The MPI environment is ready. Time to compile a parallel code. Compiling MPI code involves calling of a wrapper script "mpif90". This script launches ordinary Fortran compiler (gfortran), but also links the code with MPI libraries.

As an example, This name of the code can be anything of course.

mpif90 <source> -o <executable>

mpif90 source_code.F90 -o executable_code

This command will compile a Fortran source code source_code.F90 into an executable file called executable_file.

To run a parallel code on a number of processors write:

mpiexec -n <proc_number> <executable>

mpiexec -n 2 ./executable_file

In general you should keep your program source code in your home directory because it will be backed up every day. Designate a different output directory to e.g.

/local/<user_name>/<prog_name>/

/local/maxim/fdtd/

Specifying a local output directory will force your code to use the hard drive of a certain machine only. Using the home directory for output will synchronising the data files between all machines of the cluster and considerably slow down other people's computers. Please refrain from doing this.

The IBM Redbook on "Practical MPI Programming" is a recommended reading.

The most important Chapters are:

1: Introduction to Parallel Programming	pp. 1-10
2: Basic Concepts of MPI	pp. 11-40
Appendix B: Frequently Used MPI Subroutines Illustrated	pp. 161-206

Although the environment setting and program compilation are strongly site-dependent, you can get a flavour of parallel programming by reading the following information:

http://www.osc.edu/supercomputing/training/

https://computing.llnl.gov/tutorials/mpi/

http://fats-raid.ldeo.columbia.edu/pages/parallel_programming.html

http://www.hpcwire.com/

http://www.insidehpc.com/

http://www.clustermonkey.net/

Presentation is the activity to give(present) the audience your knowledge as a gift, not to speak about your idea which is speech.

1. Attract the audience at the first page of the slide by showing the aim and the outline of the talk
2. Keep your eye contact with the audience confidently
3. Use main and second title on each slide
4. Smile to make the mood relaxed
5. Slow down your talk so that the audience have time to guess what happens next
6. Make your conclusion concise

Technical report writing skills

1. Attract readers with the title of your report.
2. Make the structure of your report crystal clear.
3. Use as figures and tables as much as possible to support understanding of readers.
4. Produce the logical and accurate sentenses (not spoken English).
5. Check your English using ispell and plagiarism checker .
6. Conclude your report with concise statements.

LaTeX

The basic guideline on the technical report writing and The best method for presentation of research results are very useful stuff to read before you gain good amount of experience in writing technical report. Please check the marking schemes thoroughly prior to your writing. Prior to present your manuscript to me, please go through a check list for your manuscript preparation .

You do not have to worry about the formatting as LaTex does the formatting based on your style file such as muthesis.cls.

An article on Wikipedia gives a short introduction on LaTeX — a document markup language extensively used in a scientific domain.

Wikipedia also holds an entire LaTeX textbook which you can browse by topics.

There's a University LaTeX users list. If you're interested, send an email from your University email account to LISTSERV@listserv.manchester.ac.uk with the body text "subscribe latex-users".

The referencing is one of the very important part of your documentation. Please use the reference abbreviation based on List of IEEE Transactions and IEEE Editorial Style Manual.

Movie can be included in LaTeX beamer as follows:

1. Include the lines
   \mode<article>{ \usepackage{fullpage,hyperref,flashmovie} }
\usepackage{media9}
   in your latex source code
2. Copy
   /software/sl6.3/noarch-software/atbegshi.sty
/software/sl6.3/noarch-software/infwarerr.sty
/software/sl6.3/noarch-software/ltxcmds.sty
   into your directory which has your slide latex file exists
3. Convert your images to avi format via
   convert *.ppm %03d.png
ffmpeg -f image2 -r 8 -i %03d.png input.avi
4. Convert your movie to swf format via ffmpeg -i input.avi -r 6000 output.swf
The value of 6000 can be changed depending on the desired speed of your movie (the higher the value, the faster the movie).
5. Call the movie like
   \begin{frame}{1D FDTD Simulation}
\begin{center}
\includemedia[activate=onclick, width=\linewidth,height=0.6\linewidth]{}{wave.swf}
\end{center}
\end{frame}
   inside your Latex source code (see Media 9 Package )
6. Compile the latex file as usual using pdflatexfull
7. View the pdf file using acroread which has to be version 9.4.1 under Unix/Linux. You can copy the template of this type of presentation from the cluster /software/FDTDstandard/latexslidemovie
8. In order to produce the movie, copy files
   /software/FDTDstandard/TadashiMursoftMPI/output_FDTD-2d-xy-3-*.f90
/software/FDTDstandard/TadashiMursoftMPI/output_FDTD-2d-yz-3-*.f90
/software/FDTDstandard/TadashiMursoftMPI/output_FDTD-2d-xz-3-*.f90
/software/FDTDstandard/TadashiMursoftMPI/qualitymovieshell
/software/FDTDstandard/TadashiMursoftMPI/movieshell
/software/FDTDstandard/TadashiMursoftMPI/showshell
/software/FDTDstandard/TadashiMursoftMPI/pgm2ppm.f
   into the directory of your FDTD code.
   qualitymovieshell is the 2D image movie production and it needs pgm2ppm which is from pgm2ppm.f (gfortran -O4 -o pgm2ppm pgm2ppm.f)
   movieshell is the low-quality but quick movie production in 2D.
   showshell is the quick movie production in 1D.
9. If you need to produce a movie in gif format, just run convert -resize 200x400 -delay 0.2 *.ppm test.gif

To BSc and MSc Students

Practical skills such as the operating system, programming and documentation language knowledge are not going to be forced by me unless your work has a significant impact on the mainstream of our research.

In this case, you can learn Unix, Fortran, LaTeX and shell-scripting including the command-line utilities as awk, sed, tgif and gnuplot independently.

If you import some image into tgif environment, what you need to do to produce a pdf file is

1. In tgif environment,file -> print/export format->select EPSI
2. file -> print
3. In a x-terminal, epstopdf something.eps