VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 04 2013 - 11:06:58 CDT

Hi,
  In order to run Tachyon with multi-node parallelism via MPI, you will
have to re-compile Tachyon from source code, against your local MPI
installation. Unlike POSIX threads or other parallel programming
interfaces, MPI doesn't provide binary compatibility, so in practice,
one must always recompile MPI applications from source code for every
different cluster or supercomputer MPI installation you run on.
The Tachyon binaries that we ship with VMD are not compiled with MPI
enabled due to these issues, they only use threads by default. It should
be very straightforward to compile an MPI-enabled Tachyon on your machine,
but you'll have to download the source code, edit the Make-config file
as necessary, and compile it using your local MPI on your machine.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 04, 2013 at 10:51:22AM -0500, Anne Dara Bowen wrote:
> Hello,
>
> I have been trying to submit a parallel batch render (via sge on a linux cluster) using tachyon using a command like:
>
> /share/apps/vmd/1.9/lib/tachyon_LINUXAMD64 -trans_vmd +V -fullshade -aasamples 12 -rescale_lights 0.3 -add_skylight 1.0 /fullpath/test.00000.dat -o /fullpath/test.00000.tga
>
> I am specifying the number of nodes/cores in the qsub script but each time only one node is used (output using the verbose +V option...CPU Information: Node 0: 8 CPUs, CPU Speed 1.00, Node Speed 8.00 Name: c206-110.longhorn Total CPUs: 8 Total Speed: 8.000000) regardless of how many nodes I submit it to?and will still specify 8 CPUs even when I only submit the job using 1,2 or 4 cores.
>
> Is there something I am doing incorrectly or that I need to add?
>
> (I have also tried to submit the render with the flavor of mpirun the machine I am using likes: e.g. mpirun /share/apps/vmd/1.9/lib/tachyon_LINUXAMD64 therestoftheoptionsthesame and also playing with the -numthreads option but this seems to have no effect)
>
> Thank you,
> Anne
>
> 

-- 
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/