Running bio3d from HPC

[debra ragland]

Hello,

I have some pretty large md data I am trying to work with and running R from my desktop won't suffice. Therefore, I am trying to run and store some simple bio3d commands from my school cluster (lsf). I am wondering if anyone has a sample script for use of bio3d on a cluster? For instance, I have a submission script to use with the bsub command protein_network.sh

#!/bin/bash

#BSUB -J Protein_Network #BSUB -R "rusage[mem=4096]" #BSUB -W 300:0 #BSUB -q long

module load R/3.1.0

cd /path/to/protein_network.R

R CMD BATCH --no-save --quiet --slave protein_network.R prone.out

But I think my trouble is coming in with the actual R script, protein_network. R, can I just combine the commands I need; dcd <- read.dcd("wt.dcd") pdb <- read.pdb("Everything_Frame0.pdb") inds <- atom.select(pdb, resno = c(24:27, 85:90), elety = "CA") trj <- fit.xyz(fixed = pdb$xyz, mobile = dcd,fixed.inds = inds$xyz, mobile.inds = inds$xyz) cij <- dccm(trj) net <- cna(cij)

write.csv(cij, "cijmat.csv") write.csv(net, "netmat.csv")

Or are there elements missing?

[Xinqiu Yao]

Hi,

Running R codes on clusters should be no difference from running other commands, as long as you have R and all necessary packages installed properly. Yes, you can put all commands you need in one file and execute it using Rscript or R CMD BATCH. What's the problem you have here?

[debra ragland]

No problems as of yet, just didn't know if there were more arguments needed at the beginning of the R script. Thank you.