site_installation

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Installing SBGrid Software

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SBGrid installation

The SBGrid software collection can be installed on Linux and macOS computers from laptops to compute clusters. Often, in a shared computing environment, it is desirable to install the entire collection as a managed, self-updating software stack. We refer to this installation mode as a site installation. Site installations include all the software licensed by a site and can be updated automatically.

Configuration

The SBGrid Software Suite can be installed on a single computer at your site and shared via a network filesystem (NFS) with the workstations or compute nodes on your network. We refer to this computer as the site "master" server.

The master server will require at least 3Tb of free disk space, case-sensitive file system recommended. This machine and must run some variety of UNIX (Linux, macOS, FreeBSD, etc). The installation application will download the software branches and titles you select, and install a cron job that will run regularly to check for updates.

Software installation and updates are initiated from your site and initiate downloads from our servers. External access is not required to install the software and we do not require access to your computers. The HTTPS protocal is used to query our API to check for updates, and HTTPS or rsync is used to download the software. Thus outbound HTTPS is required.

The sbgrid-cli utility is used to install and manage an installation and is available for Linux and macOS. We are also using this method successfully on FreeBSD servers. See the sbgrid-cli recommened installation page for more information

NFS-based installation

Pre-Installation

Installation Requirements
Hard Drive Space ~3 Tb recommended for full installation (all titles and versions for mac & linux
Operating System Linux, macOS / OS X
Privileges Administrator account needed only to create install path (/programs)
Network Outbound https, optional rsync (ports 443 and 873 or 8080)

Approximate size per Branch

Branch size
i386-mac ~500 Gb
x86_64-linux ~2.5 Tb
shared files ~50 Gb

Size breakdown of titles in a typical installation

Email accounts@sbgrid.org to request the installation credentials for the software. Be sure to include the following information in your email:

* Lab Name
* Types of computers on site: Linux, macOS, GPUs etc.
* The names and email addresses of lab members that will use the software. One user may be designated to receive the majority of our correspondence if you would prefer not to hear from us too often.

Once the email has been received and your information has been entered into our system, we will email you credentials and instructions to begin the remote installation process. Instructions are also included below for reference.

Installation

The sbgrid-cli utility is used to install and manage an installation. See the sbgrid-cli recommened installation page for more information.

  1. Create an 'sbgrid' user on the machine that will host your software installation. This should be a normal, unprivileged user account.
  2. Log in as this 'sbgrid' user.
  3. Download the sbgrid-cli installation manager.
  4. Untar and Make the sbgrid-cli file executable with: chmod +x sbgrid-cli
  5. Run the installation: ./sbgrid-cli activate-site
  6. The applications will walk you through configuring your installation, downloading the software and installing a cron job that will keep the software updated at your site. You will need the site name and install key provided in the account creation email. The installation may take anywhere from several hours to a day, depending on your network and the number of applications available to your site.

Post-Installation Steps

  1. Add a symlink in the root directory of each machine that wants to use the software. The installation script will print the suggested syntax for the command.ln -s /path/to/sbgrid/installation /programs
  2. Any user that wishes to use the software needs to configure their shell to initialize the SBGrid shell environment. For bash and other sh-compliant shells, add the following line to your ~/.bash_profile or ~/.bashrc: . /programs/sbgrid.shrc For csh and tcsh, add the following line to your ~/.cshrc: source /programs/sbgrid.cshrc