Thursday Mar 19, 2009

Podcast: New Installer in Sun Grid Engine 6.2 Update 2

I just posted a new podcast on the new installer in Sun Grid Engine 6.2u2. Check it out.

Monday Mar 16, 2009

New Installer in Sun Grid Engine 6.2 Update 2

In my previous post, I talked about the new installer that is included with Sun Grid Engine 6.2u2. Lubos, one of our core team (as opposed to Service Domain Manager or QA) engineers in Prague, has just posted a couple of videos of the new installer. The first one shows how to make sure the new installer can be used with the machines you're planning to use for your cluster. Because the new installer can install an entire cluster at once, it has to be able to contact all the machines destined for the cluster, and that's where the setup comes in. The second one actually shows off the new installer. Lubos also has some screenshots of the new installer posted.

Thursday Mar 05, 2009

Sun Grid Engine 6.2 Update 2 Is Out!

Sun Grid Engine 6.2u2 is now available. If you're not excited, you should be. First off, don't let the name fool you. 6.2u2 is not just bug fixes. It's a full feature release, and contains some great features. What features? Glad you asked.

First and foremost, job submission verifiers (JSVs). It's a feature we added specifically for TACC, but it's one that will be useful for almost everyone. In fact, I suspect that we'll discover it's the answer to some of the classic Sun Grid Engine problems. What is it? Before 6.2u2, there was no way to prevent a job from being submitted. It was (and still is) possible to choose not to schedule a job after it's been submitted, but before 6.2u2, that's all you could do. With 6.2u2 and JSV, you now have the option to insert a step between submission and acceptance. With that step, you can choose to accept or reject the job submission, but you can also choose to modify the job before accepting it, and that's where the magic comes in.

The verification step is handled through scripts or binaries. There's a new submission option, -jsv, that adds a JSV to the submission. That means you can pick up JSVs from anywhere that you can stash a submission option: most notably the global sge_request file, your user sge_request file, and the directory's sge_request file, but also DRMAA native specification, DRMAA job category, the enigmatic -@ switch, and, of course, the command line itself. The -jsv switch is cumulative, so if you have one in several of those places, several JSVs will be run for your submission. It's worth noting that all of the above listed JSV sources are controlled by the user, except the global sge_request file, and even that can be overridden with the -clear switch.

So far, we've only talked about the client side. JSVs can also come in on the server side. In the global host configuration an administrator can configure a single JSV. Unlike on the client side where every JSV is started from scratch with every job submission, on the server side the JSV is started once and queried repeatedly. The reason is that on the client side, performance isn't a big issue, but on the server side, the cost of forking and execing the JSV for every job submission can have a huge impact. By keeping the JSV running, we save that cost. The big advantage of the server-side JSV is that users can't circumvent it. If you really need to enforce a policy with a JSV, the server side is that place to do it.

Now, if you're thinking fast, you might question the point of the server-side JSV when users can change everything about the job using qalter after it's submitted. Well, so did we. When you configure a server-side JSV, users are no longer allowed to modify jobs after submission unless you specifically grant the ability to do so, and even then it's limited to the job attributes that you allow them to modify.

JSV is a huge topic, and I could probably go on for days about it. Instead I'll save it for a white paper and move on.

The next big feature in 6.2u2 is the new installer. You now have the option of using the old interactive text-based installer or a new graphical installer. The graphical installer has several important advantages. First, it lets you install an entire cluster at once. It actually sits on top of the auto-installer and reuses that same functionality to install remote nodes. The graphical installer, however, will first verify that all the nodes are reachable before the installation starts, so the installation won't quietly hang on an unreachable node. It also accepts wildcarded host name and IP address ranges, which makes installing a huge cluster much simpler.

The third major feature is that we've added support for Microsoft Windows Vista (Ultimate and Enterprise) and Server 2003R2 and 2008. Both 32-bit and 64-bit version are available. Harald (who you should encourage to start blogging!) worked really hard on ironing out the issues with the changes in the OS. We still rely on SFU for the Windows execution daemons, except that it's now called SUA.

The fourth big feature is job-level parallel job resource requests. Before 6.2u2, whenever a parallel job requested a resource, SGE would implicitly multiply that resource request by the number of assigned slaves (because each slave requests the resource on the host where it runs). That makes sense with, say, memory, where requesting 4GB really means that every slave should have 4GB. It doesn't make any sense for other things, like some software licenses. Now with 6.2u2, the administrator can flag a resource as job level, meaning that it is not multiplied by the number of assigned slaves when requested by a parallel job. In most cases, a resource that shouldn't be multiplied in for one job, shouldn't be multiplied for any job. There may be exceptions to the rule, but I doubt there will be many. I'd love to hear your feedback, though.

