Jeff visits a few other lists in search of cluster goodies

The Beowulf mailing list provides detailed discussions about issues concerning Linux HPC clusters. In this column I report on using semi-public PC's for grid type applications and how we can handle large numbers of files. We also turn to the ganglia-developers mailings list to report on how one can add a "disk alive" metric to ganglia. You can consult the Beowulf archives, the bioclusters archives, and the ganglia archives for the actual conversations.

Using Semi-Public PCs

There was an interesting discussion a few months back on the bioclusters mailing list about using semi-public PC's for heavy computational jobs. On Feb. 15, 2004, Arnon Klein asked about running his jobs on semi-public machines that are running various flavors of Windows. Arnon is asking this question because he is doing his graduate research and needs computational power. He's already exhausted the machines easily available to him, so he was looking for suggestions about what to do next.

The first response came from Chris Dwan. Chris responded that he's in a similar boat but has managed to put together some systems from various campuses into something like a grid. He also provided a very useful ranking of systems in terms of access difficulty. For example, systems that he maintains were easiest to get into followed by systems running Linux or OS X (which Chris also runs). The lowest two ranked systems were Windows machines that either could be rebooted at night or could not be rebooted at all. Chris went on to talk about some schedulers that can steal cycles from idle workstations (e. g. SGE, torque, LSF). Although he said that integrating disparate schedulers can be very difficult. He did mention Condor from the University of Wisconsin as a possible solution. He also mentioned the grid software from United Devices, which runs on Windows machines but will use compute cycles from other machines.

Farud Ghazali also mentioned that's he's also looking for a solution to this type of problem. He pointed that there were many practical difficulties including authentication across disparate resources. Chris Dwan jumped in to explain how he has hacked up something to do authentication for him.

Ron Chen joined the conversation to mention that SGE (Sun Grid Engine) version 6.0 will integrate with JXTA which then offers Jgrid that offers P2P (Peer-to-Peer) workload management in a fashion similar to SETI@home. However he did say that SGE 6.0 won't be out until May of 2004 (and it may slip slightly from then). Until then, Ron recommended using boinc. This package starts jobs and transmits data using port 80, which makes it easier to get in and out of a firewall than other approaches. It also has versions for Windows, Linux, Solaris and OS X. John van Workum also mentioned GreenTea that offers a Java P2P client that gives grid capabilities for running jobs. Bruce Moxon also mentioned that the Cornell Theory Center, has some tools that might help with Windows machines.

While this is discussion was short it did offer some ideas that could help people in similar situations. There are many people and groups thinking about the same things that Arnon mentioned in his first posting.

Disk Alive Metric

I'm sure many readers are aware of ganglia. It is a scalable distributed monitoring system for high performance computing systems such as clusters and grids. It is open source and in use on over 500 clusters throughout the world. On December 22, 2003, on the Ganglia Developers mailing list Federico Sacerdoti asked about a metric that ganglia could watch that would report if a disk was alive or not. It seems that Federico was talking to a Purdue (my alma mater) system administrator about a cluster that is put together from old PCs. The disks in the machines keep failing but ganglia fails to report the disks as down since the ganglia daemon will still report a heartbeat even the node is basically down. Federico posted a possible solution that he worked out with the administrator but had not tried it.

Brooks Davis replied that he didn't think it would work, at least in FreeBSD, because of the way Unix and Unix-like systems work. He did offer another solution that read random blocks from a file system to make sure the drive was still functioning.

Robert Walsh responded that he has been trying to get information from the SMART (Self-Monitoring Analysis and Reporting Technology System) data in most hard drives into ganglia. Brooks Davis mentioned that he thought integrating smartmontools with ganglia might offer a solution. smartmontools is a package that allows you to control and monitor the SMART data contained in virtually all modern hard drives.

The discussion spilled over into January of 2004, where Sander van Vliet announced that he had a preliminary working version of a gmetric code that would test if the drives were alive. The code walks the /proc/mounts file looking for drives that are mounted and then attempts to write 4 bytes to the end of the current used file system to determine if the disk is alive. If there were no errors along the way, then the disk is alive. Sander then posted that he had a version of his code working that used the SMART data but the job as to be run as root. This problem was sorted out fairly quickly though. During all of the conversation, there was an effort to make the code work under Linux and the various BSD flavors, especially FreeBSD. At this point the thread died out, but it appears as though the code was working correctly for Linux and FreeBSD.