screen

Ever lost a terminal which had an active job running? Ever wanted to check in on what you'd been doing from home *and* wanted or needed the session history as well?

'screen' is your friend. If you're starting work that's important or that you may want to check from another machine it's a real time-saver. Have a look at the man page for more details than you can shake a stick at.

I've only been using it for a little while, so the only caveat I've found so far is that I have to remember to give the sessions a reasonable name before I start them. Otherwise, if you've got a lot of sessions, it's a time waster trying to find the right one. The '-t' flag sets the title for the default shell; more importantly the '-S' flag sets the session title. I've been using the same string for both (will probably set up an alias to deal with the duplication soon).

e.g.

shell1> screen -t data_loading -S data_loading
shell2> screen -ls
There are screens on:
        21802.data_loading    (Attached)
        20237.pts-10.hamilton   (Attached)
        1376.variance_analysis  (Attached)
        6639.pts-8.hamilton     (Attached)
        9881.cluster_jobs        (Attached)
5 Sockets in /var/run/screen/S-paul.

You can see from the above listing that there are 5 sessions (all currently attached). There are two listings there with no session title and I have no idea what I'm doing in them... but for the other three it's obvious (at least to me).

Code formatting for blogger

This post is very out of date now - I recommend using GitHub and Gists for adding code to blog posts.

... older post below ...
I've been meaning to look into this for a while. I'd like to be able to insert nicely formatted code into posts.

I found the follwing blog post - getting-code-formatting-with-syntax-highlighting-to-work-on-blogger and figured I'd give it a try.

Unfortunately following the instructions in the above post didn't work for me and I had to waste some time on the project site to find out what to do. This post on puffyandmishu was very helpful. I ended up with the following code in my blogger template:

1. In the <head> tag:

<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shCore.js'/>  
<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shBrushCpp.js'/>
<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shBrushBash.js'/>  
<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shBrushJava.js'/>
<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shBrushSql.js'/>
<script language='javascript' src='http://alexgorbatchev.com/pub/sh/current/scripts/shBrushPerl.js'/>
<link href='http://alexgorbatchev.com/pub/sh/current/styles/shCore.css' rel='stylesheet' type='text/css'/>
<link href='http://alexgorbatchev.com/pub/sh/current/styles/shThemeDefault.css' rel='stylesheet' type='text/css'/>

2. at the bottom of the <body> tag:

<script language='javascript'>  
SyntaxHighlighter.config.bloggerMode = true;
SyntaxHighlighter.all()  
</script>  

Let's test it out:

C - <pre class="brush:c">

int main(void)
{
    uint8_t i = 0;
    char c = 'a';
    while(1)
    {
        i++;
    }
}

Bash - <pre class="brush:bash">

for i in `ls *.c`;
  do echo $i;
done

Sql - <pre class="brush:sql">

SELECT name FROM mydb.test_table WHERE id IN (1,2,3,4,5);
INSERT INTO mydb.test_table VALUES(1) WHERE name = "test";

Java - <pre class="brush:java">

private static final class MyClass extends YourClass implements Cloneable
{
    public int mMyInt = 145;
    private String mString = "blarg";
    protected double mDouble = 23.45;

    public void main(String[] pArgs) throws Exception
    {
        System.out.println("Hi there");
    }
}

Perl - <pre class="brush:perl">

use warnings;
use strict;

my $i = 10;
for my $j (0 .. $i)
{
    print "This is line $j.  How lovely!\n";
}
warn "this does nothing.";

Line wrapping off <pre class="brush: plain; wrap-lines: false">

This is an example of a long line that shouldn't wrap.  Dwi eisio ddweud rhiwbeth yn Cymraeg ond dwi wedi anghofio popeth.  How long can we make these bars?

Now lets try it with Perl.

perl -F'\t' -lane 'print if $h{$F[0]}++;END{print "$_\t$h{$_}" for keys %h}' averyververververlongfilename.tsv

AVR delay_ms

When programming the AVR uC you have to remember that the delay_ms and delay_us functions will tie in the whole floating point library unless they are passed constants. This will always make the code too bloated to fit in anything less that 3K. So, it's right out for the ATtiny13 (1K Flash memory). I've been bitten by this twice now and the incidences were far enough appart that it took me 45 mins the second time to trace what was going on...