The last two new features aren't so much features as improvements. Starting with 6.2u2, the 64-bit Linux binaries use the jemalloc library instead of the default Linux malloc. The performance and memory footprint impact is significant, in some cases as much as 20% improvement. Also, starting with 6.2u2, the Linux binaries use poll() instead of select() in the commlib. For some flavors of Linux, the use of select() made it difficult to scale past a couple thousand hosts. With the commlib now using poll(), I've seen SGE scale well over 6000 Linux nodes.

And on top of all that, there is the usual pile of bug fixes. A handful of qmaster and scheduler issues cropped up recently in 6.2 and 6.2u1, but with 6.2u2 those should all now be resolved.

I highly recommend giving 6.2u2 a try, if for no reason other than JSV. Let me know what you think!

Wednesday Jan 07, 2009

Grid Infrastructure Infrastructure

Owen Taylor (formerly) of GigaSpaces has put together an excellent proof of concept using GigaSpaces XAP and Sun Grid Engine. Using Sun Grid Engine, the PoC is able to grow and shrink the size of the GigaSpaces cluster dynamically according to changing load conditions. The PoC monitors GigaSpaces via JMX and then uses DRMAA to submit new instances to SGE or stop existing ones. Read more about it.

Tuesday Jan 06, 2009

Connecting All the Dots

The last couple of weeks before the holidays I worked on an interesting project. It involved assembling pretty much everything Sun offers for HPC into a single coherent demo and throwing in Amazon EC2 to boot. This post will explain what I did and how I did it. Let's start at the beginning.

One of the new offerings from Sun is the Sun HPC Software. Beneath the excessively generic name is a complete, integrated stack of HPC software components. Currently there are two editions: the Sun HPC Software, Linux Edition (aka Project Giraffe) and the Sun HPC Software, Solaris Developer Edition. (A Sun HPC Software, Solaris Edition and Sun HPC Software, OpenSolaris Edition will be following shortly.) The Linux edition is exactly what the name implies. It's a full stack of open source HPC tools bundled into a Centos image, ready to push out to your cluster. The Solaris developer edition is a slightly different animal. It is targeted at developers interested in writing HPC applications for Solaris. The Solaris developer edition is a virtual machine image (available for VMware and Virtual Box) that includes Solaris 10 and a pre-installed suite of Sun's HPC products, including Sun Grid Engine, Sun HPC ClusterTools, Sun Studio, and Sun Visualization, all integrated together.

For this demo, I used the Solaris developer edition. The end goal was to produce a version of the virtual machine image that was capable of automatically borrowing resources from a local pool or from the cloud in order to test or deploy developed HPC applications. Inside the developer edition virtual machine, there are already two Zones that act as virtual execution nodes for testing applications. That's a nice start, but what about testing on real machines or a larger number of machines? That's where the resource borrowing comes in. In the end, I had a VM image that was capable of automatically borrowing and releasing resources first from a local pool and later from the cloud, on demand.

The first step was to get the developer edition running as-is. Sounded simple enough. The first wrinkle was that I was doing this demo on a Mac. The regular VMware Player is not available for Mac, so I had to download an eval copy of VMware Fusion. Once I had Fusion installed, I was able to bring up the developer edition VM without a hitch.

Step 2 was to get the VM networked. The network configuration for the developer edition beta 1 is such that the global and non-global Zones can see each other, but nobody can get into or out of the VM. Getting the networking working was probably the hardest part of the demo, and honestly, I can't tell you how I finally did it. Per the suggestion of the pop-up dialogs from VMware, I installed the VMware Tools in the VM's Solaris instance. That changed the name of the primary interface from pcn0 to vmxnet0, but didn't actually help. Solaris was still unable to plumb the interface. After twiddling the VM's network settings several times and doing several reconfiguration boots, I eventually ended up with a working vmxnet1 interface (and a dead pcn0 and vmxnet0). As usual in such adventures, I'd swear that the last thing I did before it started working should not have had any appreciable effect. Oh, well. It worked, and I wasn't interested in understanding why.

