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  • There is a folder called intro_to_linux within the /project/arccanetrain<project-name>/ folder.

  • How would you copy this folder into your home folder?

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Info

Method 01: Move to your home folder and copy into this location.

The . marks the current working directory.

Code Block
[arccanetrain]$ cd 
[~]$ cp -r /project/arccanetrain<project-name>/intro_to_linux/ .
cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied
[~]$ ls
Desktop  Documents  Downloads  intro_to_linux
Info

Method 02: Move into the /project/arccatrain<project-name>arccatrain/ folder and copy from there into your home.
Remember, the ~ is short for your home folder.

Code Block
[~]$ cd /project/arccanetrain<project-name>/
[arccanetrain<project-name>]$ cp -r intro_to_linux/ ~
cp: cannot open 'intro_to_linux/workshop_me.txt' for reading: Permission denied
[arccanetrain<project-name>]$ ls ~
Desktop  Documents  Downloads  intro_to_linux
Note

In both cases you do not have permissions to copy workshop_me.txt - this is intentional and a good remind to check the permissions/ownerships of files.

Question: What do you notice about the permissions of this file?

Code Block
# -rw-------  1 arcc<arcc-t05username> arccanetrain<project-name>      23 Oct  5 07:20  workshop_me.txt
Info

Only the owner of this file (arcc<arcc-t05username>) has permission to read/write, and thus copy this file.

Any other user can not copy this file, and thus it will not be copied as part of everything else.

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Command

Description

tail

Code Block
Usage: tail [OPTION]... [FILE]...
Print the last 10 lines of each FILE to standard output.
 -f, --follow[={name|descriptor}]
                           output appended data as the file grows;
                             an absent option argument means 'descriptor’
 -n, --lines=[+]NUM       output the last NUM lines, instead of the last 10;
                             or use -n +NUM to output starting with line NUM

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Exercise

Info

Question: Within the intro_to_linux folder, how can we view the contents of the software.csv file?

  1. How can we view the entire file?

  2. How can we view the start of the file?

  3. How can we view the end of the file?

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Answers

Info

Within the intro_to_linux folder, how can we view the contents of the software.csv file?

1. How can we view the entire file?

Code Block
[]$ cd ~/intro_to_linux/
[intro_to_linux]$ cat software.csv
[intro_to_linux]$ cat -n software.csv

[intro_to_linux]$ more software.csv
# Press spacebar to scroll through.
# Press ‘q’ to quit at any time.
[intro_to_linux]$ more software.csv
Info

2. How can we view the start of the file?

Code Block
[intro_to_linux]$ head software.csv
[intro_to_linux]$ head –n 5 software.csv
Info

3. How can we view the end of the file?

Code Block
[intro_to_linux]$ tail software.csv
[intro_to_linux]$ tail –n 5 software.csv

...

Code Block
[intro_to_linux]$ grep -r -i nvidia *
clusters/teton.html:    .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
clusters/beartooth.html:    .../788758554/NVidia+HPC+SDK">NVidia HPC SDK</a></td>
software.csv:compiler,NVidia HPC SDK,nvhpc,"beartooth,teton"...
software.csv:libraries and toolkits,cuDNN,cudnn,beartooth,The NVIDIA CUDA Deep...
software.csv:libraries and toolkits,TensorRT,,beartooth,"NVIDIA TensorRT, an...

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Exercises

Info

We will be using the software.csv file:

Lets take a quick look at it using head to view the first few lines:

Code Block
# The software.csv file takes the form:
[intro_to_linux]$ head software.csv
Type,Name,Module,Cluster,Description
application,Alphafold,alphafold,"beartooth,teton",AlphaFold...
application,Astral,astral,wildiris,ASTRAL is a tool...
application,Augustus,augustus,beartooth,AUGUSTUS is a program...
application,Avizo,avizo,loren-pre202308,Avizo is a general-purpose...
application,ANGSD,angsd,"beartooth,teton",ANGSD: is a software...
application,ANSYS,ansys,teton,"ANSYS is a general-purpose software...
Info

Questions:

  1. Which named applications are related to the words

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  1. bayes?

  2. Which files contain reference to IPA?

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Answers

Info

Question 01: Which named applications are related to the words “bayes”?

This assumes we want to find all instances of “bayes” regardless of case.

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