Node Locked License, Singularity Container
This Version of Parabricks is no longer available: This documentation page is for reference only. Versions 3.8 and earlier have been deprecated. We encourage you to use the latest version, for which no license is required. If you need access to this version of Parabricks to continue an ongoing project, please contact the Parabricks team at email@example.com.
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
This section assumes you have the installer package as parabricks.tar.gz 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
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
During the installation you'll be asked
To accept the end user license agreement.
If you want to create a symbolic link from the Parabricks installation to
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.
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
available for system-wide access. Otherwise, you can access
pbrun from your local
installation directory, which is
/opt/parabricks/pbrun by default.
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
Log in to a machine where you have
sudoaccess and Singularity 3.0 or higher.
Download the software as described above.
Unzip the package.
$ tar -xvzf parabricks.tar.gz
Do a local installation.
$ mkdir localdir $ sudo ./parabricks/installer.py --install-location localdir --container singularity
Everything will be installed in the localdir/parabricks folder. Tar this folder....
$ cd localdir $ tar -cvzf parabricks_install.tar.gz parabricks
...and copy it to the computer where you will be using Clara Parabricks. This computer must have Singularity v3.x installed.
Untar the parabricks_install.tar.gz file in the desired installation directory <INSTALL_DIR>.
$ cd <INSTALL_DIR> $ tar -xvzf parabricks_install.tar.gz