Mine the Harvest

While I am not a big iTunes fan, the analogy is at least somewhat accurate and sums up some of the key benefits of Mendeley Desktop quickly. Like iTunes, it provides a client you can use to organize, access and interact with media - in this case research papers rather than music. The cross platform client runs on Linux, OS X and Windows and can sync your research library with on-line storage you can access anywhere. Some of the key features I like are:

Features

* Search your entire library of papers very quickly. Make notes, and define tags, for papers which stay with them and can also be searched. Searching within dozens of PDFs seems to execute very fast.

* Automatic retrieval of document information based on analysis of metadata in the paper. Mendeley will scan the paper, identify the author and name of the paper, and if it finds a DOI or PMID publication catalog number it can then pull in additional metadata for the paper for you - all very painlessly. Very cool.

* Allows you to create collections which can be shared publicly (I’ve not used this feature yet.)

* On-line library of thousands of paper to browse and easily download. Note: Unlike iTunes, Mendeley is not a publishing agent per say - they simply point you to where the research can be found. Thus you may get directed to sites like the ACM or IEEE digital libraries, or various sites for medical research, which require an account to access. To make maximum use of Mendeley you may want to find out if your company or school has an account which provides access to these publications. (There are many papers available however which do not require this additional access.)

* The web site presents the current, mostly highly read papers, organized by discipline, which makes finding interesting things to read very simple.

* Web importer: A Javascript bookmarklet that imports documents you find on-line, and associated .PDFs if possible, into your library.

* Provides social network opportunities by searching for other Mendeley users, viewing their publications and bio information, and contacting them through Mendeley.

* One of the best features is integration with OpenOffice / MS Office which makes adding citations a snap. Choose your citation format and use the plug-in for your Office Suite and you can painlessly add citations with abandon. Oh the glory.

Getting Started

In addition to downloading the desktop client, I recommend reading the Getting Started Guide which will orient you on how to add existing papers you may have into Mendeley and how the metadata analysis works. It also shows how to use the OpenOffice plug-in for citing works.

Note that if you wish to synchronize your PDFs with your on-line account, you must enable this. Use the “Edit Settings” button (near the middle center of the tool bar).

You can add existing PDF simply by dragging and dropping them into Mendeley. This places them in a “needs reviewed” status during which you can have Mendeley search online for additional information. (It does this automatically, but if you need to do so manually: Right click on the document, select “mark as” and choose “Needs Review”. A dialog will now appear asking if you want to try automatically searching.)

Now, just start browsing for papers at the Mendeley site and use the bookmarklet when you are browseing to import items into your Mendeley.

Happy reading!

(Update: I’ve written the Wiki now and you can find it here.)

So I’ve been playing around with NVIDIA’s CUDA Toolkit and SDK and reading this book that just came out “CUDA by Example”. (See this Linux Journal article for some general back ground on CUDA.)

This is pretty interesting (and fun) stuff. So far I’ve gotten the toolkit installed and compiled the sample code projects in the SDK. I have to use my workstation at work as (sadly) my ancient ass NVIDIA card at home is not CUDA capable and my system is so old it is really just a type writer at this point.

Running just the sample CUDA projects is pretty impressive though. My old school GeForce 8800 at work has a meager 32 cores. (The card I just ordered has 96, and the most recent Fermi architecture ones have 448 and 6GB - yea, holy crap.) However, with only 32 cores it renders the particle, smoke and other samples quite nicely. These are rendered in 3D, allowing you to change perspective, and sometimes alter the particle density, light source, etc.  They are just examples showing how to run general purpose code (and render results in OpenGL) on the GPU.

So then I thought - I would like to forward the rendered OpenGL images to my workstation at home. Alas, SSH, VNC, et. al all actually send the OpenGL to the client to be rendered. Enter VirtualGL, which does just what you would think - it attaches a loadable module to an executable which intercepts OpenGL requests and send them to the local GPU for rendering, putting the results into a pixel buffer which then gets sent to the client. Wow. You can run your rendering in a data center and forward the results anywhere. That’s nifty!

Here is a picture of the CUDA smoke particles sample, being rendered at work, and forwarded via SSH X Forwarding with rendering handled by VirtualGL. (I think Geek Level just dinged.)

I’m going to write up a wiki on this stuff, but if you have any recent NVIDIA card (8800 or newer) , even a mobile one, you likely have the capability to run CUDA. If you are interested you can download the Toolkit and SDK and have at it. (Update: I’ve actually written the Wiki now and you can find it here.

