Node Locked License, Singularity Container

Prerequisites

Installing Parabricks via the Singularity container installer requires the following:

  • A working Nvidia driver,

  • A working Singularity setup

  • Installer package, something similar to parabricks.tar.gz

You can refer to the section Installation Requirements for more details

Software Installation

This section assumes you have the installer package as parabricks.tar.gz either through the Trial Process or through the License Portal. For node locked licenses, you should have requested a license.bin from EnterpriseSupport@nvidia.com

# Extract the installation package.
$ tar -xzf parabricks.tar.gz

# Install the software.
$ sudo ./parabricks/installer.py --container singularity

# Verify your installation.
# This should display the parabricks version number:
$ pbrun version

Note

Installing the Singularity version of Parabricks differs from installing the Docker version in the third step listed above--specifically in the addition of the --container singularity option when running ./parabricks/installer.py

During the installation you'll be asked

  1. To accept the end user license agreement.

  2. If you want to create a symbolic link from the Parabricks installation to /usr/bin/pbrun (requires sudo access).

  3. If you want to install the Ampere version or the non-Ampere version.

To check if your system has Ampere GPUs, run the following:

nvidia-smi --query-gpu=name --format=csv,noheader

Any GPU labeled with the first letter A (e.g. 'Tesla A100', 'Tesla A40') is an Ampere GPU.

Note

If your machine has more GPUs than you have licenses, you will need to specify which, and how many, GPUs to use. For example, use the following flags to select only the first two GPUs:

CUDA_VISIBLE_DEVICES="0,1" pbrun [command and inputs]  --num-gpus 2

After installation, the pbrun command will start any tool in the Parabricks software suite. Answering "yes" to the second question (about creating a symbolic link) will make pbrun available for system-wide access. Otherwise, you can access pbrun from your local installation directory, which is /opt/parabricks/pbrun by default.

Installing without sudo access

Clara Parabricks can be built on one machine where you have sudo access and then copied to a second machine where you do not have sudo access.

  1. Log in to a machine where you have sudo access and Singularity 3.0 or higher.

  2. Download the software as described above.

  3. Unzip the package.

    $ tar -xvzf parabricks.tar.gz
    
  4. Do a local installation.

    $ mkdir localdir
    $ sudo ./parabricks/installer.py --install-location localdir --container singularity
    
  5. Everything will be installed in the localdir/parabricks folder. Tar this folder....

    $ cd localdir
    $ tar -cvzf parabricks_install.tar.gz parabricks
    
  6. ...and copy it to the computer where you will be using Clara Parabricks. This computer must have Singularity v3.x installed.

  7. Untar the parabricks_install.tar.gz file in the desired installation directory <INSTALL_DIR>.

    $ cd <INSTALL_DIR>
    $ tar -xvzf parabricks_install.tar.gz