Linux util 5

Whew!! My 5th linux util post...

1) Assuming you have SLURM basics, (well, I am just a beginner, so posting this very simple solution for the problem I faced), to force salloc to release the job allocation, find the process of that command using

   a) ps ax|grep $your_name|grep salloc

   If you have reserved resources by separate salloc command (without invoking the job using srun), then
   b) kill -9 $pid

Or, If you have both salloc and srun in a single command,
  c) kill -s HUP $pid

To see the signal identification for all the signals, use

man 7 signal

Just 'man signal' will take you to the C programming API for signaling.

2) Here is a simple way to find the number of words in each line of a file using awk:

awk '$0="line"NR": "NF' filename

Guess I got this tip again from SO, but this solution was not the accepted one.

3) If you pick only few lines output from make command to selectively fix the errors or warnings, (assuming you are in bash shell):


 make -f Makefile clean; make -f Makefile 2 > &1 |grep 'error'

4) To identify the shell you are working on currently:
 ps -p $$
From what I understand from the man pages, the -p option looks for pid list and $$ get the first process which is the shell itself. This prints the pid of the shell, terminal id etc. If you would rather want a concise output, then type:
echo $0 
This was important to me change between bash and tcsh frequently when working on HPC machines of PNNL. The default login shell was tcsh, but I had do compilation and execution on bash. Most importantly, echo $SHELL did not help.

Linux Util 2

1) You can try to place a tab between the quotes if you first press "<CTR> v" then the "<TAB>" key:

cut -f1 -d'<ctrl>v <tab>' filename

This way even <tab> character can also made as delimiter in shell scripting.

2) If you have a file where first column is list of years with author names against each year, to find the count of papers in each year:

cut -f1 -d' ' fname |uniq -c

3) To find all empty lines in the standard input:
grep ^$  or  grep -v .   

4) Hmm, long live blogging: I was looking for grep command to search for a text recursively from a given directory and this blogger helped:

http://www.geekality.net/2011/04/12/unix-recursive-search-for-text-in-files/

grep -rl "your_text"

5 ) To redirect the output of time (real, sys, usr) command onto redirect_file, instead of console.

(time your_command your_args) 2>> redirect_file

6) To search for a file's contents in another file:

grep -f searchfile tobesearchedfile -n --color=auto

Can remove the color flag. Got this color tip from Nixcraft

7) To list only the duplicate lines of a file:

uniq -d filename

8) To unzip a file that is only compressed with bz2 use

bunzip2 filename.bz2

9) To unzip things thar are compressed with .tar.bz2 use

tar -xvjpf filename.tar.bz2

I got the tips 8 and 9 from linuxquestions.org

10) Many a times, to know if the server I am working in is serving a lot of users, I type w in the shell prompt. This is useful if you are going to run a resource-greedy process. Now, if you are interested to write/talk to them, you may want to know their full name. The following command helps to get their full names from an administrative database:

getent passwd "jey"|cut -d':' -f5

If you are curious, an encouraging fact is man page of getent is small :) !!
Happy linuxing!!

11) Wow, after about 5 months (it's Jan 8, 2013 today), I am glad to be updating my blog. Yup, it also means I have failed to keep track of my new findings in web in this database. Anyways, the following tip was something very important to me because I realized I am spending too much time 'Alt+tab'ing to find the window I want to work in while working from home, logging to my office machine (essentially all are xterms).

To change the title of the xterm window to indicate something useful (in this example, your_string):
unset PROMPT_COMMAND
echo -ne "\033]0;your_string\007"

I had to call unset first because by default in my .bashrc file, PROMPT_COMMAND stores the username, machine and current working directory. It is important to observe the combination of characters around "your_string" and follow them strictly.