HPCC_Instructions

#Title: Running Jobs through the HPCC
#Author: A.D. Wright, E.R. Zylstra
#Last Updated: 2/27/2019

##These instructions assume you already have an account through the HPCC and have downloaded the apppropriate software (in this case, I use the recommended MobaxTerm)
  # If you haven't done this yet, see the HPCC wiki for more information: wiki.hpcc.msu.edu
    #Go to How to Access HPCC
      #Sections "Obtain a HPCC account" & "Install SHH Client" & 'Connect to HPC system"

##
#### Logging in to MobaxTerm
##

#open terminal
#type:
  ssh username@hpcc.msu.edu
#type in MSU id password if prompted (might have to do it twice)

# To test that it is working correctly:
 #type:
 xeyes

##
#### Running a job through the HPCC 
##

## Need to log-in to development node (dev-intel14, dev-intel16, or dev-intel18 will work)
#type:
  ssh dev-intel16

## Need to load current versions of R, JAGS, and necessary GNU
  # Only necessary to do do if you plan on running the job directly on the development node, and not through a formal job submission (otherwise this information will be in your qsub file)
#Type:
  module load GNU/4.9
  module load OpenMPI/1.10.0
  module load R/3.3.2
  module load jags/4.2.0

## Need to transfer files over to MobaXterm (can drag from a Windows File Explorer folder)
  #These files should include everything in your working directory you need to run your R script, your script, and an .sb file (which is used to submit a job to the HPCC).
    #For help writing an .sb file, see file 'R-JAGS_job_template.sb'
    #Things to remember in your R script: 1) Don't set a working directory (that will be done in the sb file), & 2) Make sure you have code that saves the output/objects from the script that you want
  #If at any point you need to edit files after they've been transfered, use 'nano (file name)'
  #If at any point you need to view files after they've been transfered, use 'cat (file name)'

## Need to change directory to the folder that contains your files (R script, sb file, JAGS file, and all data files)
#type:
  cd 'folder path'
  
## Need to run sbatch command on sb file
#Type:
  sb example.sb


##
#### For more help
##

# Learn from the experts! 
  # 1) Office Hours: Monday/Thursday 1-2 PM in the BPS Building, Room 1440
  # 2) User Manual/Wiki: wiki.hpcc.msu.edu (see especially the sections labeled: Job Scheduling by SLURM and Job Management by SLURM)
  # 3) More information about running R and JAGS: https://wiki.hpcc.msu.edu/display/ITH/R+-+CentOS+7

## not sure if the following code is still current?
# To get examples for the HPCC and R:
  # Load example files
  module load powertools
  getexample R_example
  getexample intro2hpcc