Oy, this is become quite a little pain. The k2 theme rocks and I use it on my own blog where it works just fine. However, on iocean it is really really slooooooww. I’ve spent quite a bit of time looking into why this is and have tried tweaking for performance at every level: mysql optimizations, turning off plug-ins, wp-cache, etc.

I’m still not entirely sure what’s causing the sluggish performance. In the meantime, I’m reverting back (somewhat) to the previous theme, which loads a bit faster. I’m wondering whether we should install the APC (alternative php cache) extension to enable compiled php caching in apache. This could help somewhat?

I’ll wait until Mason returns in a couple weeks to figure some of this stuff out. For now, this site, although functional, will remain in a state of limbo.

Thanks for the patience.

-Shaun

This site may be a little broken for the next few days as we complete the transition to a new and improved WordPress theme.

Trust me, it will be worth it.

One of the improvements is already seen in the global navigation bar. We’d like to provide a more logical structure for the static pages contained within this site. The addition of the About, Projects, Groups, and Tools pages will give us a good framework for placing related content.

For example, the Matlab Group page is now located under Groups.

More stuff to come in time…

-Shaun

Due to the persistence of comment spam and at the requests of individuals, all email notifications involving new posts and comments have been disabled. To keep on track with the blog, I highly recommend subscribing via an RSS reader. I like using NetNewsWire on the mac. Mac users may also use Safari’s built-in rss reader. For the Firefox users, I’m sure there are tons of rss plugins available in addition to the Live Bookmarks feature.

We will continue to combat the spam on this blog (a great deal of it is filtered immediately by the blacklist words). Apologies for the email noise over the last few days.
–Shaun

UPDATE:
Additionally, I’ve disabled open registration and anonymous comments. At this point, we can manually add new users as they come along, and users need to log in to leave a comment.

Sorry for the facist-like policy. I’m ideally for open registration and anonymous comments because this lets the casual passer-byer leave his/her two cents. Unfortunately, the amount of spam greatly outweighed the amount of meaningful passer-by comments, so it’s best to shut all doors completely.

Third time’s a charm! (let’s hope)

I upgraded WordPress to version 2.0.3 from 1.5. This was my third attempt at upgrading. My previous two attempts were unsuccessful in that the blog seemed to perform much slower after upgrading.

This time around, I took all the precautions: backing up data, deactivating plugins, etc.

One by one, I will start upgrading and reactivating some plugins to get everything back to speed (ex. Archives plug-in). I also need to recode some hacks (ex. users can edit own comments).

I’ve written previously about wp2.0 after my 1st upgrade attempt. Read about it here

[NOTE]
The oceaninformatics.ucsd.edu/blog url is an alias oceaninformatics.ucsd.edu/index.php?cat=12

[UPDATE]
All plug-ins and hacks are back up. Enjoy!

In a search for some inspiration on my current project, I revisited one of my old favorite websites, the MIT OpenCourseWare website. MIT has generously posted all of the materials associated with hundreds of their classes (in theory, it should be all of them, but it sometimes doesn’t happen that way). If you want to learn about, say, Algorithms for Biological Computing, just navigate over to the computer science section of opencourseware and click on the class title. Inside are complete lecture notes, readings, tests, homeworks, projects, resources, etc. It’s a fantastic example of interoperability between departments and an open framework for the dissemination of knowledge. In essence, you have the complete lesson plans for every class at MIT at your disposal.

I suppose it’s not exactly groundbreaking or revolutionary, but Seed is a new science magazine in the same vein as Discover, Scientific American or Science. It’s not as commercialized or plastic as Discover, not as stodgy and old school as Scientific American, and not as technical as Science. What it is, however, is a periodic look into the world of science as culture. Science not solely as a method, hobby or body of knowledge, but rather science as a social binding agent and source of personal subjectivity. Much like Wired has examined the interface between society and technology, teasing out the effect one has on the other, Seed attempts to examine the overlap between society and hard science, and does so while preserving the authenticity of its subject matter.

Perhaps the most refreshing aspect of the magazine is its art design. It places photography and art at a premium, and what results is both a visual and textually interesting read. You often feel like you are reading an art magazine, with intelligent staff writing and mature layouts, yet without the looming sense of paying 6 dollars to look at pretty pictures for 20 minutes.

So, there you go. A glowing endorsement for something that doesn’t quite fit into the bounds of oceaninformatics, but is exciting enough that I think you’ll forgive me. Oh, and this month’s issue has an article about a new NOAA ship that is being built as a remote sensing operation, where ROV’s roam the ocean floor and scientists around the world can monitor the data output from their home computers. Now that’s pretty OI if you ask me…

by Lynn and Jerry

In the past, physical copies of data, articles and technical reports published at SIO were collected through the SIO Publications Committee (a sub-committee of the SIO Staff Council), given a SIO Reference Series publication number, and listed in an annually published hardcopy bibliography. This centralized system broadened community awareness of research and provided a common location for all publications independent of the scientist or lab involved in the research. Institutional support for this program ended in 2002, and with the retirement of Kitty Kuhns, the annual bibliographies ended.

Today, as demand for access to articles and data is growing, the need for a centralized, stable and accessible repository has re-emerged with some new obstacles. The web has provided the needed centralized space of which many researchers and groups have taken advantage. However, with constantly shifting URLs, servers, and funding cycles, maintaining these local access points is a laborious and frustrating task.

To fill the need, the SIO Library has assumed the local responsibility to maintain an online archive and repository called the e-scholarship Repository . This is a free service provided by a partnership between the University of California Office of the President (UCOP) and the non-profit California Digital Library(CDL). An author can submit a published paper in PDF format to the e-scholarship system through an email to siolib@sio.ucsd.edu, an email alias provided by Peter Brueggeman, Director of the SIO Library. The paper will be posted under the appropriate headers (headers include: Tech Reports, SIO Reference, etc) and given a permanent URL. Data, photos, graphs, and other file types can be submitted as well, either independently or as an ‘associated file’ to a paper. Web URLs can be included, though as websites grow, shift and age, links commonly break and are discouraged unless realistically stable for the long-term.