After testing the CUDA waters I have to say I am very impressed. I can easily see CUDA being integrated into many applications in the near future. There are already plugins to offload MS Excel formulas onto the GPU, run Mathmatica on it, etc. The integration of multi core CPUs, in even consumer class hardware, combined with the capabilities of GPUs very well might make things go from a “multi core revolution” in consumer computers and into a “massively parallel revolution”. In fact, it’s already happened. Massively parallel computing is now capable on your notebook, it just has not been fully exploited yet. (Think of the cryptographic fun you could have.) Of course once Apple catches on, it will be called iMassive.

This is just all pretty fascinating to me. My first computers had 4Mhz Motorola CPUs, 32K of memory, etc. and now I just bought a 98 core GPU which I can write code in CUDA C and run general purpose computations on. Wow. And I’m getting ready to get an i7 too - it’s all just a bit dizzying. But very fun.

If you have not checked out CUDA, I highly recommend it. It’s a good opportunity to learn more about massively parallel computing, which I think we are going to be seeing a whole lot more of.  You can easily  find the book “CUDA by Example” It requires basic to intermed iate C skills, but not OpenGL or other graphics languages at all - you learn CUDA C as you go and start writing parallel code very quickly.(Amazingly, the run time just integrates the GPU device code and host code, and you can invoke code to run on the GPU as easily as any C function. It is some hot stuff behind the scenes, but surprisingly easy to code.)

Heavy Metal Tour - 2009

Last weekend Syd and I went on a long anticipated wreck diving trip in the Florida keys. We completed our wreck and Advanced Open Water certifications two years ago, and were able to do one dive on the Spiegel Grove back in 2009. Since then we have done many other dives, and completed our Master Diver rating, but we have wanted to return to the Keys for some more wreck dives — a “Heavy Metal Tour”, and thus we jumped at the opportunity to do this trip with our friend Travis from Macs Sports in Clearwater. We had a series of unbelievable dives, managed to take some of our best diving pictures to date, dove two new wrecks, and had a wonderful time.

The deep calls

The Wreck Dives

We completed four wreck dives the first two days, then finished off the third day with two shallow reef dives. The wrecks included the USS Spiegel Grove, USCG Duane (twice) and the Eagle. Although we had planned on diving the Bibb too (a sister ship to the Duane), we were unable to obtain a mooring as the local fishermen had camped out ï¾ them, and so we did two dives on the Duane. All the wreck dives were deep dives (100′ +) on Nitrox (32 to 34 %ï¾ O2) , and ï¾ bottom times varied about :30 to :40 per dive. Visibility was 60′+ with water temp at 85 degrees and calm seas of about 1′ - in other words, the conditions were ideal. There was some moderate to strong current, most noticeable on the descent line. There was at least some penetration or swimthroughs on all the wrecks. The operator on all dives was Florida Keys Dive Center in Islamarada, and they provided well maintained boats and a professional crew. Our dive master was our buddy Travis who, as always, conducted a fun, adventurous and safe trip.

The Spiegel Grove (Day 1)

Our first dive was on the USS Spiegel Grove, diving with Joe, a dive guide from the dive shop. We decided to get a guide for this dive as this is a massive vessel - at 510 feet long there is a lot to see, and diving with someone who knows it well can really help optimize your bottom time. Our hope was to penetrate into the wreck a bit and do some exploring, as we did on our last dive on it. (Or last guided dive on the Spiegel included penetrating several rooms as passages and dropping into the hold at 110′).ï¾ Although we had a good dive on it, and did some swimthroughs, we did not get into the wreck as much as we had hoped. There were some less experienced divers tagging along who seemed to enjoy cutting us off in passages and being generally oblivious, so we had a pretty mellow dive - but don’t get me wrong, this is one stunning wreck no matter what, and there was still adventure to be had. The trip down the decent line was rather interesting as there was strong current, and you certainly had to pull your way down - if you let go you would find yourself a LONG way from the boat.ï¾ Once on the wreck the current was easier to contend with and we had a very good dive. Unfortunately we did not get too many pictures of this dive, but it was great to see this wreck again.

The Duane (Day 1)

After our surface interval we were soon moored off to our next wreck, the USCG Duane. Like the Spiegel, this coast guard cutter was intentional suck, and is also resting straight on its keel, providing a stunning profile. With the deck at 100′ you can look up at the intact tower and crows nest, and it makes for a pretty amazing sight:

USCG Duane Mast

The wreck is covered in coral - the term “artificial reef” means exactly that, it truly is a reef with a great variety of marine life living on it and all around.

These wrecks create complete ecosystems and are teaming with life.

