Latex tips 1

So, I am starting a new post for Latex related findings. My second post in 2014, thanks to getting prep-ed for KDD2014. I am surprised I have missed to update this blog on my Latex journey.

Here is an awesome tool to find a symbol in Latex:

Detexify

Linux Util 6

I inadvertently deleted the previous contents of this post. Blogger sucks :( would not allow me to revert the contents. I lost one of my precious search on the nmap command.

1) To add a column of numbers and print the sum:
 
awk '{sum += $2} END {print sum}' temp 

2) To list the contents of a local directory when inside a ftp connection:

!ls

In words, exclamatory sign followed by the actual command.

3) If you are transferring a lot of files through mput or mget and do not have the patience to hit the key 'y', then while opening the ftp connection:

ftp -i hostname

Interestingly, I would have thought -i would enable interactive mode, here is just the reverse.

4) If you have to convert from Unix time stamp to human-readable date form and vice versa, the following helps:

date -d @915149280       (to get readable date format from epoch seconds)

date +%s -d"Thu Nov 1 12:50:00 2013"         (to get the unix timestamp in seconds from normal date format)

I literally stumbled upon the second command while reading a related question and its answer from SO. This answer was both simple and complicated in its own way. I thought I am better with vim search and replace. Well, I thought wrong. So, here is the next tip. Stack Overflow rocks!!

5) If you have text file with full human-readable date string sitting between the columns, then use vim to replace them all to epoch time using the following search string.

An example line looks like this:
Jey tty8 Thu Nov 1 12:50:57 2012 - Thu Nov 1 12:51:21 2012 (00:00)

Search command (in escape mode in vim):
:%s/\v\w+\s\w+\s\d+\s\d+:\d+:\d+\s\d+/\=system('date +%s -d"'.submatch(0).'" | tr -d "\n"')/g

After replacing:
(Jey tty8 1351788657 - 1351788681 (00:00)

As you can see, after the 'system' word, sits the command I explained in point 4 above. I learnt a lot of new things from this search regular expression.
a) use of the submatch(0): this matches what you went looking for in the first half of the expression
b) tr is used for translation. In this case, it is used to delete the trailing "\n" that comes with executing the system command
c) \s is for matching a single space. What was surprising was the "+" symbol after the characters 'w' and 'd'. Without them, the command does not work.

Grace Hopper Conference

This is going to be a Life. Changing. Experience. Can't wait any more!!!

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 4

Hmm, I had to open this new post because I cannot have more than 20 tags for a post.

1) June 14, 2013: Unresponsive system administrator, connection speed is slow and I am sitting in my PNNL intern office, not knowing how to see pdf files created using pdflatex in Natty - this is for my first ever paper from my internship. 

Home directory based xpdf installation in Natty failed because of some missing software or dependencies - only admin could fix this. After losing hope here, today I tried my luck with evince, a medium-weight software, but definitely lighter than acroread, in Google for solutions to
"cannot parse arguments, cannot open display" problem.

And Bingo, thanks to StackExchange, all I had to do was to copy the evince binary from global directory to my home bin directory and set the alias for evince in bashrc. Phew!!! Wish I had known this before. Long live user Gilles!! He answered his own question, incidentally. A proper fix for this could be done only by the admin, apparently and well, then in my case, I have to wait indefinitely for this.


My months long wait is finally over :). Is it not good that we have something called home directory in linux?


2) About 8 years back (around 2006, 2007, way long back, huh), firefox used to save the bookmarks automatically to a file called bookmarks.html, that I  used to just copy to the desired location, all in the command line itself. Did not realize this has changed with the recent versions. Now, I am looking for one url (Aeolus/ganglia, specifically) available in my office natty to my PNNL box, but I find my bookmarks.html file (at ~/.mozilla/firefox/profilename/) is actually way smaller than the number of bookmarks I find in my browser. Thanks to MozillaZine, I understood that the default behavior is not to save the bookmarks and that you have to edit the config file to force firefox to do that. Here is what I did:

• find the prefs.js file in .mozilla directory (should be available in the same location as your other profile specific files). The file header says you are not to edit the file, but I tried and it worked :)
• type the following as the last line of that file:
• user_pref("browser.bookmarks.autoExportHTML", true);

• save it. Reopen firefox and close it. This will update the local files.
• Now, open the bookmarks.html file and you will find all your saved bookmarks.

