Introduction: This workshop will introduce users on how to remotely access the clusters and how to set up and personalize their environment for their computational needs. After the workshop, participants will understand:

How to (remotely) access the cluster.
How to set up various environments allowing the use of a variety of programming languages, applications, libraries and utilities.

Participants will require an intro level of experience of using Linux, as well as the ability to use a text editor from the command line.

Course Goals:

Introduce a number of ways to access the Beartooth cluster.
What is LMOD and how to use it to set up an Environment.

01: Accessing the Cluster

Topics:

Access the Beartooth Cluster
Navigate various folders.
Take a look at the basic system/cluster.

Exercises: Log on, and create and run a python script

(SSH onto a login node – if using an existing ARCC account.)
Access via SouthPass and start a shell terminal tab.
Commands: man, id, groups
Commands: arccquota
Create and run a python script.

You have an Existing Account: Log on

There are a number of ways to access the cluster: Logging Into HPC:

Open up a terminal.
Use a client such as MobiXTerm

ssh <username>@beartooth.arcc.uwyo.edu
[username@blog1 ~]$

# UW: Beartooth (blog1/blog2)

Temporarily use a test account:

Open up Chrome
Navigate to: https://southpass.arcc.uwyo.edu/
Start Beartooth Shell Access

Download Slides:

Opening Screen:

Message of the day
Storage usage - across project spaces

General Format:[<username>@<server/node-name> <folder>]$ 

[<username>@blog2 ~]$ arccquota

# ‘man’ is only available on the login nodes.
# It is not available on the compute nodes.
[<username>@blog2 ~]$ man id
[<username>@blog2 ~]$ id –-version
[<username>@blog2 ~]$ id

[<username>@blog2 ~]$ groups

Which groups?

[arcc-t05@blog1 ~]$ id
uid=10339923(arcc-t05) gid=10339923(arcc-t05) groups=10339923(arcc-t05),89997(beartooth),446824(uwit-research-arccanetraining),5735503(teton_backup),6000211(arccanetrain)

[arcc-t05@blog1 ~]$ groups
arcc-t05 beartooth uwit-research-arccanetraining teton_backup arccanetrain

Beartooth: FileSystem

Type	Location	Description
home	/home/<username>	Space for configuration files and software installations.
project	/project/<project-name>/[username]	Space to collaborate among project members. Data here is persistent and is exempt from purge policy.
gscratch	/gscratch/<username>	Space to perform computing for individual users. Data here is subject to a purge policy defined below.
node local scratch	/lscratch	Only on compute.
memory filesystem	/dev/shm	RAM-based tmpfs available as part of RAM for very rapid I/O operations; small capacity.

Home and Project Folders:

# Home folder:
[]$ cd ~
[]$ pwd
/home/arcc-t05

[]$ cd /gscratch/arcc-t05

# Shared project space
[]$ cd /project/arccanetrain/
[arcc-t05@blog1 arccanetrain]$ ls
arcc-t01  arcc-t06  arcc-t11  arcc-t16  arcc-t21  arcc-t26  brewer       mkillean
arcc-t02  arcc-t07  arcc-t12  arcc-t17  arcc-t22  arcc-t27  excotest     salexan5
arcc-t03  arcc-t08  arcc-t13  arcc-t18  arcc-t23  arcc-t28  intro_to_hpc
arcc-t04  arcc-t09  arcc-t14  arcc-t19  arcc-t24  arcc-t29  lmainzer
arcc-t05  arcc-t10  arcc-t15  arcc-t20  arcc-t25  arcc-t30  lreilly

Copy files:

[]$ cd 

[~]$ cp -r /project/arccanetrain/intro_to_hpc/ .

[~]$ cd intro_to_hpc/

[intro_to_hpc]$ ls
Intro_to_hpc.pdf  python01.py  python01.py.fixed  run_gpu.sh  run.sh

Let's run a python script:

# If you have NOT already copied the files.
# Navigate back to your home folder.
[]$ cd
[~]$ mkdir intro_to_hpc
[~]$ cd intro_to_hpc/
[intro_to_hpc]$ ls
[intro_to_hpc]$ pwd
/home/<username>/intro_to_hpc


[intro_to_hpc]$ vim python01.py
"python01.py" [New File] 

# Using vim: Press ESC followed by ‘i’ to INSERT: Start typing:
import sys
print("Python version: " + sys.version)
print("Version info: " + sys.version_info)
# Using vim: ESC followed by ‘:wq’, then Return

Let's run a python script: Fixed:

[]$ python python01.py
Python version: 3.8.16 (default, May 31 2023, 12:44:21)
[GCC 8.5.0 20210514 (Red Hat 8.5.0-18)]
Traceback (most recent call last):
  File "python01.py", line 3, in <module>
    print("Version info: " + sys.version_info)
TypeError: can only concatenate str (not "sys.version_info") to str

# Let's update the code:
From: print("Version info: " + sys.version_info)
To:   print("Version info: " + str(sys.version_info))

[]$ python python01.py
Python version: 3.8.17 (default, Aug 10 2023, 12:50:17)
[GCC 8.5.0 20210514 (Red Hat 8.5.0-20)]
Version info: sys.version_info(major=3, minor=8, micro=17, releaselevel='final', serial=0)
[]$ python --version
Python 3.8.17

02: Setting up the Environment and LMOD

Topics:

LMOD: Setting up an Environment.
What’s available.
How to find (spider) modules.
Loading / purging modules.
Dependencies.

What do we have available?

