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Bash

Info

A Bash is command-line shell and scripting language that allows users to interact with Unix-based operating systems.

Code Block
[]$ bash --version
GNU bash, version 5.1.8(1)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

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Environment Variables

# List ALL environments currently set within your environment. # There's a lot! []$ env # View an individual environment variable. []$ echo $PATH # Something of the form: /home/<username>/.local/bin:/home/<username>/bin:/
Code Block
Info

An environment variable is a user/system defined value that can read by users/scripts/applications, and be used to affect/influence how something can/should behave.

Info

Lets list everything that the session is currently aware of - there’s a lot!

This demonstrates that there is a lot of things being defined and configured, behind the scenes, to make your session run as required.

Code Block
[]$ env
Info

You can view individual environment variables:

Code Block
[]$ echo $PATH
# Something of the form:
/home/<username>/.local/bin:/home/<username>/bin:/apps/s/arcc/1.0/bin:/apps/s/slurm/latest/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin

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Info

Let’s check what’s on the system:

Code Blockinfo
#

GCC

stands

for

GNU

Compiler

Collection,

a

free

and

open-source

collection

of

compilers

#

and

development

tools

that

support

many

programming

languages,

hardware

architectures,

and

operating

systems.

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

[]$ gcc --version
gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)

# Let's look at Python:
Info

Let’s look at Python:

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

[]$ python --version
Python 3.9.18

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Let's run a Python script:

Info

Within your home, create an intro_to_modules folder and write into it the python01.py file:

Code Block
# Create a folder in your home folder:
[]$ cd
[~]$ mkdir intro_to_modules
[~]$ cd intro_to_modules/
[intro_to_modules/]$ ls
[intro_to_modules]$ ls
[intro_to_modules]$ pwd
/home/<username>/intro_to_modules

[intro_to_modules]$ vim python01.py
"python01.py" [New File] 
# Using vim: Press ESC followed by ‘i’ to INSERT: Start typing:
Info

Using vim (or some other text editor) create a file called python01.py and enter the following:

  • Press ESC followed by i to INSERT: Start typing.

  • Press ESC followed by :wq then Return to save the file.

Code Block
import sys
print("Python version: " + sys.version)
print("Version info: " + sys.version_info)
# Using vim: ESC followed by ‘:wq’, then Return

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Let's run a Python script: Fixed:

Info

Try running the Python code:

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:
Info

Update the python01.py file:

Code Block
From: print("Version info: " + sys.version_info)
To:   print("Version info: " + str(sys.version_info))
Now try running again:
 Code Block
[]$ python python01.py
Python version: 3.9.18 (main, Jan  4 2024, 00:00:00)
[GCC 11.4.1 20230605 (Red Hat 11.4.1-2)]
Version info: sys.version_info(major=3, minor=9, micro=18, releaselevel='final', serial=0)
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 Code Block
[]$ which R
/usr/bin/which: no R in (/apps/s/arcc/1.0/bin:/apps/s/slurm/latest/bin:/home/<username>/.local/bin:/home/<username>/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)

# Is it 
 Info
Is it case-sensitive?


 Code Block
[]$ which r
/usr/bin/which: no r in (/apps/s/arcc/1.0/bin:/apps/s/slurm/latest/bin:/home/<username>/.local/bin:/home/<username>/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
 Note
R is not available on the system by default.
 Infonote
But I want to use R. What can I do?
This is the reason for this module. To demonstrate how you setup your environment to make things available to you.
You Can’t Break the System
to you.
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You Can’t Break the System
 Info
Try removing something that you do not have permissions to delete:
 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 ls
[]$ pwd
/usr/bin

[bin]$ ls -al
[bin]$ ls -al python*
[bin]$ rm python
rm: cannot remove 'python': Permission denied
 Info
Check and confirm by looking at the permissions (ugo:rwx) and Ownership (user:group).
What do you notice?
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What is sudo? Can I use/request sudo?
 Info
The sudo command ("superuser do") , is a command to allow a user to temporarily elevate their privileges to run commands that are usually restricted.
 Warning
sudo: you will not be granted sudo access – do not ask!
 Info
Similarly:
 Warning
You can not use dnf or other Linux related software management commands you might come across yum, apt-get…
You won’t have permissions, and we will not provide you permission - do not ask!
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