Basic bash for NLP tutorial

Bash is a language that allows for easy manipulation of Unix-like computing environments. Frequently in NLP research, quick simple tasks like “how many lines are there in this file” or “how can I copy a file to 100 places at the same time” arise, and can best be solved with bash, and some easily-usable affiliate programs.

Beyond this, Bash is much more versatile and useful than many give it credit for, and advanced knowledge of bash can make projects involving very large systems and/or multi-step pipelines truly a joy.

When to use bash; When not to

I love bash dearly. That’s not to say it’s the answer to every problem in NLP.

Use bash when

• You need to move, and/or rename one or many files
• You need to set up folder structures, create symbolic links (more on this later), and generally change the file system.
• You want basic statistics on one or many files (e.g. “I have 3,000,000 lines of log files, and if the word ‘error’ appears, something failed. Did it ever appear?”)
• You want to submit multiple jobs to the scheduler with similar parameters
• You want to set up a “pipeline”, which means a set of processing steps that takes input files and produces output files, using multiple independent programs.

Don’t use bash when

• You need to do a lot of arithmetic computation, especially division/multiplication
• You need library support (for, say, reading TSVs, or JSON, etc.)
• You plan to make copious use of fun data structures like sets, counters, UnionFind, MyArbitraryClass, or TrieHeapMapBellmanFordImpl

File system and unix basics

As we said in use bash when, we frequently use bash to manipulate a Unix file system. The unix filesystem is a rooted tree-like data structure. Its root is /. This forward slash is known as “root”. Below is a diagram showing a selection of the root of the nlpgrid filesystem(s).

When using bash, you are always “at” one of the nodes in the filesystem tree. Every command you run is run relative to your current node, or “folder”, or more commonly, “directory.” A “path” is a list of names of folders combined with forward slashes (/) that takes you either from root (an absolute path) or from any arbitrary directory (a relative path) to some other directory.

Knowing where you are

When running bash commands, ., the period, corresponds to your current directory. When reading or writing files, the . is implicit. Let’s demonstrate this with a file. Open up a terminal and run

    touch testfile

This creates a file named testfile if it doesn’t exist, or updates the ‘last-read’ flag on the file if it already existed. Now, list the contents of your current directory with

    ls

You should see (possibly among other things) the file testfile. You can demonstrate that this is equivalent to:

    touch ./testfile
    ls .

In both cases, the . was implicit.

However, when specifying commands, the . is not implicit. For example, try running

    ./touch testfile

You should find that bash complains with a command-not-found error. This is because you told bash “look for the command touch; it’ll be in this directory.” Without the prepended ./, the command touch is found by other means, which we’ll find later.

Specifying the location of files you want to work with can be more complex than just looking in your current directory, however. For example, make a directory within your current directory with

    mkdir testfolder

Now, make a new file in that directory, and demonstrate that the file is in the directory, with

    touch testfolder/testfile2
    ls testfolder

You can also change your working directory, which changes the location from which your commands are run. For example, if we run

    cd testfolder
    ls

We should see testfile2, not testfile. To return to the directory just 1 “above” (or, closer to /) from the current directory, run

    cd ..

Where .. is short for “parent directory”.

Directory navigation quick tips

Here are some other quick commands you’d otherwise have to search for at some point:

• cd - sends you to the last directory you were in, whatever that was, and prints the name of that directory.
• ~ the tilde represents your “home” directory. On my laptop, for example, thats /home/johnhew. If you run a command with the tilde, it will be replaced by the location of your home diretory.
• * the asterisc stands for “everything within the directory I’ve just specified”. Thus ls * means “list the contents of every file/directory in the current directory.”
• pwd is a command that prints the absolute path of the current working directory
• tree is a fun commands that lists the tree structure starting from the current working directory and searching “down” (away from /).