Compilers and eco systems: GNU family, Intel’s oneAPI, Nvidia’s hpc-sdk
Languages: C/C+, Fortran, Go, Java, Julia, Perl, Python, R, Ruby, Rust
Scientific libraries and toolkits: Built with a specific compiler: GNU by default
Standalone applications and utilities: Installed using:
- Conda
- Containers: running Singularity (not Docker)
  - We can create a Singularity image from a Docker image.
- Binaries/Executables

Beartooth Software List

Setting up your environment:

Exercises

Environment variables: env, echo
Find and load modules.
Commands: module spider/load/purge/ml
Understand dependencies and compiler stacks.
Run our python script using a specific version of python.
Load R (and Python).
Default modules – why define the module version.

Environment Variables:

[]$ env

[]$ echo $PATH

What’s being used?

[]$ which python
/usr/bin/python

You can’t break the System:

[]$ ls /usr/bin

[]$ cd /usr/bin
[bin]$ ls
[]$ pwd
/usr/bin

# Permissions (ugo:rwx) and Ownership (user:group)
[bin]$ ls -al
[bin]$ ls -al python*

You can't break the system.
[bin]$ rm python
rm: cannot remove 'python': Permission denied

sudo: you will not be granted sudo access – do not ask!

What’s available?

[bin]$ cd ~
[~]$ cd intro_to_hpc/

[]$ ml
[]$ module avail

[]$ module load gcc/12.2.0
[]$ ml
[]$ module avail

# What is different compared to the first time we called ml?


[]$ module load gcc/11.2.0
# What happened?

What’s available? Compiler tree:

[]$ module load gcc/11.2.0
# What happened?
Due to MODULEPATH changes, the following have been reloaded:
  1) gmp/6.2.1     2) mpfr/4.1.0     3) zlib/1.2.12     4) zstd/1.5.2

The following have been reloaded with a version change:
  1) gcc/12.2.0 => gcc/11.2.0

# You can only have one compiler loaded at a time within a session.

[]$ ml
[]$ module avail

[]$ module purge
[]$ ml
# What do you notice?

What’s available? Modules loaded by default:

[]$ module purge
The following modules were not unloaded:
  (Use "module --force purge" to unload all):
  1) slurm/latest   2) arcc/1.0


[]$ ml
Currently Loaded Modules:
  1) slurm/latest (S)   2) arcc/1.0 (S)
  Where:
   S:  Module is Sticky, requires --force to unload or purge

Module load/spider: Dependencies:

[]$ module load python/3.10.6
Lmod has detected the following error:  These module(s) or extension(s) exist but cannot be loaded as
requested: "python/3.10.6"
   Try: "module spider python/3.10.6" to see how to load the module(s).

What’s different between these command-lines?

[]$ module spider python/3.10.6

[]$ module spider python/3.10.8

What’s different between these command-lines? Dependencies:

[]$ module spider python/3.10.6
----------------------------------------
  python: python/3.10.6
----------------------------------------
    You will need to load all module(s) on any one of the lines below before the "python/3.10.6" module is available to load.
      arcc/1.0  gcc/12.2.0
    Help:
      The Python programming language.


[]$ module spider python/3.10.8
----------------------------------------
  python: python/3.10.8
----------------------------------------
    You will need to load all module(s) on any one of the lines below before the "python/3.10.8" module is available to load.
      arcc/1.0  gcc/11.2.0
    Help:
      The Python programming language.

Setup Python environment:

[]$ module purge
[]$ module load gcc/12.2.0
[]$ module load python/3.10.6
[]$ python –version


# Single line:
# Order matters:
[]$ module purge
[]$ module load python/3.10.6 gcc/12.2.0
vs
[]$ module load gcc/12.2.0 python/3.10.6

What’s happened to the PATH environment variable?

[]$ module purge
[]$ echo $PATH


[]$ module load gcc/12.2.0 python/3.10.6
[]$ echo $PATH
[]$ which python
/apps/u/spack/gcc/12.2.0/python/3.10.6-7ginwsd/bin/python

Can we use the R language?

[]$ module purge
[]$ r
[]$ R

# Can we find an 'R' module?
[]$ module avail
[]$ module spider r

# What do we see and why?
[]$ module load r/4.2.2

# How do we fix it?

Can we use the R language? Fixed:

[]$ module purge
[]$ r
[]$ R

# Can we find an 'R' module?
[]$ module avail
[]$ module spider r

# What do we see and why?
[]$ module load r/4.2.2

# How do we fix it?
[]$ module load gcc/12.2.0 r/4.2.2
[]$ ml
[]$ R --version

Can we also use the Python language?

[]$ module load python/3.10.6
[]$ python --version
Python 3.10.6

# Where’s the gcc/12.2.0?

# What happens if we:
[]$ module load gcc/11.2.0 python/3.10.8
[]$ python –-version
[]$ R --version

Remember:

Only one compiler/version can be loaded into your environment at a time.
Can only load languages/applications built with the same compiler.
But, even this can introduce dependency issues.

Defaults:

[]$ module purge
[]$ module avail
[]$ module load python
[]$ python --version
Python 2.7.18 :: Anaconda, Inc.

Defaults:

Modules change and are updated.

The defaults will change and update – you might not realize.

Please define the version of a module you’re using.

Helps to replicate and triage.

Advanced: Why do versions matter?

Consider Python Packages installed using pip:

You install a package with respect to the version of python you are using.
A packages is not automatically available/installed across different versions.
If you start using python/3.9 and then swap to python/3.10 you will need to re-install any packages.

# Example:
[lib]$ pwd
/home/<username>/.local/lib

[]$ ls
python2.7  python3.10  python3.6  python3.8  python3.9
# These folders will only be created if you use that version.

# Each child folder has its own site-packages folder.

It is the same concept for R libraries.

Summary

LMOD: Setting up an Environment.

Intro to Accessing the Cluster and the Module System

01: Accessing the Cluster

02: Setting up the Environment and LMOD