â Â installed). For 1.9.3 in the past I always found it would crash
> when
> >>Â Â trying to use more than around 1.1 - 1.3 GB of memory.
> >>
> >>Â Â What's more is that I can't use frame striding to get around it.
> In 1.9.3
> >>Â Â and 4a48 I can open up my 100 GB files using striding, but I
> can't open
> >>Â Â the 2.9 GB in a50 using striding.
> >>
> >>Â Â I also repeatedly opened a 750 MB DCD in a50 until task manager
> indicated
> >>Â Â 4.5 GB usage by VMD, so not a 32-bit memory limit. I also tried
> to open
> >>Â Â the files from HDD vs NVME in case it was a hardware issue.
> >>
> >>Â Â The error given is:
> >>
> >>Â Â dcdplugin) Could not access file
> 'E:/temp/6yb7_NPT_Production-2.dcd'.
> >>Â Â ERROR) Could not read file E:/temp/6yb7_NPT_Production-2.dcd
> >>
> >>Â Â Cheers,
> >>
> >>Â Â -
> >>Â Â Jason Smith
> >>Â Â Post-Doctoral Fellow
> >>Â Â Robert N. Young Lab, Simon Fraser University
> >>Â Â 8888 University Drive, Burnaby, BC, V5A-1S6
> >>Â Â 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
> > [6]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> > [7]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:jerome.henin_at_ibpc.fr
> 2. https://github.com/Colvars/colvars/commit/4382319c9a676596ec57c07aa32f7946b559c069
> 3. mailto:jason_smith_18_at_sfu.ca
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd-l_at_ks.uiuc.edu
> 6. http://www.ks.uiuc.edu/~johns/
> 7. 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/