Duane Deck

Of course, these pictures hardly do it justice. There is abundant life all around this wreck, a mountain of steel and coral to explore.

Duane Ladder

The current on this wreck was also quite strong on the descent line, but manageable on the wreck. Just where the descent line started there were a number of dives who seemed to be meditating peacefully, and quite motionlessly. One had lost a fin which I snagged as it floated past and returned it to him. After a few minutes of waiting we had to just move past them. Unfortunately in so doing I made an interesting discovery. Fire coral not only thrives on the wreck but apparently also enjoys a healthy existence on floats on the mooring line as well. Interesting. As I passed around the the divers and float I managed to contact the float with my forearm and upper arm. The sting was a bit strong immediately, and within a minute was throbbing nicely at depth, giving me something to look forward to. Oh well - I now know to give those floats much wider clearance in the future. (The scarlet rash got nice and sticky for a day or two, and then just itched good for a week and is now almost gone. Nasty little beastie that coral - amazing stuff really.)

Current? Naw. . .

Once on the wreck we had a great time exploring it. It has such a great profile, and many rooms, windows and passages to look in - filled with fish and painted in coral, it is like a ghost ship that keeps luring you around new corners. We made several passes in and around the main decks of the superstructure. Syd caught this picture as I was advancing up the wreck port side:

Pete on the Duane

The Duane is a great wreck dive, offering many swimthroughs, an intriguing profile, and lots of things to look at. You could dive this wreck many times and have nothing but new experiences on it.

The Duane (Day 2)

Since our plan to dive the Bibb had to be scrubbed, we returned again to the Duane for our first dive of the day. While we had looked forward to the Bibb as another new wreck, and the opportunity for a bit deeper dive at 130′ feet, it was hard to be disappointed to return to the Duane. This time we dropped onto her bow and worked our way toward the superstructure, where we explored for quite a while. We did several swimthroughs and once again got some excellent pictures:

After we turned the dive and headed back to the ascent line though it took everything you had to swim against the current. We almost dropped to the deck to hand-over-hand the way back along the edge, or try to get out of the current by getting out of the open water and skimming just above the deck, but we were able to make just enough headway to just angle up toward the line.

Entering the Duane

We had nice, slow ascents from both dive with deep stops at 50′ and then a normal safety stop at 15′ to 20′. Here is a group of divers all hanging out on the safety stop:

Divers on ascent line

The Eagle (Day 2)

Or last dive on our wreck tour was the Eagle. Unlike the first two, this one sets on her side with her hull broken completely in half. This makes for an excellent figure eight tour allowing you to see all sides of her and offering several swimthroughs and places to explore. There were many great things to investigate, such as this wench, completely covered in corals:

Eagle Wench

Here is a picture of Syd just before we started into exploring the Eagle - she would have brought the Explorers Club flag, but it was not feasible due to the current:

Ready to Explore

This ended the wreck diving portion of our trip, and we were completely happy with these dives. The conditions were very good, the dives offered good challenges, we got to use several different skills, and we even managed to come away with some respectable photos this time. Underwater photography, we have learned, is a fickle bitch - and either we are getting better, or just got lucky this trip.

Syd near Eagle’s Mast

Here is a picture of Syd near the mast of the Eagle - note how thick the coral growth is on this wreck, the entire structure is covered in extensive growth such as this. The flashlight high intensity LED flashlight helps bring out the natural colors of the coral, even in the day light. At 100′ down, the colors are nearly gone.

Although our Heavy Metal Tour was over, our trip was not. This night we went out with our dive group, heading to Wahoo’s on Islamorada per Travis’ recommendation. It sites oceanside, with a wonderful patio providing the idyllic Florida Keys view. We sat with a wonderful couple we had just met on this trip and had a great time visiting with them. Having a beer on the deck on a summer evening after some awesome wreck diving was not a bad way to end off this part of the trip, and put us in a perfect mood for the reef dives yet ahead.

The Reef Dives

You sometimes can forget how beautiful these dives can be. Our diving through the winter and spring had all been inland cavern diving. Then you get back to the reefs and remember how amazing these ecosystems are. On our first dive, I was delighted to get a decent shot of three lion fish hiding under a coral outcropping. While lion fish are unfortunately an invasive specie in the Keys, and are a definite problem, I still love seeing them - it always amazes me watching them, they are so beautiful and exotic. One of my early goals as a diver was to see lion and stone fish, and I am still thrilled every time I do.

Evil, yet beautiful.

