VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 04 2022 - 15:11:39 CDT

Chris,
  Can you show me your VMD startup messages? It should help clarify
if your binary was properly compiled and how MPI startup proceeded.

Best,
  John

On Mon, May 02, 2022 at 07:49:45PM -0700, Chris Taylor wrote:
> I'm experimenting with the example from the tutorial and have a SLURM sbatch script like this:
>
> $ cat vmd-text.sbatch
> #!/bin/bash
>
> #SBATCH --nodes=3
> #SBATCH --ntasks-per-node=1
> #SBATCH --cpus-per-task=4
>
> module load ospray
> module load mpich
> module load vmd-mpi
>
> srun vmd -dispdev text -e noderank-parallel-render.tcl
>
> It starts my MPI-enabled VMD and runs this script:
>
> $ cat noderank-parallel-render.tcl
> set noderank [parallel noderank]
>
> puts "node $noderank is running ..."
> parallel barrier
>
> mol new 5ire_merged.pdb waitfor all
> puts "node $noderank has loaded data"
> parallel barrier
>
> rotate y by [expr $noderank * 20]
> render TachyonLOSPRayInternal test_node_$noderank.ppm
> puts "node $noderank has rendered a frame"
>
> parallel barrier
> quit
>
> But, in the output I only see node 0 rendering one frame. What am I missing? Thanks 

-- 
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/