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Users are encouraged to install their own software (applications, application dependencies, libraries, scripts, etc.) in their accounts.

Another option is to use the "unsupported" environment on Ocelote, or "contrib" on Puma.  The advantage is that you can share the software built here with other users. This is created by sending a request to HPC Consult who will create an unsupported / contrib group in which you can build software and add users.

Using "unsupported / contrib" software is done with:
module load unsupported or module load contrib
module load softwareName 

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.

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.


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:
     
    wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz
  2. Unzip and unpack the "tarball"
      
    tar -zxf gromacs-4.5.5.tar.gz
  3. Read the instructions for installing the software
       cd gromacs-4.5.5
       more README
  4. Here, the README file is a text file containing information and instructions, and it might have a different name like INSTALL or SETUP. Alternatively, the installation instruction may be posted on the website from which I downloaded the software.
  5. Setup your environment for compiling the software
       module add gcc/4.4 mpich2/1.4 fftw/2.1.5-double
  6. 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. Now I'm ready to begin compiling my software.
  7. Run the configure script
    Typical Linux installations will make use of a script named "configure" that allows me to specify details about how I want the installation to proceed. This step should be described in your software's installation instructions.
       ./configure --prefix=/home/u1/galen/gromacs/4.5.5 --disable-float --enable-mpi --without-x --disable-shared
    Here, I'm specifying that I want my software to be installed in my /home directory (specifically, /home/u1/galen/gromacs/4.5.5).
    Also, I'm specifying a few other options such as the choice of not installing a graphical interface (--without-x), which may not be used on the cluster.
  8. 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).
     
    make
  9. Install the newly compiled software
      make install
  10. At this point, the new software will be installed in my specified /home/u1/galen/gromacs/4.5.5 directory.
  11. Configure environment settings
    Now that I've installed a new software package, I can customize my environment so I'll be able to access the new software automatically. This usually involves appending the location of the new software to my existing PATH, LD_LIBRARY_PATH, INCLUDE, or other environment variables. Or I may need to add new environment variables. The installation instructions for my software package should explain what needs to be done. Here are a few examples of the syntax I might use in my /home/galen/.bashrc file, or in my PBS job script, so I can use my newly installed software:
       

       module add gcc/4.4 mpich2/1.4 fftw/2.1.5-double
       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


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