Basic Linux

Linux information FAQs

Where do I find basic unix/linux resources?

There are many web based tutorials and howto's for anything linux oriented. Some sites of interest:

What are some of the basic linux and related commands?

Most usage is centered around a dozen or so commands:

ls, more, less, cat, nano, pwd, cd, man, bsub, bkill, bjobs, ps, scp, ssh, cp, chmod, rm, mkdir, passwd, history, zip, unzip, tar, df, du, head, tail, grep

See the man pages for complete documentation. Here is a short description of some.

Basic Unix Commands

Action Needed	Command	Usage
Display contents of a file	cat	cat filename
Copy a file	cp	cp [-op] source destination
Change file protection	chmod	chmod mode filename or chmod mode directory_name
Change working directory	cd	cd pathname
Display file (/w pauses)	more	more filename
Display first page of text	less	less filename
Display help	man	man command or man -k topic
Rename a file	mv	mv [-op] filename1 filename2 or mv [-op] directory1 directory2 or mv [-op] filename directory
Compare file	diff	diff file1 file2
Delete file	rm	rm [-op] filename
Create a directory	mkdir	mkdir directory_name
Delete a directory /w files in it	rmdir -r	rm -r directory_name
Delete a directory	rmdir	rmdir directory_name
Display a list of files	ls	ls [-op] directory_name
Change the password	passwd	passwd
Display a long list (details)	ls -l	ls -l directory_name
Display current directory	pwd	pwd
Display mounted filesystems	df	df

What text editors are available?

nano, nedit, vi, vim, emacs

How do I strip out ^M embedded characters in my files I transferred from my PC?

Use the dos2unix command on the file. There is man page documentation available for further info. Also check this page for additional tips.

> man dos2unix

What is a man page?

man pages are linux/unix style text based documentation. For example, to obtain documentation on the command cat:

> man cat

> xman
is the command for the x-based interface to man.

> man man
is the man documentation.

> man -k graphics
finds all related commands concerning graphics.

Are the compute nodes named differently from the old cluster compute nodes?

Yes. You should not hard code the names anywhere.

How can I verify that my requested storage is mounted?
Use the df command.

How can I view my most recent files?

> ls -lt

I sometime notice that my job duration can vary when I rerun a program with exactly the same inputs, condition, etc... Why?
The cluster has a mix of several different Intel CPUs and motherboard combinations. The absolute performance potential is similar among them but given the mix of other jobs sharing nodes, your results will vary. This is not something that is predictable when the cluster is well loaded.

How do I convert mixed case file names in a directory to lower case?

Issue the following in the directory of interest:

> find . -name "A-Z" \| cut -c 3- - \| awk '{print $1,tolower($1)}' \| xargs -i echo "mv {}" \| csh

This will find everything with uppercase letters and rename it to the
same thing with all lowercase.

How do I uncompress and extract many .gz and corresponding tar files?

> ls -1 *.gz \| xargs -n 1 -r -I {} tar zxf {}

Sometimes I get a cryptic message about too many open files, what is that?
There are several resource settings associated with a default account. To see the settings:

-bash-3.2$ ulimit -a

The default setting is 2048 for the open files parameter. A user may increase it up to 10K in 1024 increments. To set it to 4096:

-bash-3.2$ ulimit -n 4096

However, this shows what has happened on the headnode only.

Since jobs execute on compute nodes you should include this in a simple shell script along with your sbatch command, so that the new setting takes effect on the compute node as well.

Sometimes I would like to have multiple shells available on the login node, how do I do this?

There are many ways. Most often you may just login two or more times from your desktop. Or, refer to the slurm section with examples using srun.

It is best not to ssh into the cluster while you are on the login node of the cluster.

I compiled a program locally in my account and I would like to add the location of the executables to my PATH, how do I do this?

Suppose your software directory is located in you home directory and your username is jdoe02. Your software directory is flight_program/ and there is a bin subdirectory located within containing executables.

$PATH is a global environmental variable defined for the cluster for general access to important locations. You may add to it by pre-pending the path you wish to be searched.

PATH=/cluster/home/j/d/jdoe02/flight_program/bin:$PATH

export PATH

To see if it got updated:

> printenv \| grep PATH