Now that I had a functional network interface, the next step was to reinstall the Sun Grid Engine product. The VM comes with a preinstalled instance, but this demo requires features not enabled in a default installation, like what the VM provides. I left the original cell (default) intact and installed a new cell (hpc) with the -jmx and -csp options. -jmx enables the Java thread in the qmaster that serves up the JGDI API over JMX. I needed JGDI so that the demo GUI that I was building could receive event updates from the qmaster about job and host changes. With Sun Grid Engine 6.2, I was unable to successfully connect to the JMX server unless I installed the qmaster with certificate-based security, hence the -csp option. After the installation was complete, I then had to do the usual CSP certificate juggling, plus a new wrinkle. In order to connect to the JMX server, I also had to create a keystore for the connecting user with $SGE_ROOT/util/sgeCA/sge_ca -ks <user>. There's a quirk to the sge_ca -ks command, though. By default, it fails, explaining that it can't find the certificates. The reason is that the path to the certificates is hard-coded in the sge_ca script to a ridiculous default value. To change it to the correct value, I had to use the -calocaltop switch. After the certificates were squared away, I installed execution daemons in both Zones. At least that part was easy.

The next thing I did was to create some more Zones. Yes, I know this demo was supposed to be using real machines from a local pool and the cloud. Because it's a demo on a laptop, the "local machines" had to be equally portable. Because of firewall issues, I also wanted to have a backup for the cloud. In an effort to be clever, I moved the file systems for the two existing Zones onto their own ZFS volumes. I wanted to create the new Zones as cloned snapshots of the old Zones. Unfortunately, it turns out that even though the man page for zfs(1M) says that it's possible, the version of Solaris installed in the VM is the last version on which it isn't possible. After chasing my tail a bit, I decided to just do it the old fashioned way instead of trying to force the new fangled way to work.

Now that I had six non-global Zones running, the next step was to get Service Domain Manager installed. It is neither installed nor included in the developer edition VM, so I had to scp it over from my desktop. Technically, I could probably have managed to download it directly from the VM, but I had already downloaded it to my desktop before I started. For the Service Domain Manager installation, I followed Chansup's blog rather than the documentation. Chansup's blog posts detail exactly what steps to follow without the distraction of all the other possibilities that the docs explain. Following the steps in the blog, I was able to get the Service Domain Manager master and agents installed with little difficulty. The hardest part is that the sdmadm command has extremely complicated syntax, and it took a while before I could execute a command without having the docs or blog in front of me as a reference. To prove that the installation worked, I manually forced Service Domain Manager to add one of the new Zones to the existing Sun Grid Engine cluster, and much to my shock and wonderment, it worked.

The last step of VM (re)configuration was to configure the Service Domain Manager with a local spare pool and a cloud spare pool and a set of policies to govern when resources should be moved around. This step proved about as tricky as I expected. As one of the original architects and developers of the product, I had a good idea of what I wanted to do and how to make it happen, but the syntax and the details were still problematic. The syntax was the first hurdle. The docs have issues with both understandability and accuracy, and Chansup's blog was too narrowly focused for my purposes. After I poked around a bit, I figured out how to do what I wanted, but actually doing it was the next challenge. What I wanted to do was create two MaxPendingJobsSLO's...

We interrupt your regularly scheduled blog post to bring you a public service announcement. Please, for your own well being and the well being of others who might use your software, test all of your code contributions thoroughly on all supported platforms, and have them reviewed by an experienced member of the development team before committing, especially if you're working on the Firefox source base. This point in the blog post is the last time I saved my text before completing the post. Before I could save it, Firefox segfaulted causing me to loose a significant amount of work. What follows is a downtrodden, half-hearted attempt to complete the post again. We now return you to your regularly scheduled blog post.

What I wanted to do was create two MaxPendingJobsSLO's for the Sun Grid Engine instance. The first would post a moderate need (50) when the pending job list was more than 6 jobs long. The second would post a high need (99) when the pending job list was more than 12 jobs long. I also wanted to have a local spare pool with a low (20) PermanentRequestSLO and a low FixedUsageSLO, and a cloud spare pool with a moderate (60) PermanentRequestSLO and a moderate FixedUsageSLO. The idea was that when the Sun Grid Engine cluster was idle, all the resources would stay where they were. When the pending job list was longer than 6 jobs, resources would be taken from the local spare pool. When the pending job list was longer than 12 jobs, additional resource would be taken from the cloud spare pool. When the pending job list grew shorter, the resources would be returned to their spare pools. In theory. (The philosophy of setting up Service Domain Manager SLOs is a full topic unto itself and will have to wait for another blog post.)

