Revision as of 17:15, 3 December 2014

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Installation Woes

• Python packages (ex: sympy)
• GNU Autotools + make-based process (ex: FFTW)
• Cmake: a developer-friendly (not user-friendly?) alternative (ex: cgal)
• Non-standard makes (ex: NAMD2 and NWChem)
• Tinkering with open-source
• The DL on Software Licenses
  • Apache, BSD, GPL, Microsoft, FDL, Creative Commons
  • The open-source that isn't: Canvas

The single most important idea for compiling and installing new software is to remember that the installation works for the developer's environment, and it will for you, too if your environment is setup correctly. Often times this is easier said than done.

1. Package Dependencies (pdftk depends on libgcj)
   • and versions of those packages - this is usually the worst part
2. Shell variables
   • PATH, CFLAGS, LDFLAGS, LD_LIBRARY_PATH
3. Compiler version
4. Machine architecture

Tips:

To find a package owning a file (on linux systems with rpm)

rpm -qf /usr/lib64/libfftw3.so.3

To find all files associated with a package

rpm -ql fftw-3.2.1-3.1.el6.x86_64

Example 1

Installing pdftk (developer Makefile)

mkdir ~/build && cd ~/build
wget https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk-2.02-src.zip

Unpacking the zip file can (and often does) clobber files in your current directory, so it's always safest to unpack it in a new directory:

mkdir pdftk && cd pdftk
unzip ../pdftk-2.02-src.zip
ls

In this case, pdftk was nice enough to put all their files in a subfolder, so we can get rid of the temp directory.

cd ..
mv pdftk/pdftk-2.02-src .
rmdir pdftk

If you read the license information, you'll note that pdftk is covered by a GPL copyright. This means you have the freedom to modify and re-distribute the source (but not to change the license). The GPL is sometimes called a 'copyleft', since it is a clever hack on copyright perpetrated by Richard Stallman, the founder of the GNU project.

Make is a small language that lists the shell commands required to 'make' the 'targets'. A make target can be anything, but usually is the name of an executable file (or a file at an intermediate step) that will be built during the compilation process. Pdftk has installation instructions on its website, which outline a make-based process commonly seen for development on small projects. pdftk is large-ish because the pdf file format can do a lot, but the build process is small because it is based on java. Some standard options to make are

make -f Makefile.Redhat -j 8 -C $PWD install

The '-j 8' flag tells make to run in parallel on 8 processors. The '-C' flag tells make what directory to run make from. Here, it's for illustration, since the default is to run in the current directory. The name 'install' is the target to build. It is not a real file, but instead just has a list of commands that copy the compiled program into the filesystem. The great thing about make is that it knows what order to make all the files in.

In this instance, make will build the executable, pdftk, but will not install it - since it tries to copy it into /usr/local/bin. You should read Makefile.Redhat to find the install target. You'll notice that it's not there, but at the bottom the Makefile includes Makefile.Base. Looking at that file, you will find the install target. It is run with a single line that installs (carefully copies) pdftk from the current directory into /usr/local/bin. make install will work if you change /usr/local/bin to $(HOME)/bin. You may also consider installing the manpage (pdftk.1 from the main pdftk directory).

cd ..
cp pdftk.1 $HOME/share/man/man1
export MANPATH=$MANPATH:$HOME/share/man

Example 2

Installing fftw (autotools)

A quick search turns up the main page for fftw, the Fastest Fourier Transform in the West.

mkdir ~/build && cd ~/build
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4.tar.gz

This is a tar (tape archive) that has been gzipped (usually given the endearing name 'tarball'). You can read the contents with

tar tzf fftw-3.3.4.tar.gz | less
tar xzf fftw-3.3.4.tar.gz

The first command lists the contents. It is really helpful to make sure that all the files in the tarball are in their own directory. Most tarballs should be packed this way. Ones that aren't will put files in your current directory, and may clobber other files you had there before.

cd fftw-3.3.4
less README

The second line is absolutely critical, since almost every package has some installation quirk that you won't know about until it's too late -- or until you read the instructions, either way. You'll notice this file says configure, make, make install. This means the package uses gnu autotools!

Autotools are a standard set of installation scripts that follow the general install commands above. The configure part is the most important, since it gives you a chance to put in details about your own environment. In addition to reading all install instructions, you should also run

./configure --help

This will give you a list of options that tell the compile process what compilers to use and where to find libraries and include files that the package may well depend on. The standard ones (CFLAGS, etc.) are shown in the graphic at the top of this page.

./configure --with-pic --enable-float --prefix=$HOME 

The second part of autotools is (sometimes GNU) make, covered above.

make -j4 install

Example 3

Installing gromacs (CMAKE)

Fourier Transforms

Read through the page on Fourier transforms.

The Monte Carlo Method

• Integrals of the form: <math>\int \frac{f(x)}{g(x)} g(x) dx</math>
• Computing pi
• Parallelizing with MPI4Py