From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Jun 29 2016 - 22:26:58 CDT

Sorry John, forgot to mention the output of commands you requested. In case
you need them:
$ uname -a
Linux <domain_name> 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/issue
CentOS release 6.6 (Final)
Kernel \r on an \m

Sorry for lengthening the thread.

Regards,
Kevin

On Thu, Jun 30, 2016 at 11:23 AM, Kevin C Chan <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> 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/
>>
>
>