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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 set up various environments allowing the use of a variety of programming languages, applications, libraries and utilities.

Course Goals:

  • What is LMOD and how to use it to set up an Environment.

Topics:

  • LMOD: Setting up an Environment.

  • What’s available.

  • How to find (spider) modules.

  • Loading / purging modules.

  • Dependencies.

...

Note
Note

Notes:

  • Participants will require an intro level of experience of using Linux, the ability to use a text editor from the command line, and knowledge on how to access the cluster.

Table of Contents
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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

Code Block
[]$ env

[]$ echo $PATH

What’s being used?

Code Block
[]$ which python
/usr/bin/python

Context: Run a Python Script on the System

Copy files:

Code Block
[]$ 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:

Code Block
# 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:

Code Block
[]$ 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

You can’t break the System

Code Block
[]$ 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
Warning

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

What’s available?

Code Block
[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

Code Block
[]$ 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

Code Block
[]$ 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

Code Block
[]$ 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?

Code Block
[]$ module spider python/3.10.6

[]$ module spider python/3.10.8

What’s different between these command-lines? Dependencies

Code Block
[]$ 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

Code Block
[]$ 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?

Code Block
[]$ 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?

Code Block
[]$ 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

Code Block
[]$ 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?

Code Block
[]$ 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

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

Defaults: Why Consider?

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.

Code Block
# 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

  • We have tried to make the examples as generic as possible. You will need to replace <project-name> and <username> with appropriate values that apply to you.

  • Versions on the System might change after scheduled maintenance and before these trainings can be updated. The context of the training and what is being demonstrated still apply. Versions of commands are correct as of 20240727.

  • This tutorial is available for download as a PDF here.

...

Sections

  1. Your Basic Environment: Demonstrate what a default session starts as.

  2. The Module System and What’s Available: Introduce the LMOD Module System and the concept of dependencies.

  3. Setting Up Environments: Understand how to load modules, reset your environment by purging, and potential dependency issues.

  4. Using Modules: Considerations and Defaults: Highlight the modules have defaults, and good practices such as purging and defining module versions.

  5. Using Modules: FAQs: Present a list of commonly asked questions that might not be addressed specifically during the workshop.

  6. Required Software is Not Available: Discuss approaches and process for when software isn’t available and/or users bring their own scripts/code.

  7. Using Modules: Summary: Provide a summary of concepts and commands covered.

...

All Trainings

Trainings

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Your Basic Environment