Some things to note:

• Though you might have typed the 'user_pref' line towards the end, after the open-close of firefox, you will find that line sitting in a different place.

• Please follow the instructions at the header of the file prefs.js and the mozilla's about:config page, if you are not comfortable editing the .js file directly.

3) I got a coupon from Quiznos for a free small sub and I didn't expect the machine I was given at PNNL will not have the option of selecting an area of the window to do screenshot. Here is what I did to print only the coupon (remember, my entire yahoo account screen was taken as screenshot).

•  Open the image in gimp and note the pixel information of the top, left and bottom, right corners. (Just hover your mouse to these places and you will see the pixel information in the bottom left corner in gimp changing.) Let us say you got, x1, y1 for top left and x2, y2 for bottom right.
• Calculate the width and height of the image from this information (subtract the smaller left value with larger left value and right with right). x2-x1 is the width, y2-y1 is the height.
• mogrify -crop widthxheight+x1+y1 imagename.png

That's all.....

Note the letter 'x' between the width and height values, it is not '*', the asterisk. Warning: the original image will be modified. Image quality was not modified at all.

Thanks to the stackoverflow question for this.

Linux Util 3

1) To kill all processes of a process tree, say a bunch of  child processes spawned by a parent process (note that all the child processes have pids greater than that of parent's):

kill -9 -(ppid)

where ppid stands for parent pid. (just a negation symbol before the parent process id)

Another way to find the parent id (is same as process group id):

ps -eo "%p %r %c %a"
 
stackoverflow-page helped to solve this problem.

2) If you work by logging to your office machine (Linux server) from windows client machine using NoMachine (NX), and when you open lot of xterms, it is oftentimes confusing what each xterm window corresponding based just on the title of it. Just follow these steps to get new informative title (but this is active only for this session of your login)

unset PROMPT_COMMAND (assuming you have this env variable set in your .bashrc)
echo -ne "\033]0;title\007"
It is important to blindly follow the characters and their sequence in the echo command. Obviously, they mean something, but to keep the brevity, I am refraining from giving the explanation here.

3) If you want to do copy/paste operation in xterm, 

   a) highlight the text using mouse
   b) use middle button/scroll wheel of mouse to paste or
   c)  shift+insert to paste or when there is no middle button,or
   d) simultaneously click both mouse buttons to emulate middle-button click

Thanks to Ubuntu Forums for this help. 

4) All along I have been using pdftops - psselect - ps2pdf combination to select pages from a pdf document, but Today (Jan 23, 2013) I learnt about pdftk from
LinuxJournal to select pages from pdf document directly without converting to ps first. How nice!!

pdftk A=100p-inputfile.pdf cat A22-36 output outfile_p22-p36.pdf  

Input file is 100p-inputfile.pdf. Though the name sounds confusing, there is no need to prefix the name with 100p (100 pages).  It is just for this particular example. This command selects pages from 22 to 36 and creates an output file with just those pages.

5) April 17, 2013: Found this tip while wanting to put all docx files of submitted student homeworks in one directory to upload to google drive and open them there in order not to miss pictures or other openoffice incompatible things.
Thanks to Nixcraft I could do this and this is the first time I really found a way to use xargs command.

find . -name "*.docx" -print0 | xargs -0 -I file mv file onlydocs/


6)  To sync a local directory to a remote directory:

rsync -r -a -v -e "ssh -l yourname" local/directory/path remote.machine.address:remote/directory/path

You will be prompted to enter the password to the remote machine. If all else is correct, this should sync the files. Thanks to Nixcraft for this tip.

More python

Well, in less than one day, I came to know about two important python based software systems:

1) scikit-learn : thanks to my surfing, profile creation and eventual posting of a question in Stack-Overflow, I got to know this nice tool when I was trying hard for better python based ML tools.
2) Cython came as a surprise when I was reading about the efficiency of graph algorithms in Networkx. So, there is a way out if my experiments are going to take lot of time, which I am expecting to happen. Hopefully I should have time to fiddle with Cython.