OSCAR and Bioinformatics

With new cluster deployment and management tools, you can set up a 64-node cluster in an hour, then put it to work on your research.
Walk-Through of a Typical OSCAR Installation

Installing a cluster with the OSCAR Toolkit is a straightforward process. If you have installed Linux before, you should have little trouble.

Currently, the OSCAR Project supports three Linux distributions: Red Hat 8.0, Red Hat 9.0 and Mandrake 9.0. The main Linux installation requirement is that an X windowing environment such as KDE or GNOME is installed; otherwise, a typical workstation install with software development tools should be sufficient.

After Linux is installed and configured on the head node, you can download the OSCAR tarball from the projects page, untar it and do the configure, make, make install routine.

OSCAR, by default, is installed to /opt/oscar. You can change this using the --prefix flag with configure. After OSCAR has been installed, you can start the OSCAR Wizard, which provides step-by-step installation menus for setting up your cluster.

To invoke the wizard, go to /opt/oscar and type ./install_cluster ethX. Here, ethX refers to the interface that is on the cluster network.

Figure 1. The OSCAR installation main menu. In less than ten steps the cluster is ready to compute!

OSCAR comes with many prebundled packages. Other packages available from the various repositories also may be of interest. To download those, simply click on Download Additional OSCAR Packages in the OSCAR Wizard and choose the package(s).

Next, you can select the packages you want to install. Packages have three main categories: core, provided and third party. Core packages must be installed and cannot be deselected. Provided packages are the ones the OSCAR team recommends you install, and third-party packages are all the remaining packages available from the repositories.

Figure 2. OSCAR Package Downloader—additional packages can be downloaded in this menu.

Configuration changes can be made to packages using the Configure Selected OSCAR Packages menu.

The next stage is to Install OSCAR Server Packages. This is non-interactive and basically sets up packages for use on the server. When it is done, you are alerted by a pop-up window.

Figure 3. Non-interactive step where server packages are installed.

Now the fun part begins. You can build a client image with the Build OSCAR Client Image step. In this step, you select a few options for the client image you want to build. This image then is pushed to your client nodes. You can provide a list of RPM packages to be installed on the base image, and you also can decide how to partition the hard drive and assign IP addresses. Lastly, you can choose the post-image action, such as rebooting the machine when imaging is done.

Figure 4. Create a client image based on a user-provided package list and partition table.

In the Define OSCAR Clients step, you can specify the domain name, base name of your clients, the number of nodes you want to bring up for this session and other network settings. After you click the Add clients button, these definitions are configured and the cluster is almost ready to be rolled out.

Figure 5. Cluster nodes and network settings are defined here.

Next, you will want to set up networking for your cluster. Here, you can boot up your client nodes with PXE or floppy disk, and the OSCAR head node then collects the MAC addresses and you can assign them to particular hosts. Once this is done, the client nodes are imaged immediately. Typically, it takes anywhere from 10–30 minutes to image each node, depending on the speed of your hard drive. When deploying a cluster, multiple nodes can be imaged at the same time. We usually start up ten nodes to be imaged at a time so the head node does not get heavily loaded. With this staggered approach, you should be able to deploy a 64-node cluster within an hour.

Figure 6. Cluster nodes are network-booted, and their MAC addresses assigned to host entries.

After the nodes are imaged and rebooted, you can continue with the next step, which is to Complete the Cluster Setup. This again is a non-interactive step in which final installation configurations and other clean-up functions are performed.

Figure 7. Non-interactive step where final installation configurations and clean-up functions are performed.

Lastly, you may want to Test Cluster Setup. This runs a series of tests for the cluster install as well as for individual packages. If all goes well, you will pass all the tests, thus confirming your cluster setup is complete and ready to run computations.

Figure 8. All systems go—cluster is ready to rock and roll.

The OSCAR Toolkit is easy to install and, in general, works with most hardware. However, if you run into problems, two mailing lists are available for help. The oscar-users list is the first place you should ask questions. Most of the core team frequently reads the list, and other users help out too. However, if you have questions regarding the development of OSCAR, there is the oscar-devel list. Both lists are closed lists; you need to subscribe before you can post to them.


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