Job is killed when loading the trajectory netcdf file

[Former user]

Hi, I am using R/4.1 and I encounter a problem that the job is killed when loading the trajectory. My script is :> library(bio3d)

netfile<- "prod_500ns.nc" traj <-read.ncdf(netfile) And it showed that [1] "Produced by program: pmemd" [1] "File conventions AMBER version 1.0" [1] "Frames: 6250" [1] "Atoms: 51430" /apps/R/4.1/bin/launch_r: line 3: 25333 Killed singularity exec -B /apps,/opt/slurm,/var/run/munge:/run/munge "${HPC_SINGULARITY_IMAGE}" "$@"

In the output file, it said the job is killed for no reason.

library(bio3d) netfile<- "prod_500ns.nc" traj <-read.ncdf(netfile) [1] "Reading file prod_500ns.nc" [1] "Produced by program: pmemd" [1] "File conventions AMBER version 1.0" [1] "Frames: 6250" [1] "Atoms: 51430" Killed

Could you help me out? Thanks!!

-Qianchen

[Xinqiu Yao]

It is possibly too much memory usage. Try to reduce your trajectory by, for example skipping a few frames at a certain interval or only taking the backbone/CA atoms.

[Liu Qianchen]

Thanks!