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Common Pitfalls#

This page highlights common pitfalls in Linux usage, offering insights into potential challenges users might face. By understanding these pitfalls, you can avoid unnecessary hurdles.

Location#

If you receive an error message which contains something like the following: 

No such file or directory

It probably means that you haven't placed your files in the correct directory, or you have mistyped the file name or path.

Try and figure out the correct location using ls, cd and using the different $VSC_* variables.

Spaces#

Filenames should not contain any spaces! If you have a long filename you should use underscores or dashes (e.g., very_long_filename).

$ cat some file
No such file or directory 'some'

Spaces are permitted, however they result in surprising behaviour. To cat the file 'some file' as above, you can escape the space with a backslash ("\") or you can put the filename in quotes:

$ cat some\ file
...
$ cat "some file"
...

This is especially error prone if you are piping results of find:

$ find . -type f | xargs cat
No such file or directory name ’some’
No such file or directory name ’file’

This can be worked around using the -print0 flag:

$ find . -type f -print0 | xargs -0 cat
...

But, this is tedious, and you can prevent errors by simply colouring within the lines and not using spaces in filenames.

Missing/mistyped environment variables#

If you use a command like rm -r with environment variables you need to be careful to make sure that the environment variable exists. If you mistype an environment variable then it will resolve into a blank string. This means the following resolves to rm -r ~/* which will remove every file in your home directory!

$ rm -r ~/$PROJETC/*

Typing dangerous commands#

A good habit when typing dangerous commands is to precede the line with #, the comment character. This will let you type out the command without fear of accidentally hitting enter and running something unintended.

$ #rm -r ~/$POROJETC/*

Then you can go back to the beginning of the line (Ctrl-A) and remove the first character (Ctrl-D) to run the command. You can also just press enter to put the command in your history so you can come back to it later (e.g., while you go check the spelling of your environment variables).

Copying files with WinSCP#

After copying files from a windows machine, a file might look funny when looking at it on the cluster.

$ cat script.sh
#!/bin/bash^M
#PBS -l nodes^M
...

Or you can get errors like:

$ qsub fibo.pbs
qsub: script is written in DOS/Windows text format

See section dos2unix to fix these errors with dos2unix.

Permissions#

$ ls -l script.sh # File with correct permissions
-rwxr-xr-x 1 vsc40000 vsc40000 2983 Jan 30 09:13 script.sh
$ ls -l script.sh # File with incorrect permissions
-rw-r--r-- 1 vsc40000 vsc40000 2983 Jan 30 09:13 script.sh

Before submitting the script, you'll need to add execute permissions to make sure it can be executed:

$ chmod +x script_name.sh

Help#

If you stumble upon an error, don't panic! Read the error output, it might contain a clue as to what went wrong. You can copy the error message into Google (selecting a small part of the error without filenames). It can help if you surround your search terms in double quotes (for example "No such file or directory"), that way Google will consider the error as one thing, and won't show results just containing these words in random order.

If you need help about a certain command, you should consult its so-called "man page":

$ man command

This will open the manual of this command. This manual contains detailed explanation of all the options the command has. Exiting the manual is done by pressing 'q'.

Don't be afraid to contact hpc@ugent.be. They are here to help and will do so for even the smallest of problems!

More information#

  1. Unix Power Tools - A fantastic book about most of these tools (see also The Second Edition)

  2. http://linuxcommand.org/: A great place to start with many examples. There is an associated book which gets a lot of good reviews

  3. The Linux Documentation Project: More guides on various topics relating to the Linux command line

  4. basic shell usage

  5. Bash for beginners

  6. MOOC

Please don't hesitate to contact in case of questions or problems.