The first problem I ran into was that Service Domain Manager does not allow a spare pool to have a FixedUsageSLO. An issue has been filed for the problem, but that didn't help me set up the demo. The result was that I had no way to force Service Domain Manager to take the local spare pool resources before the cloud spare pool resources. The best I could do was set the averageSlotsPerHost value for the SLO for the MaxPendingJobsSLO's to a high number so that Service Domain Manager only would take hosts one at a time, rather than one from each spare pool simultaneously.

The nest problem was quite unexpected. With the SLOs in place, I submitted an array job with 100 tasks. I waited. Nothing happened. I waited some more. Still nothing happened. I turns out that the MaxPendingJobsSLO only counts whole jobs, not job tasks like DRMAA would. The work-around was easy. I just had to be sure the demo submitted enough individual jobs instead of relying on array tasks.

The last problem was one that I had been expecting. After a long pending job list had caused Service Domain Manager to assign all the available resources to the cluster, when the pending job list went to zero, the borrowed resources didn't always end up where they started. Service Domain Manager does not track the origin of resources. Fortunately, the issue is resolved by an easy idiom. I created a source property for every resource, and I set the value of the property to either "cloud", "spare", or "sge". I then set up the spare pools' PermanentRequestSLO's to only request resources with appropriate source settings. I also added a MinResourceSLO for the cluster that wants at least 2 resources that didn't come from a spare pool, just to be complete.

With the SLOs in place, the configuration actually did what it was supposed to. When the cluster had enough pending jobs, hosts were borrowed first from the local spare pool and then from the cloud. When the pending jobs were processed, the resources went back to the appropriate spare pools. To make the configuration more demo-friendly, I changed the sloUpdateInterval for the Sun Grid Engine instance to a few seconds (from the default of a few minutes). I also changed the quantity for the spare pools' PermanentRequestSLO's to 1 so that they would only reclaim their resources one at a time, rather than all at once. With those last changes made, I was ready to move on to the UI.

The idea of the demo was to present a clear graphical representation of what was going on with Sun Grid Engine and Service Domain Manager. From past experience building a similar demo for SuperComputing, I knew that JavaFX™ Script was the best tool for the job. (OK. It's not the best tool for the job in a general sense, but I'm a long-time Java™ geek, I don't know Flash, and I didn't have any budget to buy tools. Under those constraints, it was the best I could do.) Before I could get to building the UI, though, I first needed a JGDI shim to talk to the qmaster. Richard kindly provided me with some JGDI sample code, and from there it was pretty easy. The hardest part was figuring out what the events actually meant. In the end, my shim registered for job add events (to recognize job submissions), task modified events (to recognize job tasks being scheduled), and job deleted events (to recognize job completions). It also registered for host added and deleted events to recognize when Service Domain Manager reassigned a host.

With the shim working smoothly, I turned to the actual UI. Given the complexity of the animations that I wanted to do, it was shockingly simple to achieve with JavaFX Script, especially considering that there was not yet a graphical tool equivalent to Matisse for Swing. Every bit of it was hand-coded, but it still was fast, easy, and came out looking great. In the end, the whole UI, counting the shim, was about 1500 lines of code, and about 500 lines of that was the shim. (JGDI is rather verbose, especially when establishing a connection to the qmaster.)

And with that, I ran out of time. The next step would have been to actually populate the cloud spare pool with machines provisioned from the cloud. Torsten graciously provided me a Solaris AMI that included Sun Grid Engine and Service Domain Manager. The plan was to pre-provision two hosts to populate the pool and then create a script that would provision an additional host each time the cloud pool dropped below two hosts and release a host every time it grew larger than two hosts. Now that the demo has been presented, the pressure is off, and other things are higher priority. I do plan, however, to eventually come back and put the last piece of the puzzle in place.

Below is a video of the demo, showing how jobs can be submitted from the Sun Studio IDE, and how Sun Grid Engine and Service Domain Manager work together with the local spare pool and the cloud to handle the workload. The job that is being submitted is a short script that submits eight sleeper jobs. Because the MaxPendingJobsSLO ignores array tasks, I needed to submit a bunch of individual jobs, but I didn't want to have to click the submit button multiple times in the demo.

Filming the video turned out to be an interesting challenge unto itself. I did the screencap using Snapz Pro on the Mac. It has no problem with JavaFX Script or with VMware VMs, but it apparently can't film JavaFX Script running inside a VMware VM. I ended up having to twiddle the UI a bit so that I could run it directly on the Mac. That's why in the demo, when I switch from Sun Studio to the UI, I swap Mac desktops instead of Solaris workspaces. The voice over and zooming effects are courtesy of Final Cut, by the way.

