Bash extract function

Extract function for bash. Put in .bashrc

function extract() # Handy Extract Program.
{
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
*.tar.gz) tar xvzf $1 ;;
*.bz2) bunzip2 $1 ;;
*.rar) unrar x $1 ;;
*.gz) gunzip $1 ;;
*.tar) tar xvf $1 ;;
*.tbz2) tar xvjf $1 ;;
*.tgz) tar xvzf $1 ;;
*.zip) unzip $1 ;;
*.Z) uncompress $1 ;;
*.7z) 7z x $1 ;;
*) echo "'$1' cannot be extracted via >extract<" ;;
esac
else
echo "'$1' is not a valid file"
fi
}

epstopdf

It's epstopdf joe not eps2pdf

Fixing backspace on edred vim

To fix the backspace key on the vim on edred add this to .vimrc

set backspace=indent,eol,start

latex figures

To get rid of strange behaviour in latex where it does weird things with figure numbers its has to be done in a strict order.

\begin{figure}
\begin{center}
\includegraphics{...}
\end{center}
\caption{...}
\label{...}
\end{figure}

I think caption can go above \begin{center} but it must be outside of the centre section

Gnuplot PDF+Latex files

To create a pdf file from gnuplot with latex text do the following:

In the plot use the terminal:

set terminal epslatex

Then convert the eps to a pdf file.

Include the figure using

\input{figure.tex}

Printing variables from gnuplot to a file

To output variables such as fitting parameters from gnuplot use.

set fit errorvariables # creates a_err type variables for fitting errors

set print "tmp.dat"

print a,a_err,b,b_err

Labeling figures in Latex

If labeling of figures has gone wrong in latex it's probably because the \label{} must be at the end of the figure block after the includegraphics and caption.

Compiling OpenMPI with Intel Compilers on Ubuntu

Compiling OpenMPI with Intel compilers can be a bit of a nuisance, and so the following seems to work with version 11.074 Intel Compilers, OpenMPI v 2.8.1 and Ubuntu 8.10:

1) Install The Intel Compilers with defaults
2) Put iccvars.sh and ifortvars.sh into /etc/profile.d, and comment out the lines referring to non 64 bit binaries
3) source /etc/profile
4) Unpack the OpenMPI
5) Run ./configure --with-fortran CXX=icc FC=ifort LIBS=-lstdc++
6) type LANG=C
7) make all
8) sudo make all install
9) sudo ldconfig
10) type mpiCC --showme to verify the compiler wrappers are working correctly

Awk Scripting, combining columns

If you have multiple files named filename.< a number > e.g. filename.0, filename.1, filename.2,filename.3 etc then you can take an average of multiple columns using awk as below:

you need to know how many files you have, in this num_files=16, and you need to know the total number of columns per file in this tot_num_cols=13. Here I wanted to average colums 1 and 4. Using the paste command which pastes a number of files to the screen side by side and piping to awk the script will output the average of columns 1 and 4 to a file called anewfile.txt

paste filename.* | awk 'BEGIN{num_col=4;num_files=16;timecol=1;tot_num_cols} {c=0; for (j=0;j < num_files;j++){c+=$(timecol+tot_num_cols*j)}}; s="0;" i="0;i < ="num_files;i++){s+="$(num_col+tot_num_cols*i)};" > | anewfile.txt

Bash number formatting

Use printf as in c. For zero padding add a 0 infront of the field length, eg: %06i

So to delete more files than rm can handle

for i in `seq 0 100`; do file=`printf "%06i" "$i"`; echo $file; done