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HPCC_Instructions
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#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