VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Thu Jun 30 2016 - 09:16:51 CDT

Good to know the libraries were shipped with the downloaded file. Yes I
found them under lib/redistrib/lib_LINUXAMD64. After manually added the
path into LD_LIBRARY_PATH, the vmd_LINUXAMD64 recognized it.

Oh, wait, interesting. I have successfully installed it by typing "make
install" instead of "make" in src/. Then even if the vmd_LINUXAMD64 still
show not finding any OptiX lib, it would NOT affect the launch of the
wrapped binary under $install_bin_dir specified in configure.

Problem solved. Thanks all of you for your valuable experience shared.

Benchmark of my rendering of a ~100k atoms VDW representations was ~25s per
snap and ~90s if transparent presents (e.g. GlassBubble). Is it normal?

Kevin

On Thu, Jun 30, 2016 at 8:57 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Hi Kevin,
>
> Those two libraries are going to be the big problem, as they are the optix
> library that you need for the super-mega-awesome GPU ray tracer. I could
> have sworn that the binary download includes them. Have you looked there?
> Maybe in the lib directory?
>
> Josh Vermaas
> Director’s Postdoctoral Fellow
> National Renewable Energy Laboratory
> joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>
>
>
>
> On Jun 29, 2016, at 9:23 PM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk
> <mailto:cchan2242-c_at_my.cityu.edu.hk>> wrote:
>
> ​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<mailto:
> 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<mailto: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<mailto: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<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.vallejos.cl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=asS68yK4w_ytuTVQXO_fIxmAd0602DA8LBoIXQasLx8&s=Ie4131uuh8MC6GEcM3P31yG8cOxaeyLuptC_C5a4Ey8&e=
> >
> > > Labo web: http://www.shinshu-u.ac.jp/faculty/engineering/kaneko-group/
> <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.shinshu-2Du.ac.jp_faculty_engineering_kaneko-2Dgroup_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=asS68yK4w_ytuTVQXO_fIxmAd0602DA8LBoIXQasLx8&s=vw2oQxW0Gmm2EbpmUYcD0J8cjALCvJecYNvNx6pNzOQ&e=
> >
> > >
> > >
> > >
> > > On Jun 29, 2016, at 12:14 PM, Kevin C Chan <
> cchan2242-c_at_my.cityu.edu.hk<mailto: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
> <mailto: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/<
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> Phone: 217-244-3349<tel:217-244-3349>
> http://www.ks.uiuc.edu/Research/vmd/<
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