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Installing Software

Installing Software

Dec 11, 2023

Overview

While users cannot add or update system software or libraries using tools that require root privileges such as yum, many software packages can be installed locally without needing to be a superuser. Frequently linux packages make use of the "configure, make, make install" method and an example of how to do this is shown under Example Installation below.

Contents

Contrib Installations

One option to build your own software on HPC is to use the "contrib" environment. This is essentially a way to build your own module that you maintain and can share with other users. To create a contrib space, send a request to HPC Consult who will create a contrib space for your group. To see and use contrib software, use:

module load contrib
module load group_name/software_name

It should be noted that to see, access, and build software, you will need to be on one of the cluster's compute nodes. These can be accessed using the command interactive. More details can be found in our SLURM documentation.

When installing software, users are invited to use the compilers and libraries available through the module system (see previous section of this guide), but that is not necessary. If a software package you wish to install requires a specific version of the MPICH2 libraries, FFTW libraries, or even GCC compilers, you can install those packages for yourself.

Example Installation

  • Software is not available on the login nodes. To install custom software, log into an interactive session.

  • For a typical Linux installation, the default settings may attempt to install files in system directories outside your directories. This is not permitted, so the installation process (specifically, the "configure" step) needs to be changed so that files are installed in a specified location.  There is frequently a --prefix=/path/to/software option.

 configure/make/make install

Here is a typical example of installing software on a Linux cluster: Installing GROMACS (molecular simulation software):

  1. Get the software
    I usually download a software package to my laptop, then transfer the downloaded package to my /home directory  for installation. Alternatively, if I have the http or ftp address for the package I need, I can transfer that package directly to my /home directory while logged in using the wget utility:

    Download the software
    wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz


  2. Unzip and unpack the "tarball"

    Unpack the archive
    tar -zxf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5

  3. Set up your environment for compiling the software.
    Here, to compile a parallel build of GROMACS, I need the MPICH2 libraries. Compiling GROMACS also requires some version of the GCC compilers and the FFTW libraries:

    Load dependencies
    module load gnu8/8.3.0 mpich/3.3.1 aocl-fftw/2.2

  4. Run the configure script.
    Typical Linux installations will make use of a script named configure that allows for customization. The --prefix option allows you to specify a custom install location. This allows you to run a make install without targeting a system location (which requires root privileges).

    More options should be described in your software's installation instructions. In this example, a few other options are also used, such as the choice of not installing a graphical interface (--without-x).

    configure
    ./configure --prefix=$HOME/gromacs/4.5.5 --disable-float --enable-mpi --without-x --disable-shared


  5. Run make to compile the source code
    Typical Linux installations involve the process of compiling the software so it will run with the particular hardware and software available. The make command uses a special file called Makefile to guide the process of compiling large numbers of source code files (instead of just compiling one or a few source code files).

    Compiling the software
    make


  6. Install the newly compiled software
    In this case, the executables, libraries, and other software files will be installed to the directory specified with the --prefix flag in step 4.

    Install the software
    make install


  7. Configure environment settings
    Now that the new software package has been installed, you can customize your environment to give you access to your new software automatically. This usually involves appending the location of the new software to your existing environment variables, such as: PATH, LD_LIBRARY_PATH, INCLUDE. You may also need to add new environment variables that are specific to your software package. The installation instructions should explain what needs to be done. If you add these to the hidden file ~/.bashrc in your account, the environment variables will automatically be set each time you log in.

    Configuring your environment
    module load gnu8/8.3.0 mpich/3.3.1 aocl-fftw/2.2
export PATH=/home/u1/galen/gromacs/4.5.5/bin:$PATH
export LD_LIBRARY_PATH=/home/u1/galen/gromacs/4.5.5/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/home/u1/galen/gromacs/4.5.5/lib:$LIBRARY_PATH
export C_INCLUDE_PATH=/home/u1/galen/gromacs/4.5.5/include:$C_INCLUDE_PATH
export CPLUS_INCLUDE_PATH=/home/u1/galen/gromacs/4.5.5/include:$CPLUS_INCLUDE_PATH
export MANPATH=/home/u1/galen/gromacs/4.5.5/share/man:$MANPATH
export MPI_HOME=/opt/mpich2/1.4
export FFTW_HOME=/opt/fftw/2.1.5-double
 cmake