VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Dec 18 2020 - 09:51:52 CST

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 plugins
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 <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 are outdated.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:
>
> 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/
>
>