I was trying this:

delay_ms(delay);
if(i==0)
delay--;

but should have been increasing/decreasing the delay time by wrapping the delay call in a loop of variable length instead.

Legends in R plots

I've just spent about 45 mins trying to get a decent results plot from R. I wanted to include a legend for clarity and this gave me some trouble. It turns out the co-ordinate system was using values from the x and y plot rather than pixels... weird. Happily, for simple plots, there's an easy way to position the legend. From the R man page:

The location may also be specified by setting 'x' to a single
keyword from the list '"bottomright"', '"bottom"', '"bottomleft"',
'"left"', '"topleft"', '"top"', '"topright"', '"right"' and
'"center"'. This places the legend on the inside of the plot frame
at the given location.

So, I ended up with something like this:

R --vanilla --slave <<<"d=read.table('data1.csv', sep=',', header=F);e=read.table('data2.csv', header=F, sep=',');png('results.png');dh=hist(d\$V2, plot=F);eh=hist(e\$V2, plot=F);xlim=range(dh\$mids, eh\$mids);ylim=range(dh\$counts, eh\$counts);plot(dh, main='', xlab='value', col='orange', xlim=xlim, ylim=ylim);plot(eh, col='lightblue', add=T);legend('topright', legend=c('label1', 'label2'), fill=c('orange', 'lightblue'));q()"

Pre-calculating the range for the x and y axes (using the range operators) prevents you from cutting off data from one of the plots.

MySQL bash shell one-liners

This is a useful thing to know if you're ever trying to use data in files to grab data from a MySQL database: You can feed in SQL query strings to the mysql client in the bash/shell standard way:

bash> mysql -u paul -h myhost -pmypass test_paul <<< "SELECT id from a_table where a_name='boo-yah';" 

Which means that you can put this in a shell script (or Perl script, or whatever). For example, to print out the addresses associated with a set of names:

for name in `cat names.list`;
   do address=`mysql -u paul -h myhost -pmypass test_paul <<< "SELECT address from a_table where a_name='$name';"`;     echo "$name -> $address";
   done

Perl subroutine references

I just found this useful for generating a dispatch/lookup table. You can create a hash table with the values being references to subroutines.

Here's a simple example:

> perl -le '$a = sub { 5 * $_[0]};print &{$a}(23);'
> 115

A better example is to use this as a look-up table. Here's another simple example:

%table = (
 "+" => sub { $_[0] + $_[1] },
 "-" => sub { $_[0] - $_[1] },
 "*" => sub { $_[0] * $_[1] },
 "/" => sub { $_[0] / $_[1] },
);

print &{$table{"+"}}(12,24), "\n";
print &{$table{"-"}}(24,12)), "\n";

This would output 36 and 12 respectively. This is very handy for more complex processing and parsing (which is what I'm using it for).

Command line R

Sometimes I just want to print out a histogram from a file, or create a simple summary of some numeric data. It's good to be able to just bash off an R script from the command line to do this for you.

There are a couple of easy ways to invoke R to run in 'batch' mode (i.e. non-interactive):
1. R CMD BATCH <scriptname>
2. R --vanilla --slave <scriptname>

For 1. the output is saved in a file named <scriptname>.Rout, in 2. the output comes to STDOUT - which, for me, is much more useful.

Also, you can use the standard shell 'tricks' to create quick scripts without having to save a script file:

e.g.

1. Create a numeric summary of the input data (in this case for a file with the format - "name,value"):

R --vanilla --slave <<< "d=read.table('data.scores', sep=',');summary(d);q()"
V1
Min. :1.333
1st Qu.:4.037
Median :4.651
Mean :4.634
3rd Qu.:5.282
Max. :8.000


2. Create a histogram for the data and save to a PNG (don't forget to escape any special shell characters).

R --vanilla --slave <<< "d=read.table('data.scores', sep=',');png('data.png');hist(d\$V1);q()"