HPC Intermediate

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We assumes you have some experience with:

  • The Linux command-line
  • Loading software using the module command
  • Using sbatch to submit jobs

If you are in the workshop classroom, sign-in as a student to UCONNHPC on socrative.com

Unix Shell automation

Commands below assume you are using the bash shell. Equivalent commands are given after the bash commands in case you are using the csh shell instead.

Check for the shell you are using with:

echo $0


Save yourself typing; create aliases:

# the command we want to alias
# one way
alias htop='htop -u $USER' # for csh, no =
type htop                  # for csh, use `where` instead
# another way
alias htop="htop -u $USER" # for csh, no =
type htop                  # for csh, use `where` instead
# ignore alias
command htop               # for csh, use \htop
# remove alias
unalias htop
type htop                  # for csh, use `where` instead

Our sjobs command is an alias!

type sjobs                 # for csh, use `where` instead

Challenge 1: Create an alias to `cd` to the scratch directory by typing `scratch`


cp /scratch/lesson-intermediate ~
cd ~/lesson-intermediate
# for bash
cat watch-sbatch.sh
source watch-sbatch.sh
# for csh
cat stail
set path = (`pwd` $path)

Job troubleshooting

cd slurm-troubleshooting
# Let's see what nodes are free
sinfo -s
# Try out stail
stail bash-fail.slurm

Challenge 2: Why did the job fail?

# What does success look like?
stail bash-success.slurm

There are two useful debugging features enabled in "bash-debug.slurm"

# Getting debug information
stail bash-debug.slurm
# Why is this stuck in pending?
stail bash-pending.slurm
# Use Control + C to cancel out.
# To find why, see the output of:
squeue -u $USER
stimes -u $USER
# Related and also useful
sprio -u $USER
# Cancel our job
scancel -u $USER
make clean
srun --partition=phi hostname


Ctrl + R Reverse history search of shell history.

Ctrl + G to exit search mode.

mkdir my-descriptive-long-name

Retype last word:

  • Bash: Alt + . (Use ESC on OSX for Alt)
  • csh: Alt + Shift + _

Multiple windows using tmux and screen

The RedHat version of tmux is too old, so we have a module:

module load tmux

Shortcuts (all shortcuts are prefixed by Ctrl + B):

  • " Split window horizontally
  • % Split window vertically
  • Arrow keys Move between windows (Wait a second or two before recalling commands)
  • Space Cycle pane layouts
  • Ctrl + C Create new window
  • N Go to next window
  • , Rename window
  • D to disconnect
# Reconnect to detached session
tmux attach -d

Environmental variables

Challenge 3: How do you make your program use an environmental variable?

  1. Create the variable in a terminal and restart the program # Learner does not understand how the environment is set
  2. Export the variable and restart the program # Learner does not understand that environment needs to be selectively imported
  3. Read the environmental variable from the program # Correct answer
  4. Use the variable name "ENVIRONMENT" # Does not understand the concept of environment

Set the environmental variable TERM to xterm to enable color:


Job optimization

$ sacct
$ sacct -l
# Lots of info!  Let's break that down.
$ man sacct
$ type sjobs
$ cat /scratch/lesson-intermediate/job-aliases.sh # or .csh
$ source /scratch/lesson-intermediate/job-aliases.sh # or .csh
# CPU usage
$ job-cpu
$ job-cpu 761842
       JobID      NCPUS    Elapsed     MinCPU      CPUTime 
------------ ---------- ---------- ---------- ------------ 
761842               96   05:50:33             23-08:52:48 
761842.batch         24   05:50:33   00:00:00   5-20:13:12 
761842.1             96   05:50:31   05:49:57  23-08:49:36 
# Memory usage
$ job-mem 761842
       JobID  MaxVMSize     MaxRSS     AveRSS 
------------ ---------- ---------- ---------- 
761842.batch    652640K      7548K      7548K 
761842.1        502984K     94908K     40215K
# Disk usage
$ job-disk 761842
       JobID  MaxDiskRead MaxDiskWrite MaxPages 
------------ ------------ ------------ -------- 
761842.batch           2M           1M        0 
761842.1             119M        4850M        0
# Exercise
# See disk usage for 760356
# See CPU usage for 576568

In summary, SLURM is good for disk usage, but not as useful for memory and CPU. htop is better for run-time performance profiling (RES in htop = RSS in SLURM).

Install software

cd ~/lesson-intermediate/install-apps
bash python-example
# Loading the module in the subshell did not affect our current environment
module list
cutadapt # error
~/.local/bin/cutadapt -h
PATH="~/.local/bin:$PATH" cutadapt     # bash only
env PATH="~/.local/bin:$PATH" cutadapt # csh only
cutadapt # error again: change to PATH was temporary
export PATH="~/.local/bin:$PATH" # bash only
setenv PATH "~/.local/bin:$PATH" # csh only
cutadapt # now works

Compile and install software

Compilers / module name

  • GCC - gcc
  • Intel - intelics
  • PGI (Portland Group) - pgi


  • MPICH (MPI "Chamelion" started by Argonne National Labs) - mpi/mpich
  • MVAPICH (InfiniBand optimized version by Ohio State University) - mpi/mvapich and mpi/mvapich2
  • OpenMPI - mpi/openmpi
  • Intel MPI - intelics

Shell script

Let's compile some software

To compile on a node, try using the debug partition and limiting the architecture.


LAMMPS error - remove MPI



Challenge 1

# bash
alias scratch='cd /scratch/$USER'
# csh (no equal sign)
alias scratch 'cd /scratch/$USER'

Challenge 2

There is a typo in the submission file. Because of the space character between bin and /bash, SLURM is looking for an executable file called bin in the root directory and passing it the first argument /bash

$ diff -u bash-fail.slurm bash-success.slurm 
--- bash-fail.slurm	2017-03-19 22:13:31.473867000 -0400
+++ bash-success.slurm	2017-03-19 22:15:09.780362131 -0400
@@ -1,4 +1,4 @@
-#!/bin /bash
 # Submit a 1 minute job.
 #SBATCH --partition=phi
 #SBATCH --time=1:00

Challenge 3

Challenge 3: Answer = 3

  1. Create the variable in a terminal and restart the program - The environment is not always set by the terminal. It may be set by other programs
  2. Export the variable and restart the program - The environmental variable needs to be selectively imported
  3. Read the environmental variable from the program - Correct answer
  4. Use the variable name "ENVIRONMENT" - An environment is comprised of several variables, not a single variable named "ENVIRONMENT"