File copying and movement

To copy a file located at oldloc to a new location newloc, use the `cp command as follows:

    cp oldloc newloc

Seems simple enough. oldloc and newloc can each be an absolute path, like /nlp/data/johnhew/expts/realgooddata.txt.png, or a relative path like realgooddata.txt.png. The semantics of cp allows you to copy multiple files to one location, but not copy 1 file to multiple locations. By this I mean when you run:

    cp loc1 loc2 loc3 loc4 loc5

You’re copying loc1 through loc4 all into loc5. If loc5 is a directory and loc1,loc2,loc3,loc4 all have unique filenames, all 4 files will be copied into the loc5 directory. If loc5 is a file (or didn’t exist previously), each file will be copied sequentially into loc5, squashing all old files. In other words, all you’ll end up with at loc5 is (in this case) loc4.

If you don’t want to keep the old file locations, use the mv (move) command instead of cp.

Reading, editing, analyzing files

Moving files is great, but actually working with files contents is great too.

An optional aside : vim

To integrate file editing into your bash workflow, I highly suggest putting in the time to learn vim, the world’s best text editor. There’s a bit of a learning curve, but many things are googleable, and I’ll start you off with two things:

• Use :q to quit.

• Here’s a good starter vimrc, which is a configuration file. Google for more info.

   filetype indent on
   filetype plugin on
   set expandtab
   set mouse=a
   set pastetoggle=<F2>
   syntax enable
   set tabstop=2
   set shiftwidth=2
   set softtabstop=2
   set autoindent
   set whichwrap+=<,>,h,l,[,]
   set cursorline
   set number
   set hlsearch
   set lazyredraw
   set omnifunc=syntaxcomplete#Complete
   set grepprg=grep\ -nH\ $*
  

Printing and streams

To pring a file’s contents, run the cat command. (This stands for “concatentate”. If you run cat on multiple files, it prints them all out, one after the other.)

    cat file1 file2 file3

What we’ve siad so far about “printing” has been pretty self-evident: text shows up in your bash terminal. However, it is useful to know a bit more about how this works. Any program has access to two “streams”, known as stdout and stderr, for “standard output” and “standard error”. (To learn more about their true nature, take CIS 380 : Operating Systems.) When a program prints, it writes data to stdout. By default, stdout is printed to your terminal (as is stderr.) However, we can “redirect” these streams to, for example, concatentate 3 files:

  cat file1 file2 file3 > fileall

This has just printed all of files 1,2,3 into the file fileall. The > character is called a “redirection”; it redirects the stdout stream to the file specified after it.

Streams quick tips

• to redirect stdout not to a file, but to another program, use a pipe, |, as such:

   cat file1 file2 file3 | sort | uniq 
  

• to redirect stderr, use the following: 2>

• to redirect stdout to a file, but also see the output on your terminal, use the tee command, as follows:

   cat file1 file2 file3 | tee fileall
  

Searching and analysis

To search for a string string within files file1, file2, file3, use the program grep as follows:

    grep string file1 file2 file3

This will print out lines in each file that have the string string.

If your string has a space in it, you must enclose it in quotes (either single or double,) as in:

    grep "error happened" file1 file2 file3

Grep is more powerful than this; instead of using a string, you can search for an arbitrary pattern, described by Regular Expressions. (That’s worth a tutorial in itself.)

To count “things” in a file, use the program wc as follows:

    wc file1

This will print the number of characters, number of words (whitespace-delimited) and number of lines in the file.

Similarly, you can run both wc and grep on output piped from some other process, as in:

    cat file1 file2 file3 | sort | uniq | grep "error found" 
    cat file1 file2 file3 | sort | uniq | grep "error found" | wc

wc and grep quick tips:

• grep -c will print the number of lines that matched, instead of the lines themselves. This is equivalent to piping through wc -l.
• grep -n will print the line numbers of the matching lines (along with the matching lines)
• grep -r pattern dir will recursively grep through a given directory dir.
• wc -w will just give the word count, similarly wc -l will just give the line count.

Shortcuts and efficiency

Working with files in bash can be much faster than using a GUI. These shortcuts will help you get up to speed.

Tab completion

Typing out long paths and filenames is very tedious, and prone to error. Bash provides a solution to both of these problems in “tab completion”.

As you type a file name, bash knows all the files in the directory you’ve specified so far, and knows which files you could be referring to, based on the prefix you’ve written so far. At any time as you’re writing a filename, if you press <tab>, bash will determine whether it can unambiguously fill in any portion of the rest of the filename.

