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Now that the qmaster is set up and NFS is set up, I can finally set the machines up as execution hosts. I’m doing it in parallel on both machines. cd /usr/local/gridengine, sudo -s, and finally ./install_execd, and we’re on our way to another bulleted list describing lots of screens…

• Welcome Why, thank you!
• Checking directory Looks good: /usr/local/gridengine
• Cells Also good: algore
• Checking hostname resolving This worked fine out of the box on the qmaster machine, but on the PowerBook the Bonjour name wasn’t getting resolved properly. So I added an entry to /etc/hosts on astor.local: [local IP address] darwin.local. That fixed things.
• Local spool directory configuration No local spools.
• Creating local configuration Done!
• execd startup script Yes! Done!
• execution daemon startup Started up!
• Adding a queue for this host Done on both. Looks like the 2-processor G5 detected two processors, and the 1-processor PowerBook detected 1. Smarty smarty. But a problem: “unable to resolve host [‘darwin’ | ‘astor’]”…I hope this doesn’t mean everything breaks.
• The rest… is just information already shown during the other installation. I hope that name-resolution problem doesn’t bite me in the ass.

Well, it looks like everything’s done. Testing…tomorrow. Time to sleep.

Turns out you have to have an NFS share for your SGE_ROOT directory. So I set up NFS.

I followed the GUI instructions from this one. In short, you add an /exports entry to NetInfo with settings for the directory you want to export. I couldn’t get the exports to show up right for a long time, but restarting the machine fixed that problem.

To set up an NFS automount on the PowerBook, there’s some more setup to be done, described here. The gist is to set up a NetInfo entry in /mounts for the server.

End result: my /usr/local/gridengine on darwin.local maps to the same directory on astor.local.

Fresh from a nice Memorial Day picnic lunch in Dolores Park, it feels like time to take a nap. But I’m going to install the Grid Engine instead! Here comes the installation part of the installation process.

Getting the Software

I downloaded the Grid Engine 6.0u8 common files and Mac OS X binaries linked from here and unpacked the contents of each into /usr/local/gridengine on both of my machines.

Then I set the $SGE_ROOT environment variables in the system-wide /etc/bashrc file, and added the binary directory to the standard $PATH:


export SGE_ROOT=/usr/local/gridengine
export PATH=$SGE_ROOT/bin/darwin:$PATH


and did a source /etc/bashrc to update my session’s environment variables.

Setting up the Master Host

Making sure I was in the $SGE_ROOT directory and in a sudo -s session, I ran this on good-old Astor:

./install_qmaster

I followed through some screens:

• Admin user At the first screen, I said OK to use ebaskerv (my user account) as the admin user.
• root directory The root directory was right.
• TCP/IP services As requested, I added sge_qmaster to my /etc/services file, and in anticipation added one for sge_execd:
  sge_qmaster 781/tcp
sge_execd 782/tcp
• Cells Named my cell algore, as promised.
• qmaster spool directory Default is fine: /usr/local/gridengine/algore/spool/qmaster
• Windows Execution Host Support Are you going to install Windows Execution Hosts? Are you kidding me? At least, by Judas, the default is no.
• File permissions I said no when asked if I had already verified and set file permissions. My guess is these would need fixing. I said yes at the next screen (please verify and set my permissions) and all looked hunky-dory (“Your file permissions were set”).
• Hostname resolving method This asks if all my hosts are in one DNS domain. I’m going to cross my fingers and hope that the zeroconf pseudo-domain local. will work, and answer yes.
• Making directories This seemed to go fine. (“Mrs. Crabapple and Principal Skinner were in the closet making directories, and I saw one of the directories, and the directory looked at me!”) RETURN!
• Setup spooling I chose classic spooling, because I had this suspicion that BerkeleyDB wasn’t ever installed properly on my machine. I’m looking for simplicity, not performance. The spooling database seemed to be initialized properly on the next screen.
• Group id range For some strange reason, the Grid Engine needs a range of UNIX group ids to assign dynamically to jobs. I’m pretty sure the example range 20000-20100 is free and large enough, so I’ll use that.
• Cluster configuration First up: execd_spool_dir. The default seems fine. Then, administrator email: I gave it my email, but I don’t think email sending is even set up right on my machine, so it probably won’t work.
• Creating local configuration This seemed to work…
• qmaster/scheduler startup script Apparently, it knows how to set up a startup script. I’ll let it go ahead and try…wow! It put something in /Library/StartupItems! Clever girl.
• qmaster and scheduler startup Started up successfully!
• hosts This is easy: just two for now. astor.local. and darwin.local., maybe more later. (They misspelled “separated” in “Please enter a blank seperated list of hosts.”) This seemed to go correctly. I said no to a shadow host, partially because I like to live dangerously, and mostly because my grid consists of two computers. Then, the default queue and hostgroup were added: just astor.local.—maybe I have to add darwin.local. manually later.
• Scheduler tuning Went with Normal.
• Using gridengine Looks like they provide a nice script to set all the environment variables. So I replaced my old bashrc line with:
  . /usr/local/gridengine/algore/common/settings.sh
• Messages FYI, messages logged to:
  /tmp/qmaster_messages
/tmp/execd_messages
/usr/local/gridengine/algore/spool/qmaster/messages
[execd_spool_dir]/[hostname]/messages
  and startup scripts are at:
  /usr/local/gridengine/algore/common/sgemaster (qmaster and scheduler)
  /usr/local/gridengine/algore/common/sgeexecd (execd)
• Almost done “Your Grid Engine qmaster installation is now completed” says the friendly screen. Now I get to start the execution host installation. Next post.

