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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 |
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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. |
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Sections
The Module System and What’s Available: Dependencies
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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
Setting up your environment
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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 |
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[]$ env
[]$ echo $PATH |
What’s being used?
| Code Block |
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[]$ which python
/usr/bin/python |
Context: Run a Python Script on the System
Copy files:
| Code Block |
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[]$ 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 |
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# 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 |
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[]$ 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 |
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[]$ 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 |
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sudo: you will not be granted sudo access – do not ask! |
What’s available?
| Code Block |
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[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 |
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[]$ 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 |
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[]$ 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 |
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[]$ 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 |
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[]$ module spider python/3.10.6
[]$ module spider python/3.10.8 |
What’s different between these command-lines? Dependencies
| Code Block |
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[]$ 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 |
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[]$ 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 |
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[]$ 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 |
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[]$ 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 |
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[]$ 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 |
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[]$ 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 |
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[]$ 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/3.9and then swap topython/3.10you will need to re-install any packages.
| Code Block |
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# 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
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