VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Jun 29 2016 - 22:23:03 CDT

​Thank you John for your quick reply.

I am using CentOS 6.6 (​actually it is a Rocks OS). Well yes I could get
the directly downloaded Text-only binary work (which is the binary I am
using in most of the time), it seems compatible in that case. However the
directly downloaded "LINUX_64 OpenGL, CUDA, TachyonL-OptiX" binary give two
problems:
1) $ ldd LINUXAMD64/vmd_LINUXAMD64
        ...
liboptixu.so.1 => not found
liboptix.so.1 => not found
        ...
   (which I have no idea where to find them.)
2) $ cd src/
   $ make
   make: *** No rule to make target `y.tab.h', needed by `vmd_LINUXAMD64'.
Stop.
   (which did not happen for Text-only binary, although they seems to have
the same dependency.)

Thanks,
Kevin

On Wed, Jun 29, 2016 at 10:29 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Kevin,
> What version of CentOS are you running? The OptiX-enabled binaries
> of VMD 1.9.2 should work fine with CentOS 5.x and later. You should not
> need to recompile from source, and in general I would not recommend it
> unless
> you are an expert in software development due to the need for all of the
> toolkit and GPU library versions associated with CUDA and OptiX and so on
> to
> match up precisely. What do you get when you run these commands
> on your system?:
> uname -a
> cat /etc/issue
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 29, 2016 at 10:14:01PM +0800, Kevin C Chan wrote:
> > Thanks so much for the reply. That's what I am asking for.
> >
> > However when I want to try out Fernando's script, I found that I could
> not
> > get a VMD binary with TachyonOptiX to work. I thought it was built-in,
> but
> > the RHEL binary seems not compatible with my CentOS, saying "make: *** No
> > rule to make target `y.tab.h', needed by `vmd_LINUXAMD64'. Stop." when I
> > typed make.
> >
> > Also it is surprisingly difficult to find a compilation guide for VMD.
> >
> > I am wondering whether I could obtain a binary TachyonOptiXInternal and
> > execute it using a Text-only VMD on the cluster/nodes.
> >
> > Thanks,
> > Kevin
> >
> > On Wed, Jun 29, 2016 at 12:16 PM, Fernando Vallejos-Burgos <
> > nandobike_at_gmail.com> wrote:
> >
> > > Hi Kevin,
> > >
> > > I use a very simple TCL script for rendering animations remotely.
> > > It goes something like this, for example, for 1000 frames rendering in
> > > TachyonOptiX after you set the viewpoint:
> > >
> > > display shadows on
> > > display resize 1280 720
> > > display ambientocclusion on
> > > display aoambient 0.80
> > > display aodirect 0.50
> > > for {set i 0} {$i < 1000} {incr i 1} {
> > > display update
> > > animate goto $i
> > > set filename ./snap_[format "%04d" [expr $i]].tga
> > > render aasamples TachyonLOptiXInternal 256
> > > render TachyonLOptiXInternal $filename
> > > }
> > >
> > > then I just source the TCL file and call this procedure.
> > > For me, it runs quite fast in GPU.
> > >
> > > Hope this can help!
> > >
> > > Fernando
> > >
> > >
> > > -------
> > > Dr. Fernando Vallejos-Burgos
> > > Researcher at Center for Energy and Environmental Science
> > > Shinshu University, Wakasato, Nagano 380-8553, Japan
> > > Personal web: http://www.vallejos.cl
> > > Labo web: http://www.shinshu-u.ac.jp/faculty/engineering/kaneko-group/
> > >
> > >
> > >
> > > On Jun 29, 2016, at 12:14 PM, Kevin C Chan <
> cchan2242-c_at_my.cityu.edu.hk>
> > > wrote:
> > >
> > > ???Thanks for your reply. ???I am wondering what pseudo code would it
> be like.
> > > Simply
> > >
> > > source visualization state
> > > tachyon_binary ...
> > >
> > > ? As I used to do it through GUI, I have to
> > > 1) tune the visual angle
> > > 2) turn on AO
> > > 3) render > tachyon/tachyon_internal > type BMP as extension
> > >
> > > How could all these be done using a script?
> > >
> > > Thanks,
> > > Kevin
> > >
> > > On Wed, Jun 29, 2016 at 12:34 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > >
> > > Hi,
> > > Hi, sorry for the slow reply, I just returned from international
> travel
> > >
> > >
> > >
>
>
> --
> 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/
>