SIO has a separate space in the e-scholarship Repository and allows further subdivision into ‘centers’ and ’series’. The OceanInformatics group for instance can request designation as a ‘center’ with all submissions falling under this hierarchical step. A center can have multiple series which group submissions by designated subjects.

All files in the repository are stored on the servers at the CDL. The CDL is responsible for moving files and maintaining the permanent URLs through server upgrades, etc.

A note about copyrights:

To post a published article as part of the SIO Repository, the lead author must be granted permission through the publishing house or agency. While many journals have denied copyright releases for online access, a few have begun to open up to the idea. Anecdotally, the Elsevier journals (including Continental Shelf Research, Progress in Oceanography and others) will grant authors permission to post their articles online. The research society journals (i.e., those published through the AMS, AGU, etc.) have tended to be less cooperative in this regard though AGU will consider allowing pre-prints to be posted. Authors should investigate any copyright restrictions before posting a published work, the SHERPA/ROMEO list is an excellent place to start.

On 6 March, 2006 there was an alert from iocean regarding probable failure with the RAID disk system:


==============================================================
A problem has been detected on this server.

Drives:
Drive 1 (disk2) : Normal
Drive 2 (disk1) : Normal
Drive 3 (disk0) : Warning
==============================================================


Over the course of the few days leading up to the failure warning, a number of users reported slow database performance in some web applications and services provided by iocean (Hlab Forum, etc.). The data disk[s] on iocean (/Volumes/iodata) is a RAID 1 (mirrored) diskset consisting of two (disk0 and disk2) of the three disks on the server (the third disk, disk1, is a standalone volume, ioceanHD, which contains the operating system and applications). The RAID volume, iodata, is a software-based RAID.

iocean is under AppleCare warranty which provides hardware support for up to three years after purchase. We ordered a new disk from Apple through the Upper-Campus Tech Services and it arrived late afternoon on 7 March. We replaced the failed disk with the new disk the next morning, 8 March, and tried to start rebuilding the RAID array using the Disk Utility (GUI) tool on iocean. This is accomplished by dragging the new disk icon into the RAID window. However, this didn’t work. The GUI tool gave no indication as to why this failed. We next went to the commandline tool, ‘diskutil’ to diagnose the problem. Using the command:


===========================================
iocean:~ jrw$ diskutil list
/dev/disk0
#: type name size identifier
0: Apple_partition_scheme *233.8 GB disk0
1: Apple_partition_map 31.5 KB disk0s1
2: Apple_Boot 128.0 MB disk0s2
3: Apple_RAID 233.6 GB disk0s3
/dev/disk1
#: type name size identifier
0: Apple_partition_scheme *76.7 GB disk1
1: Apple_partition_map 31.5 KB disk1s1
2: Apple_HFS ioceanHD 76.6 GB disk1s3
/dev/disk2
#: type name size identifier
0: Apple_partition_scheme *233.8 GB disk2
1: Apple_partition_map 31.5 KB disk2s1
2: Apple_Boot 512.0 KB disk2s2
3: Apple_RAID 233.8 GB disk2s3
/dev/disk3
#: type name size identifier
0: Apple_HFSX iodata *233.6 GB disk3
===========================================


This showed that the old disk, ‘disk2′ (formated in Panther) had a slightly different partition mapping than the new disk, ‘disk0′. The disk2 had a smaller “Apple_Boot” (disk2s2) partition than the new disk formatted with Apple Disk Utility, thus, the main data partition (disk2s3) was larger than the old disk. The software RAID application won’t allow RAIDs with disks of dissimilar partition maps.

The solution:

Create a single filesystem disk out of the new disk using the Disk Utility partitioning option (HFS+ w/Case Insensitivity and Journaling) .

Copy the current filesystem running on the remaining disk of the degraded RAID set over to the newly formatted disk using Carbon Copy Cloner (or the Restore tab of Disk Utility).

Create a new unpaired mirror RAID set on the new disk, using the “enableRAID” command under the commandline ‘diskutil’ application.

Delete the old RAID array (do this with extreme caution because all of the data on this disk will be erased, i.e., make sure all of the data on this disk has been copied to the new unpaired RAID array before taking this step) using either Disk Utility (GUI) or diskutil (commandline).

Repartition the old disk (the remaining good disk in the old RAID array) so it matches the partition map of the new disk

Using the “repairMirror” option of the commandline ‘diskutil’ application, or by dragging the newly partitioned old disk into the new RAID set in Disk Utility, this disk is incorporated into the newly established RAID array.

The RAID repair, or rebuild, is run as a background process, which means that the computer continues to function online, though with somewhat degraded performance, throughout the rebuild. All user activity should be unaffected. If the problem with the different partition maps hadn’t cropped up, the entire process outlined above could have happened without ever taking the system offline. The physical disks are “hot-swappable” (they can be removed and inserted without taking the system offline) so they can be replaced and the RAID rebuilt without a break in service.

Mason and I have moved the dev CCE LTER into the Production area. Both the dev and production areas are versioned under Subversion. This makes it much easier to keep both sites in sync (with content, etc.).

The CCE LTER Site location is: http://cce.lternet.edu/

This afternoon I moved the new CCE LTER site to the ccelter-dev site, and in the process put the site under subversion. Anyone looking at the websvn site might notice a small jump in version numbers as I import the site and stumble around, correcting my initial errors. The old site has been preserved in the CCE LTER project space.