Here goes trying to install the open-source Grid Engine 6.0u8 on Tiger. It would be nice if there were a Mac OS X installer package…if I have extra time (ha) maybe I’ll put one together.

I can already see that Xgrid is an infinitely simpler system. Apple wins on ease-of-use already—just based on the instructions in the Plan the Installation section of the Grid Engine manual.

SGE, on the other hand, looks way more powerful. Sophisticated scheduling, intelligent matching of available resources to job needs, etc., etc. I like.

For my own personal use, Xgrid looks great. But I’m going to slog through, because I think I’d better get some hands-on use of the reference implementation of DRMAA before writing my own new implementation.

First, some preliminary notes on how the Grid Engine works…

Definitions

master host

Runs master daemon and scheduler daemon—basically, controls the system. Equivalent to the Xgrid controller. By default, also an administration host and submit host.

shadow master host

A system that can detect a failure of master and take over. Despite my mission-critical enterprise-grade infrastructure, I won’t bother dealing with these.

execution host

Systems that execute jobs. Equivalent to an Xgrid agent.

administration host

Systems that carry out any “administrative activity.” I guess this means editing jobs, adjusting controller settings, etc.?

submit host

Systems that allow users to submit batch jobs. Like an Xgrid client.

queue

Container for jobs that can run on one or more hosts concurrently. Sort of a sub-grid. Can include any subset of hosts on the system.

Daemons

sge_qmaster

The master daemon. Handles all controller activity except scheduling decisions.

sge_schedd

The scheduling daemon—decides where to send jobs, how to order & priorities.

sge_execd

Execution daemon—actually runs jobs. Runs on execution hosts.

With this background, I can actually start thinking about how the hell to set up my own system! Here are the decisions I made for my giant 2-host grid:

Decisions

• Single cluster My system will be a single cluster, rather than a collection of sub-clusters. My system consists, at last count, of my personal machines: a G5 and a four-year-old PowerBook. I’ll try to convince my roommates to let me use their machines too. At least they’re all connected via InfiniBand! Ha, just kidding.
• Hosts The G5 will be everything: master, administration, submit, and execution. The PowerBook will be everything except a master.
• Users “Ensure that all users of the grid engine system have the same user names on all submit and execution hosts.” This isn’t a decision! It’s an order!
• Software Directories I guess I’ll put a full directory tree on both machines so I don’t have to think about what to install and what not to install.
• Queue Structure One grid, one cluster, one queue; will include all (2) execution hosts. Easy peasy.
• Network Services I have no idea what an NIS file is (Solaris thing?), so I guess that means I’ll set things up as “local to each workstation in /etc/services”.
• Gathering Information Another command: “Use the information in this chapter to gather the information necessary to complete the installation worksheet.” Decisions my ass.

I guess I’ll fill out their silly little worksheet. It looks like it might be useful…

Necessary Information

This post is getting very long. Ah well, I press on.

Aw, fuck, I just noticed they have a guide to all of those table entries. Let’s see if that changes anything…well, they use 536 and 537 as ports in their example. Maybe those are free. And perhaps interactive installation will be better.

Well, it looks like it’s time to start installing. I’ll cover that in the next post.

Today I begin work on GridSweeper. (Which, I learned through Google, shares a name with what looks like a MineSweeper clone, detailed about halfway down this page. I’m not particularly worried about confusion.)

I’m not going to write any code of significance this week: rather, I’m going to get really familiar with Sun’s Grid Engine system, DRMAA, and test out doing manual runs of Repast, etc. with Xgrid and the Grid Engine, just to see what it will take.

I was worried about how the Grid Engine DRMAA implementation worked in Java—at first glance, I saw classes in org.ggf.drmaa and worried that Sun’s DRMAA packages were implemented inside that package. In fact, it’s nicely separated: the DRMAA interface is in org.ggf.drmaa, and com.sun.grid.drmaa contains the Sun implementation. So I can just put an Xgrid implementation in com.edbaskerville.xgrid-drmaa or something like that—and you’ll be able to select between the two grid systems *at runtime*!

To elaborate on the deliverables listed in the proposal, these are the pieces I plan to build:

• GridSweeper The actual project. See the proposal.
• Xgrid DRMAA implementation (C) This will be the meat of my DRMAA work. It will wrap the Objective-C XgridFoundation library in the standard DRMAA C interface, all packaged up in XgridDRMAA.framework.
• Xgrid DRMAA implementation (Java) Mirroring the SGE Java implementation, this will just be a JNI wrapper for the Xgrid DRMAA implementation in C. Packaged in com.edbaskerville.xgrid-drmaa, class files included in XgridDRMAA.framework.
• Objective-C DRMAA interface If I have time, an Objective-C wrapper for the C API. (Not useful for GridSweeper, but just a nice thing to have, and not very much work!) I’ll propose this to the drmaa-wg as a standard interface. Yes, that’s right: this will be an Objective-C wrapper for the DRMAA C interface layer to the Objective-C XgridFoundation API. But I’ll also make this play nice with SGE—in short, mirror the structure of the Java APIs, allowing you to select from different implementations at runtime. This will be included in XgridDRMAA.framework.

The goal with the Xgrid DRMAA stuff is to have Apple roll it into Mac OS X someday, replacing my C wrapper to their Objective-C API with something that connects directly to the Xgrid internals. It would be nice for all this stuff to be in XgridFoundation someday.