Let’s look at a few examples to make this concrete. In a new directory, type the following commands:

    touch file1
    touch file2

Now, type in vim fi and then hit <tab>. Notice that bash completes to vim file without any work. Because these were the only files in the directory, bash knew that when you wrote fi, you meant either file1 or file2. It won’t complete further than that because it can’t be sure which of the two you mean. So, you have to fill in the rest of the file name.

Note that if you have a directory with only one file in it, the empty prefix is unambiguous, and a <tab> completion will fill in the whole filename for you. Further, use tab completion not only on files, but also on long directory paths. For example, instead of typing out all of

    /nlp/users/johnhew/common-crawl/corpusplz/src/core/corpus_filter.py

I generally tend to write:

    /nlp/u<tab>/joh<tab>/co<tab>/cor<tab>/src/c<tab>/cor<tab>

Even here, the forward slashes / aren’t typed by me, since the tab completion includes them, saving a lot of work.

Command history reverse-search

Typing out long lists of commands over and over again is a pain. Thankfully, bash includes a finite history of commands, and a nice search interface.

First, as you might figure out accidentally, pressing the up arrow key returns you to the last command you ran. This is very helpful, but scrolling through tons of commands to find something you ran yesterday can be tedious.

This is where the reverse-search comes in handy. It allows you to search for commands in your history that include a substring you specify. Type ctl-r in the terminal (hold ctl and press r), and you’ll notice your command prompt is replaced with (reverse-i-search). Now, type in a few letters that you remember were a part of the command, and it’ll search through your history to find the first command that matches your query.

For example, I might look for the last time I qsub‘d something to the scheduler with ctl-r followed by qsub. If the first matching command isn’t what you’re looking for and you want to keep looking back through more matching commands, hit ctl-r subsequent times to move back through them.

A few notes:

• If you keep hitting ctl-r and the command you see doesn’t change, or if you type in a prefix and you don’t see a matching command appear, it means you don’t have any (more) commands that match your query.
• If you want to keep the command you found with reverse search, I tend to use the escape key.
• Ify ou want to discard the command you found with reverse search, I tend to use ctl-c.

Typing and modifying commands

Many “move my cursor to another position” tips are, unfortunately, operating system- (or desktop environment-) dependent. For example on linux with i3, I use ctl+left\_arrow or ctl+right\_arrow to move one word to the left or right in the commands I’m typing.

However, there are a few excellent shortcuts to cut your command typing time:

• ctl+k erases everything from your cursor to the end of the line.
• ctl+a jumps your cursor to the start of the line.
• ctl+e jumps your cursor to the end of the line.
• ctl+w deletes a word to the left of your cursor.

Note that you’ll have to get a feel for what a “word” means to bash. For example, whitespace separates words. Hyphens (-) do not separate words, and neither to underscores (_).

!-prefix

This one is dangerous; proceed with caution.

• !! runs the last command again,
• !string runs the last command that starts with `string again.
• !$ runs the last word of the previous command.

Epilogue: compression

If you find files with the extension .tgz .tar.bz2, .tar.gz, never fear. These are your friends in the unix environment.

A tar file is an archive – that is, someone took a directory or a bunch of files, and stuck them together into one file for ease of transport. A gzipped or bzipped file is a compressed file; that is, someone used awesome compression algorithms to make a single file take up less space on disk. These strategies are frequently used together, leading to the file extensions seen above. Let’s look at what do to:

• “I have a .tar.gz, and I want to get what’s inside it”

    tar xzvf file.tar.gz
  

• “I have a folder and/or some files file1, directory3, etc. , and I want to make it into an archive:

    tar czvf file.tar.gz file1 file2 directory3 directory4
  

• “I want to know what xzvf and czvf mean”. Good question. -x means “extract” (i.e., from the archive). -z means “use gzip compression” -v means “be verbose; that is, tell me what files you’re working on compressing/extracting right now by printing their paths to stdout.” -f means “I’ll specify the file that you’re going to work with, and it’s coming up next.”