Platform for the Accelerated Realization, Analysis, & Discovery of Interface Materials

An NSF Materials Innovation Platform

MATERIALS BY DESIGN TOOLBOX

Basic Linux Commands
  • mkdir – make directories

Usage: mkdir [OPTION] DIRECTORY…
eg. mkdir paradim

  • cd – changes directories

Usage: cd [DIRECTORY]
eg. cd paradim

  • ls – list directory contents

Usage: ls [OPTION]… [FILE]…
eg. ls, ls ­l, ls paradim

  • pwd –  print name of current working directory

Usage: pwd

  • vim – Vi Improved, a programmer’s text editor

Usage: vim [OPTION] [file]…
eg. vim myscript.txt

  • cp – copy files and directories

Usage: cp [OPTION]… SOURCE DEST
eg. cp myscript.txt myscript_duplicate.txt

  • mv –  rename/move files

Usage: mv [OPTION]… SOURCE DESTINATION
eg. mv myscript.txt directory
eg. mv myoldscript.txt mynewscript.txt

  • rm ­ remove files or directories

Usage: rm [OPTION]… FILE…
eg. rm myoldscript.txt , rm ­rf directory

  • find – search for files in a directory hierarchy

Usage: find [OPTION] [path] [pattern]
eg. find myscript.txt, find ­name myscript.txt

  • history – prints recently used commands

Usage: history

  • ps – report a snapshot of the current processes

Usage: ps [OPTION]
eg. ps,  ps ­el

  • kill – to kill a process

Usage: kill [OPTION] pid
eg. kill ­9 2275

Sample job submission scripts
Maryland Advanced Research Computing Center (MARCC)
#!/bin/bash -l
#SBATCH --job-name=job-1
#SBATCH --time=00:30:00
#SBATCH --partition=parallel
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=12
#SBATCH --mem-per-cpu=2000MB
mpirun -np 12 pw.x -npool 4 < silicon-1.in > silicon-1.out
The Extreme Science and Engineering Discovery Environment (XSEDE)
#!/bin/bash 
#SBATCH -J myMPI                             # job name 
#SBATCH -o myMPI.o%j                    # output and error file name (%j expands to jobID) 
#SBATCH -n 32                                    # total number of mpi tasks requested 
#SBATCH -p development                # queue (partition) -- normal, development, etc. 
#SBATCH -t 01:30:00                          # run time (hh:mm:ss) - 1.5 hours 
#SBATCH --mail-user=username@tacc.utexas.edu 
#SBATCH --mail-type=begin             # email me when the job starts 
#SBATCH --mail-type=end                 # email me when the job finishes 
ibrun ./a.out                                         # run the MPI executable named a.out
NIKOLA server at Clark Atlanta University
 #Please contact PARADIM support team
PARADIM server at Clark Atlanta University
 #Please contact PARADIM support team