Introduction

This is the tenth and final blog post in a series of articles about using the CCEB cluster. An overview of the series is available here. This post includes all the commands and references used throughout the series.

Commands

The commands presented below are sometimes generalizations of what was presented throughout the series.

Command Line

# Change the working directory
cd 
# List folders/files in a directory
ls 
# Report working directory
pwd 
# Move files or directories
mv 
# Copy files or directories
cp
# Summons the manual
man 
# Create a directory
mkdir 
# Removes a directory
rmdir 
# Removes files or a directory
rm 
# Clear the screen/command board in Terminal
clear 
# Uses all files with the pattern indicated in the command applied
*pattern* 
# Creates an empty text file
touch

Log On

ssh -X pennkey@scisub

Screen

# Screen the session while on the scisub host
screen
# Check how many screens you have open 
screen -ls
# Resuming a screen
screen -r

Interactive Session

# Full bsub for an interactive session
bsub -Is -q cceb_interactive -m "silver01" -n 8 -R  "span[hosts=1] rusage[mem=5000]" -M 10000 "bash"

# R code to detect the number of cores requested by bsub
# Recall parallel::detectCores() does not report the proper number
Sys.getenv('LSB_DJOB_NUMPROC')

Normal Session

bsub -q cceb_normal \
-J "jobname[1-n]%5" \
-m "silver02" \
-R "rusage[mem=5000]" \
-M 10000 \
-n 8 \
-o /project/taki3/amv/cluster/normal_session_examples/example_output.txt \
Rscript /project/taki3/amv/cluster/normal_session_examples/normal_example.R

# Get the normal batch job index in R
Sys.getenv("LSB_JOBINDEX")

Quality Control

# Show queues
bqueues -u alval
# List execution host information
bhosts
# Check a queues traffic
bjobs -u all | grep cceb
# List all your jobs (pending and running)
bjobs
# List all running jobs
bjobs -r
# List all pening jobs
bjobs -p
# List all suspended jobs
bjobs -s
# List summary information
bjobs -sum
# Estimate run time
bjobs -WF
# Check history of current jobs running
bhist
# Use the job name to peek
bpeek -J "jobname[38]"
# Use the job ID to peek
bpeek 2147852[38]
# Suspend or pause a job
bstop
# Resume a job
bresume
# Kill a job 
bkill
# Check live machine usage -- must be run on execution host (i.e. after bsub)
top