How to sumbit jobs on HiperGator

• preparation
  • FileZilla
  • terminal (Mac, Linux)
  • putty (Windows)
• scripts:
  • URL: https://caleb-huo.github.io/teaching/2018FALL/lectures/week4_hiperGator/hiperGator/example.zip
  • HiperGator: /ufrc/phc6068/share/zhuo/
• account
  • apply https://www.rc.ufl.edu/access/account-request/

How to login HiperGator (Windows)

• putty
  • Host Name: hpg2.rc.ufl.edu
  • Port: 22
  • Protocal: SSH
  • Open
• username and passwd

How to login HiperGator (Mac, Windows)

• terminal
  • ssh user@hpg2.rc.ufl.edu
  • enter your password

Your HiperGator Home directory

• /home/yourUserName
  • same as ~
• /ufrc/phc6068/yourUserName
  • This one will be temporary, will be deleted at the end of this sememster
  • If you already have hiperGator account, you can replace phc6068 with your sponser’s group name

Common linux commands:

• pwd: currect working directory
• ls: list all files in current working directory
• mkdir afolder: create a folder named afolder
• cd afolder: get into afolder
• cd ..: go back one folder
• cd ~: go to your home directory
• top: monitor CPU/memory usages

Common linux commands:

• cd /ufrc/phc6068/share/zhuo/testR ## go the the folder with all test files
• cp saveCars.R /ufrc/phc6068/your directory
• cat saveCars.R: print everying
• more saveCars.R: interactive print
• head saveCars.R: head of the contents
• cat saveCars.slurm

FileZilla

FileZilla

• Host: sftp://sftp.rc.ufl.edu
• username:
• password:
• Port: 22
• connect

You can transfer files between your local computer and hiperGator

Login node and working node

Login node and working node

• You are not allowed to do any computing at the login node
  • If the login node crushes, nobody can use hiperGator
• Three ways to access the working nodes
  • Interactive session
  • Xrpa: remote Rstudio
  • Submit slurm jobs.

Open an interactive session on HiperGator

## open interactive R session
srun --account=phc6068 --qos=phc6068 -c 1 --mem=8gb  --time=04:00:00 --pty bash -i 

module load R ## load R

R

• this is shell script
• need to specify account and qos
• -c specifies number of CPUs
• mem specifies memory you want to claim. The entire class shares 128G.
• –time specifies how long you want to claim for the interactive session.
• -i specifies interactive session.
• module load R: will load R software
• R: open R software

Open an interactive session on HiperGator

## do the following on hiperGator
getwd()
dir()

head(cars)
mycars <- cars
write.csv(mycars, "mycars.csv")
dir()

• Try to transfer the file back to local PC

Open R studio on HiperGator

module load ufrc ## otherwise, hiperGator is not stable
module load gui

## at your home directory, or anywhere you are able to write
launch_gui_session -a phc6068 -m 12 -p 1 --time=04:00:00 -n --module rstudio/1.1.453 -e rstudio
xpra_list_sessions

• -a: account
• -m: memory
• -p: number of CPU
• -n: no wait
• xpra_list_sessions: get an xpra code, copy to your local PC

Open R studio on HiperGator

• On the terminal of your local PC:
  • Direct copy from the xpra code you obtained
  • Make sure you have installed xpra
    • See next slde about how to install xpra
  • Paste the xpra code in the terminal
    • MAC has imbedded terminal
    • Windows need to install MotaXterm. (Next slides)

cd '/drives/c/Program Files/Xpra' ## make sure xpra is executable (here by setting working directory)
./xpra attach ssh:zhuo@i21a-s3.rc.ufl.edu:3049 ## an example, you need your own code

Install xpra

• MAC:
  • xpra: https://help.rc.ufl.edu/doc/Xpra_MacOS_X_Installation (suggest use brew)
  • terminal: already installed
• Windows:
  • xpra: https://help.rc.ufl.edu/doc/Xpra_Windows_Installation
  • MobaXterm: https://mobaxterm.mobatek.net

Submit a job (I)

1. R script (saveCars.R): contains your R code
2. SLURM job script (saveCars.slurm): coordinate your job with the server
3. submit: sbatch the slurm file

Prepare R script (a simple one) (I)

• Save the following code into saveCars.R

WD <- "/ufrc/phc6068/share/zhuo/testR" ## change to your own directory
dir.create(WD, re=T) ## force to create this folder

setwd(WD) ## set to your own directory!
mycars <- mtcars
write.csv(mycars,"mycars.csv")

Prepare SLURM job script (I)