Friday Dec 19, 2008

Mapping the World's Fastest Supercomputers

A colleague just sent me link to an interesting article from the New York Times. It's a graphical representation of the relative sizes and locations of the world's top 100 supercomputers. It also includes a graph that shows how compute power has increased over the years on a per-region basis. Very neat stuff.

Announcing Grid Engine 6.2 Update 1

Grid Engine 6.2 Update 1 is now ready for download.

Thursday Dec 18, 2008

The Perfect Holiday Gift

Wondering what to get for that special someone who has everything? How about a sneak peek at soon-to-be-released Sun Grid Engine 6.2 update 2? That's right! Nothing says 'I love you,' like the SGE 6.2u2 Beta, and it's available just in time for the holidays. It makes a great stocking stuffer, and it's fun for the whole family. Download the SGE6.2u2 Beta today!

Thursday Nov 06, 2008

My Own Personal Easter Egg

There was a semi-recent post to TechCrunchIT by Steve Gilmore about how software companies are transitioning from big bang product releases to a rolling thunder model. In that post, Steve includes a video interview with Jonathan Schwartz. OK, it's really a puppet of Jonathan, and it's highly entertaining. I don't want to spoil the video for you, so I'll avoid details, but in the video Jonathan tells people to go to Well, I did, and all I got was a 404. Pretty lame. So, I contacted the web team that manages and suggested that they put something at that address. Lowe and behold, they did. It's a redirect to It's really encouraging to me to see that Sun still has a sense of humor. Sometimes I wonder...

Monday Nov 03, 2008

SGE Blog Planet

There's a new Grid Engine blog aggregator on The idea is to capture all of the relevant Grid Engine blogs in a single place for easy access. It's similar to the aggregator on the OpenSolaris HPC Community site, except that the HPC one also contains general HPC blogs and blogs on other Sun HPC products as well. If you have suggestions for a blog that should be included in either, let me know.

Wednesday Oct 01, 2008


I recently rediscovered a hidden qconf option. I remember talking with the engineer when he implemented the option years ago, but because it was never documented, I forgot that it existed. A recent customer eval reminded me that it's there, and I think it's one worth sharing.

The hidden option is qconf -bonsai. It is a human-readable equivalent of qconf -sstree, which if you've looked at you'll know isn't even remotely human-readable. It prints the current share tree configuration using spacing to represent hierarchy.

Let's look at an example. This is the output from qconf -sstree for my home test cluster:

# qconf -sstree

This is the output from qconf -bonsai for the same cluster:

# qconf -bonsai

Now, as for why it's an undocumented feature, I suspect it's historical. It was originally added on a whim by one of the engineers and was just never fully embraced. I remember there being talk about changing the name of the switch and making it a documented feature, but I suspect that plan just got lost in the shuffle.

HPC Publications from the APSTC

Just wanted to point out the great papers available from the APSTC. Have a look at their list of publications, reports, and briefs.

Thursday Sep 18, 2008

Cheap at Twice the Price

We've just added pricing to the Sun Store for Sun Grid Engine 6.2. Just go to the Get It tab, scroll down to the media kit, perpetual licenses, or subscription licenses section, and click the Get It button. On the Sun Store page you'll find the complete pricing information for that option.

Wednesday Sep 03, 2008

Sun HPC ClusterTools 8.0 Now Available

The 8.0 release of Sun HPC ClusterTools is finally out. ClusterTools is our OpenMPI implementation. Aside from boosting the scalability and adding support for Linux, 8.0 includes:

  • Based on Open MPI 1.3
  • Plug-ins for Sun Grid Engine (SGE) and Portable Batch System (PBS)
  • Support for Linux (RHEL 4&5, SLES 9&10), Solaris 10, OpenSolaris
  • Support for Sun Studio compilers and tools and GNU/gcc toolchains on both Solaris and Linux OSes
  • MPI profiling support with Sun Studio Analyzer, plus support for VampirTrace and MPI PERUSE
  • Infiniband multi-rail support
  • Mellanox ConnectX Infiniband support
  • DTrace provider support on Solaris and OpenSolaris
  • Enhanced performance and scalability, including processor affinity support
  • Support for InfiniBand, GbE, 10GbE, and Myrinet interconnects
  • Full MPI-2 standard compliance, including MPI I/O and one sided communication

Go check it out!




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