Downloading and installing software for this class¶
It is assumed that you are on a Unix-like machine (e.g Linux or Mac OS X). For some flavors of Unix it is easy to download and install some of the required packages using apt-get (see Installing software with apt-get (Debian or Ubuntu Linux)), or your system’s package manager.
If you must use a Windows PC, then you should download and install [VirtualBox] for Windows and then run the vm to provide a Linux environment.
If you are using a Mac and want to install the necessary software, you also need to install Xcode developer tools, which includes necessary compilers and make, for example.
Some of this software may already be available on your machine. The which command in Unix will tell you if a command is found on your search path, e.g.:
$ which mpif90
/opt/openmpi/bin/mpif90
tells me that when I type the mpif90 command it runs the program located in the file listed. Often executables are stored in directories named bin, which is short for binary, since they are often binary machine code files.
If which doesn’t print anything, or says something like:
$ which xyz
/usr/bin/which: no xyz in (/usr/bin:/usr/local/bin)
then the command cannot be found on the search path. So either the software is not installed or it has been installed in a directory that isn’t searched by the shell program (see Shells) when it tries to interpret your command. See PATH and other search paths for more information.
Individual packages¶
gfortran¶
GNU fortran compiler (see fortran).
You may already have this installed, try:
$ which gfortran
Open MPI¶
Message Passing Interface software for parallel computing (see MPI).
Some instructions for installing from source on a Mac can be found at here.
LAPack¶
Linear Algebra Package, a standard library of highly optimized linear algebra subroutines. LAPack depends on the BLAS (Basic Linear Algebra Subroutines); it is distributed with a reference BLAS implementation, but more highly optimized BLAS are available for most systems.
See http://www.netlib.org/lapack/
ScaLAPACK is a parallel version of LAPack. See: http://netlib.org/scalapack/
Installing software with apt-get (Debian or Ubuntu Linux)¶
On a recent Debian or Ubuntu Linux system, most of the software for this class can be installed through apt-get. To install, type the command:
$ sudo apt-get install PACKAGE
where the appropriate PACKAGE to install comes from the list below.
NOTE: You will only be able to do this on your own machine or a computer on which you have super user privileges to install software in the system files. (See sudo)
You can also install these packages using a graphical package manager such as Synaptic instead of apt-get.
| Software | Package |
|---|---|
| gfortran | gfortran |
| OpenMPI libraries | libopenmpi-dev |
| OpenMPI executables | openmpi-bin |
| LAPack | liblapack-dev |
| ScaLaPACK | libscalapack-mpi-dev |
Many of these packages depend on other packages; answer “yes” when apt-get asks you if you want to download them. Some of them may already be installed on your system, in which case apt-get will tell you that they are already installed and do nothing.
The script below can be used to install software in Ubuntu (or on a Ubuntu virtual machine running with VirtualBox:
# $/notes/install.sh # sudo apt-get update sudo apt-get upgrade sudo apt-get install gfortran sudo apt-get install openmpi-bin sudo apt-get install libopenmpi-dev sudo apt-get install liblapack-dev sudo apt-get install libscalapack-mpi-dev
For other versions of Linux, apt-get will not be available, and you will need to use the appropriate native package manager (e.g. rpm for Red Hat Linux). If you are using a new installation of Linux (say, on a virtual machine), you may want to install a text editor like gedit: sudo apt-get install gedit.
Installing software on Mac OS X¶
As noted above, you will first need to install Xcode developer tools. Then, download the gfortran tarball, gfortran-4.9-bin.tar.gz (40 MB, Mavericks or Yosemite). For more information, or to get files for earlier OS X versions, got to http://hpc.sourceforge.net. The rest of the installation process can be done from the terminal (go to Applications –> Untilities –> Terminal to open a terminal).
Installing gfortran
First, install XCode command-line tools:
$ xcode-select --install
Then, install/extract gfortran:
$ sudo tar -xvf gfortran-4.9-bin.tar.gz -C /
Now, typing:
$ which gfortran
should output:
/usr/local/bin/gfortran
Installing MPI:
$ curl http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.5.tar.gz -o openmpi-1.8.5.tar.gz
$ tar zxf openmpi-1.8.5.tar.gz
$ cd openmpi-1.8.5
$ ./configure --prefix=/opt/openmpi 2>&1 | tee config.out
[...lots of output...]
$ make -j 4 2>&1 | tee make.out
[...lots of output...]
$ sudo make install 2>&1 | tee install.out
[...lots of output...]
$ export PATH=/opt/openmpi/bin:$PATH
$ ompi_info
[...see output from newly-installed Open MPI...]
Now, typing:
$ which mpif90
should output:
/opt/openmpi/bin/mpif90
Lapack and Scalapack
Lapack is included with OS X, but scalapack is not. For scalapack:
$ curl http://www.netlib.org/scalapack/scalapack-2.0.2.tgz -o scalapack-2.0.2.tgz
$ tar zxf scalapack-2.0.2.tgz
$ cd scalapack-2.0.2
$ cp SLmake.inc.example SLmake.inc
$ make all
The final step will take a few minutes, but at the end you should have the scalapack library file, libscalapack.a in the directory.
Installing software for Windows¶
The author of these notes does not use windows, so please be aware that you may have to figure some things out for yourself. There are two options. The first, using cygwin, is easier, but will be mostly unsupported by the class instructor. The second is more complicated, but will give you a working linux virtual machine on your computer which you can use for many things outside of this class.
Cygwin The gfortran binary can be downloaded here. Openmpi packages can be found here. To obtain lapack and scalapack libraries, see http://icl.cs.utk.edu/lapack-for-windows/.
Virtual Machine The basic steps are:
- Download and install virtualbox
- Download XUbuntu (linux) operating system (~900mB)
- Create a XUbuntu virtual machine within virtual box using the XUbuntu download
- Run the XUbuntu vm, open a terminal, and install gfortran and openmpi using apt-get as described above: Installing software with apt-get (Debian or Ubuntu Linux).
Instructions for steps 1-3 can be found here. Overall, you will need about 6 gB on your hard drive.