Installing binary applications

This tutorial is done on Puhti, which requires that:

💬 In some cases software developers offer ready-made binary versions of their software.

  • If the binary version runs, you don’t need to compile the software yourself.

☝🏻 It should be noted that ready binary versions are typically not optimized for CSC supercomputers.

  • The performance difference will depend on the code and on how the application was compiled.
  • Often the difference is just a few percent, but in some cases it can be more substantial.

‼️ Especially all MPI codes need to be compiled on the machine they will be run on to ensure correct operation.

Make the installation in your own folder in the /projappl directory of your project

  1. Move to the /projappl directory of your project:

    cd /projappl/<project>   # replace <project> with your CSC project, e.g. project_2001234

  2. If not done already, create your own folder under your project’s /projappl directory:

    mkdir -p $USER

  3. Move to your folder:

    cd $USER

Example: Installing the GCTA software

💬 In this example we’ll install the binary release of the GCTA software.

  1. Go to the GCTA download page.
  2. Identify the Linux version.
    • If several Linux versions are offered, try to find one with “x86” in the name.
    • If versions are offered by Linux distribution, try first the versions made for CentOS or RedHat if present.
    • Sometimes you may have to try different versions to find one that works.

  3. Here is the link for the Linux version. Download the .zip file by running:

    wget https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.4-linux-kernel-3-x86_64.zip

  4. Unzip the file:

    unzip gcta-1.94.4-linux-kernel-3-x86_64.zip
  5. The software is now ready to use, but you will have to tell the computer where to find it.

  6. Trying just the following will result in a command not found error because you are not accessing the right folder yet.

    gcta64

  7. Try instead:

    gcta-1.94.4-linux-kernel-3-x86_64/gcta64

  8. Or:

    cd gcta-1.94.4-linux-kernel-3-x86_64
./gcta64
  9. The result shows that the software runs.
    • The error message is just about missing arguments, which is normal.

    💡 Instead of providing the full path in the command line, you can also add the application to your $PATH.

  10. Move to ./gcta-1.94.4-linux-kernel-3-x86_64 if not there yet.

  11. Add the current working directory to $PATH:

    export PATH=$PWD:$PATH

  12. You can now run the program from any directory simply with:

    gcta64

Some notes

💡 When adding paths to $PATH, always remember to append the current $PATH, otherwise some of your normal shell commands etc. will stop working.

☝🏻 To add paths automatically, you can add the export command to your $HOME/.bashrc file. Instead of $PWD, use the full path:

export PATH=/projappl/<project>/$USER/gcta-1.94.4-linux-kernel-3-x86_64:$PATH   # replace <project> with your CSC project, e.g. project_2001234

‼️ If you make changes to your environment (e.g. edit .bashrc), it is possible that there will be conflicts with applications pre-installed by CSC.

💭 If you encounter problems after modifying your environment, it is possible to restore it to the default state permanently or temporarily using the csc-env command.