VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 11 2017 - 14:43:24 CDT

Hi Stefan,
  Okay, that's useful information. The GeForce 4xx and 5xx GPUs (Fermi generation hardware)
are no longer supported by current versions of CUDA or OptiX, so the only way to make a new
build of VMD that runs on them is to compile against old versions of CUDA. If you expect these
machines to be taken out of service soon, then it may not be worth the trouble to compile a
special VMD build for them, but if you think they'll be used for another year or more, then
it might be useful to have a new VMD build for them. While I have already set the VMD 1.9.4
build scripts to use the current versions of CUDA, etc, you could in principle still compile
it for older toolkit versions. If you're interested in doing this, let me know. If you think
these machines will go away soon, then I wouldn't worry about it much. If you wanted to
recompile just the VMD webpdb plugin, that would let the most common web-based PDB download
work for you. I can tell you how to do that (or do it for you) and it's much less of a
time/effort investment than recompiling all of VMD and its associated dependencies.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 11, 2017 at 09:01:56PM +0200, Stefan Boresch wrote:
> John,
>
> thank you for the detailed reply (as always) and offer of help.
>
> We have several old student machines
> with GTX 4xx and GTX 5xx cards. vmd-1.9.3 runs, but occasionally
> crashes (e.g. for quick surface -- this was, I believe, discussed on
> this list a while ago).
>
> Now, these machines really are for introductory course work only, used, e.g., to
> visualize structures before/after manipulating them in some manner
> outside vmd (we are a CHARMM/charmm-gui 'shop'). Thus, while I install
> 1.9.3 (or now 1.9.4) on new machines or on my desktop, I saw no
> reason so far to upgrade these ancient course machines.
>
> In any case, don't loose time over this; chances are good that these
> machines will die of 'old age' sooner than later ..
>
> I was really curious whether the 'webpdb part' of 1.9.2 could be 'patched'
> to work again ..
>
> Best regards,
>
> Stefan (Boresch)
>
>
> On Wed, Oct 11, 2017 at 09:46:50AM -0500, John Stone wrote:
> > Hi,
> > The script below is helful, but it only addresses the 'webpdb' part of the VMD updates we had
> > to make for the RCSB web site changes. To correct the behavior of VMD 1.9.4, updates were made
> > to a few places in VMD's webpdbplugin, qwikmd, and autopsf, pdbtool, etc.
> >
> > Stefan, how old are the GPUs you said have trouble with VMD 1.9.4? What generation are they?
> > You can query them by running 'nvidia-smi' and it will report both the hardware and the
> > driver version number. If you can tell me what you've got I could estimate how difficult it
> > would be to either build a VMD 1.9.4 for your hardware, or to get your machines in sync with
> > current drivers so they can run VMD 1.9.4.
> >
> > Best regards,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Oct 11, 2017 at 09:18:41PM +1300, Ashar Malik wrote:
> > > I posted a fix for earlier builds a couple months back. Here
> > > Â ([1]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html)
> > > it is again.
> > > Save the following code in a script file.
> > > -----------------------------------------------------------------------------------------Â
> > > puts -nonewline "Enter PDB code: "Â
> > > flush stdoutÂ
> > > set name [gets stdin]Â
> > > puts "Getting $name"Â
> > > package require httpÂ
> > > set handle [::http::geturl [2]http://files.rcsb.org/view/$name.pdb]Â
> > > set pdb_file [open $name.pdb a]Â
> > > puts $pdb_file [::http::data $handle]Â
> > > mol load pdb $name.pdbÂ
> > > -----------------------------------------------------------------------------------------Â
> > >
> > > * you will have to save it into the working directory of vmdÂ
> > > * start vmdÂ
> > > * in the tkconsole or the shell at the VMD prompt typeÂ
> > > * source name_of_the_script_fileÂ
> > > * it will ask for a PDB code -- only enter the 4 letter IDÂ
> > > * it will do some webpage parsing - download the file to your working
> > > directory and also as the last line of the code read load it into
> > > VMD as well.Â
> > > * At the time I wrote this, I did not test it. Neither is it tested
> > > now so use cautiously. Â
> > >
> > > On Wed, Oct 11, 2017 at 7:40 PM, Stefan Boresch
> > > <[3]stefan_at_mdy.univie.ac.at> wrote:
> > >
> > > Hi everyone,
> > >
> > > I understand that some months ago the PDB changed its website layout,
> > > breaking the automated dowload of pdb structures into vmd. I know that
> > > this is fixed in the 1.9.4 series.
> > >
> > > However, I have several older machines, mostly running 1.9.2, at most
> > > 1.9.3,
> > > which hardware wise (old nvidia gpus etc) either don't play nice with
> > > 1.9.4
> > > or where updating is 'painful'. Is this (out of vmd's control) broken
> > > pdb load functionality in some TCL script, which I could update; in
> > > other
> > > words, is there a (relatively) easy way to restore the functionality in
> > > vmd versions prior to 1.9.4?
> > >
> > > Thanks,
> > >
> > > Stefan (Boresch)
> > >
> > > --
> > > Best,
> > > /A
> > >
> > > References
> > >
> > > Visible links
> > > 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28754.html
> > > 2. http://files.rcsb.org/view/$name.pdb
> > > 3. mailto:stefan_at_mdy.univie.ac.at
> >
> > --
> > 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/ 

-- 
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/