• Save the following code into saveCars.slurm

#!/bin/sh
#SBATCH --job-name=serial_job_test    # Job name
#SBATCH --account=phc6068             # your own sponser or account from this class
#SBATCH --qos=phc6068                 # your own sponser or account from this class
#SBATCH --mail-type=ALL               # Mail events
#SBATCH --mail-user=xx@xx.xx          # Where to send mail  
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=12gb                     # Memory limit
#SBATCH --time=04:00:00               # Time: hrs:min:sec
#SBATCH --output=serial_test_%j.out   # Output and error log 

pwd; hostname; date 

module load R 

echo "Running save cars script on a single CPU core" 

R CMD BATCH saveCars.R ## make sure saveCars.R is at your current working directory
## R --no-save --quiet --slave < saveCars.R ## alternative way

date

submit the job (I)

cd /ufrc/phc6068/share/zhuo/testR
sbatch saveCars.slurm ## submit job

1. Submit the slurm job (saveCars.slurm)
2. The slurm job will submit the R job (saveCars.R)
3. The R job will return the result

Check log file (I)

• Linux log file:

cd /ufrc/phc6068/share/zhuo/testR
cat serial_test_25280301.out ## you may have your own log file name
head serial_test_25280301.out ## you may have your own log file name
more serial_test_25280301.out ## you may have your own log file name

• R console history

cd /ufrc/phc6068/share/zhuo/testR
cat saveCars.Rout

• R/Slurm job output

cd /ufrc/phc6068/share/zhuo/testR
cat mycars.csv

Exercise (I)

1. Copy the saveCars.R and saveCars.slurm into your own working directory
2. Submit the job
3. Try to revise the saveCars.R
   • Just try to output any other results, and save them.
4. Try to revise the saveCars.slurm
   • Try to specify your email, revise time and memory
5. Submit your job again

cp /ufrc/phc6068/share/zhuo/testR/saveCars.R 

Submit a job with external argument (II) (optional)

• R script (saveCarsArgs.R): contains your R code
• SLURM job script (saveCarsArgs.slurm): coordinate your job with the server
• submit: sbatch the slurm file

R script (with external arguments) (II)

• Save the following code into saveCarsArgs.R

args = commandArgs(trailingOnly = TRUE) ## pass in external argument

rowID <- args[1]
aarg <- as.numeric(rowID)

setwd("/ufrc/phc6068/share/zhuo/testR2")
mycars <- mtcars[aarg,]
filename <- paste0("arg",aarg,".csv")
write.csv(mycars,filename)

SLURM job script (II)

• Save the following code into saveCarsArgs.slurm

#!/bin/sh
#SBATCH --job-name=serial_job_test    # Job name
#SBATCH --account=phc6068             # your own sponser or account from this class
#SBATCH --qos=phc6068                 # your own sponser or account from this class
#SBATCH --mail-type=ALL               # Mail events
#SBATCH --mail-user=xx@xx.xx          # Where to send mail  
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=12gb                     # Memory limit
#SBATCH --time=04:00:00               # Time: hrs:min:sec
#SBATCH --output=serial_test_%j.out   # Output and error log 

pwd; hostname; date 

module load R 

echo "Running save cars script on a single CPU core" 

R --no-save --quiet --slave --args 1 < saveCarsArgs.R 

date

submit the job (II)

cd /ufrc/phc6068/share/zhuo/testR2
sbatch saveCarsArgs.slurm ## submit job

1. Submit the slurm job (saveCarsArgs.slurm)
2. The slurm job will submit the R job (saveCarsArgs.R) with extra argument
3. The R job will return the result

Check log file (II)

• Linux log file:

cd /ufrc/phc6068/share/zhuo/testR2
cat serial_test_25280860.out ## you may have your own log file name

• R console history
  • no R console history if you use

  R --no-save --quiet --slave --args 1 < saveCarsArgs.R 

• R/Slurm job output

cd /ufrc/phc6068/share/zhuo/testR2
cat arg1.csv

Submit a job with loops (III) (optional)

• R script (saveCarsArgs.R): save as (II)
• SLURM job script (saveCarsArgsLoops.slurm): coordinate your job with the server
• submit: sbatch the slurm file

SLURM job script (III)

• Save the following code into saveCarsArgsLoops.slurm

#!/bin/sh
#SBATCH --job-name=serial_job_test    # Job name
#SBATCH --account=phc6068             # your own sponser or account from this class
#SBATCH --qos=phc6068                 # your own sponser or account from this class
#SBATCH --mail-type=ALL               # Mail events
#SBATCH --mail-user=xx@xx.xx          # Where to send mail  
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=12gb                     # Memory limit
#SBATCH --time=04:00:00               # Time: hrs:min:sec
#SBATCH --output=serial_test_%j.out   # Output and error log 

pwd; hostname; date 

module load R 

for i in {2..10}
do
echo "Running save cars" $i 
R --no-save --quiet --slave --args $i < saveCarsArgs.R 
done

date

submit the job (III)

cd /ufrc/phc6068/share/zhuo/testR3
sbatch saveCarsArgsLoops.slurm ## submit a loop job