But that is not all we saw on these dives: Several eels (moray and spotted), and innumerable lobsters were also about. Here is a picture of me fencing with a big one. If you put your finger out and lure them toward you, you can get them riled up a bit and wanting to fight you. Ummm . . . tasty, tasty bugs. . .

Killer Lobster

There were tons of lobsters on these dives, hiding under coral ledges, in crevaces and even just out in the open. They are a bit fiesty, and you can get them to spar with you. When they have had enough though they can really move! Good thing these things are lower on the food change and smaller then us. (Think Alien vs. Predator vs. Lobster.)

The lighting improved on the second dive as the morning rain clouds drifted back to where ever they had come, letting far more light down to the bottom. This allowed Syd good opportunity to catch some pictures of a few of the tropicals and corals you get to see on these dives.

Purple Sea Fan

She really scored on getting some great shots, including this purple sea fan - it is hard to get a picture of these that maintains some of their beautiful color.

Venus Fly Clam?

Tomorrows Dives

This was a great trip to the Keys, with excellent dives, good wreck diving practice, calm seas and great visibility. After doing these dives Syd and I are more interested than ever in doing some more wreck diving. We would love to do the newly sunk USS Vandenburg off Key West, and of course the USS Oriskeny air craft carrier near Tallahassee.ï¾ Perhaps someday we can even return to Micronesia and dive the Nuclear Fleet off Bikini atoll.

Thanks for reading, and we hope you like the pictures. If you like, leave a comment - we would love to hear from you.

We have wanted a wireless printer for our home, and I’ve been waiting for the prices to become reasonable. Then last weekend we scored on a refurbished Photosmart Premium C309g-m at CompUSA. Normally $199, we got it with a -$120 instant savings for a total of $79 at the register. For a 802.11g + Bluetooth enabled, reasonable quality photo printer and scanner, $79 just was a damn good deal. Especially considering it uses separate CMYK cartridges - it’s exactly what we were looking for. Best. Price. Ever.

But the best thing about it really is the fantastic Linux drivers HP provides via the HP Linux Imaging and Printing (HPLIP) software. You can download the latest version at the official HPLIP site, but you might very well find it is already installed in your Linux distro, it commonly is these days. Just check to see if you have commands such as hp-setup, hp-wirelessconfig or hp-toolbox already. If not, see if hplip is available in your distors repository, or download it using the above link.

Once installed you will have an HP icon in your systray for quick access to your printer settings:

 

I first used HPLIP about two years ago at work and was delighted to see how complete it was. It provides a full set of tools to interface with HP devices from Linux and provides a delightful user experience.

On my device, which is a relatively new product, nearly all functions are supported: Wireless printing of course, photo printing (see tips below) and even wireless scanning - which really surprised me. Overall, using this printer in Linux- like many other HP products - is very well supported. Way to go HP!

I did however run into a few little issues which had to be worked though, and you may encounter the same. So here are some notes on what  I did to resolve the snags I encountered.

(continue reading…)

With Lucid, the standard Ubuntu repos no longer contain the Sun version of Java, having opted instead to just go with openjdk. While I can certainly understand the desire to have openjdk be the truly open solution, I am accustomed to the Sun version. Also, when using java-6-openjdk , I ran into a very annoying situation where apt kept running into the following issue when you attempted any transaction:

error adding signet.pl/signet_ocspklasa3_pem.crt
error adding signet.pl/signet_pca2_pem.crt
error adding signet.pl/signet_pca3_pem.crt
error adding signet.pl/signet_rootca_pem.crt
error adding signet.pl/signet_tsa1_pem.crt
error adding spi-inc.org/spi-ca-2003.crt
error adding spi-inc.org/spi-cacert-2008.crt
error adding telesec.de/deutsche-telekom-root-ca-2.crt
failed (VM used: java-6-openjdk).
dpkg: error processing ca-certificates-java (–configure):
subprocess installed post-installation script returned error exit status 1

In addition, I was having trouble with the openjdk in Eclipse with Subversive and was longing for the Sun Java version. But it was nowhere to be found in the repos. Sigh.

I Googled about and saw a lot of similar difficulties and frustration that the Sun version was not available. Sure, you can install it and the browser plugins, etc. manually, but really - why? Fortunately, I was able to find a simple solution to install sun-java6-jdk on Lucid!

This very simple fix came from this blog site.

Just remove openjdk if you already installed it:

sudo apt-get remove  openjdk-6-jre icedtea6-plugin

Now, set up the partners repo and install Sun Java from there:

sudo apt-get install python-software-properties
sudo add-apt-repository “deb http://archive.canonical.com/ lucid partner”
sudo aptitude update
sudo aptitude install sun-java6-jdk

Done!