Just a few rss feeds

spoofedpacket
IPv6 addresses not available at boot

One of things that’s always bugged me regarding Linux and IPv6 is the
behaviour that’s exhibited during boot time. Specifically, the short delay before IPv6 addresses transition from their “tentative” state on an interface to being fully available for use by various daemons and services. With IPv4, you can be pretty much guaranteed that you can bind to any of the configured addresses at boot time, under normal circumstances.

With IPv6 on Linux, things aren’t so straightforward. Duplicate Address Detection (DAD), which basically does what it says on the tin, introduces a short delay before addresses are fully configured, the address has been added to the network interface, but not really.

I recently came across this whilst attempting to get BIND to listen on some secondary service addresses on a particular machine. BIND would not er, bind, to the IPv6 addresses at boot, failing with messages like this:

bind9 could not listen on UDP socket: address not available

Modifying /etc/init.d/bind9 to print the output of “ip addr show” to a file at the time BIND attempted to start up showed the tell-tale “tentative” flag on each IPv6 address being added to eth0. Since the addresses are in this state, BIND or other daemons will refuse to listen on them.

The problem has become very noticeable since parallel boot systems such as Upstart have become the default in quite a few Linux distros. Daemons will often fire up before the network is fully ready and in some extreme cases network filesystems that reference hostnames may fail to mount if you are using an IPv6 DNS resolver. Of course this isn’t the case across the board, some daemons and services appear to handle the unavailability of an IPv6 address somewhat gracefully, backing off and trying again a short time later rather than simply giving up on the first go.

Anyway, a simple “hairy hack” to get over this problem is to add something like the following to your startup script:

sleep 5

Yes, a one line sleep command to make the daemon wait a short while before actually starting. This seems to ensure that the IPv6 address has moved out of the tentative state, but it’s still somewhat silly..

spoofedpacket
Dubs From Hell

Techno Police

At Eirtakon this year I presented a panel on a particular interest of mine, awful anime dubbing. It’s one of these things that always gets a good few laughs, especially when you present clips of some anime dubs that, whether through accident or design, are just hilariously inept, completely nonsensical, or downright offensive.

Quite a few people approached me after the panel and asked could they have copies of the clips I played. Since all of them are actually available on youtube, I thought I’d post some of the highlights here.

So we start off with some of the attempts that companies localising anime made to translate the opening for a particular show. Some of these were valiant attempts, others were just epically bad.

So that about sums it up… or does it? If you find this kind of thing hilarious, I recommend you check out Bad American Dubbing from the Corn Pone Flicks guys, or Mike Tool’s Dubs That Time Forgot panels. I stole some of my funnier content from these guys ;)

googlereader
Tahoe-LAFS 1.9.0
Tahoe-LAFS (Least Authority File System) is a decentralized data store. It distributes your filesystem across multiple servers, and even if some of the servers fail or are taken over by an attacker, the entire filesystem continues to work correctly and to preserve your privacy and security.

Changes: This release offers a new mutable-file format (more efficient for large files), a file blacklisting feature, and a "drop-upload" feature. It includes several bugfixes and other improvements.

Release Tags: Major

Tags: Communications, File Sharing, Clustering/Distributed Networks, Archiving, backup

Licenses: GPL, Transitive Grace Period Public Licence

Posted
googlereader
Online Checkout - In Real Life
I liked a YouTube video: Shopping online is meant to be easy. Find out where your customers are "checking out" with Google Analytics.
Posted
googlereader
What's Cooking This Weekend? Weekend of October 29-30, 2011

Happy Friday, folks, and happy almost-November. We hope that you enjoyed Soup Week as much as we did. I'm certainly enjoying my soup leftovers (doesn't soup make the best leftovers? Always better than the day before). What is cooking in your kitchen this weekend? We'd love to hear what you have planned! Also, take a look at a few posts that you may have missed from the past week.



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googlereader
Canning Homemade Soup: Is It Safe?

2011_10_28-soupjars.jpgHomemade soup is so much tastier than the store-bought canned stuff (and often healthier, too). Fortunately, it's possible to can your own soups from chicken stock to carrot soup to chili, and for the most part it's pretty simple ... but there are a few important guidelines.



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googlereader
Easy Entertaining With Soup: Asian Hot Pots

2011_10_28-HotPot.jpgCold-weather entertaining doesn't get much easier — or cozier — than throwing a hot pot dinner party. Not only is a hot pot dinner an economical, low-stress way to feed a group, eating bowl after bowl of soup warms you to the core, making this the ideal meal for chilly evenings. The only work involved is making the broth, gathering the equipment, and prepping the ingredients beforehand.



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googlereader
NAMD 2.8
NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

Changes: Numerous enhancements.

Release Tags: Enhancements, Stable

Tags: Scientific/Engineering, Bioinformatics, Chemistry

Posted
googlereader
Man Drives Honda 1 Million Miles

Honda threw a surprise parade for a Maine car owner who became the first ever documented driver to rack up one million miles on the odometer. He did so behind the wheel of his 1990 Accord, which he's kept running smooth all this time.

The Portland Press Herald reports that the parade included marching bands from the local high school and middle school and the high school's varsity cheerleaders. Dancers rolled tires up and down the street and lofted oversized photos of the man, Joe LoCicero. A plane flew overhead carrying a banner that said "Way to Go Joe!"

Then Miss Maine USA Ashley Marble delivered Joe his prize: a brand new 2012 Accord, cobalt blue, just like his trusty million-mile-surpassing original car.

"Joe is a testament to what you can do if you maintain your car," the director of operations for a local auto body shop told the Portland Press Herald. "Thankfully, not many people do it or we'd be out of business."

The car's seat belts, steering wheel and upholstery have all been replaced, along with the fuel pump. But the engine and transmission are original.

Joe is an ex-mechanic and he did most of the work on it. His secret to keeping the car alive so long? Following regular maintenance schedules, using only good parts, and obeying the rules for safe driving.

Honda goes the distance: 1 million miles [The Portland Press Herland]

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spoofedpacket
The strange world of the Coffee Syphon

At the risk of exaggeration, there are almost as many ways to make coffee as there are different blends of the stuff. From the French Press and the humble filter, to the Espresso Machine and the innovative Aeropress. But for sheer theatrics, nothing beats the weird-as-all-get-out Coffee Syphon.

It’s certainly not the most convenient method to make your cup of joe, best approached on a quiet Sunday afternoon, but it does produce an amazingly clean and balanced brew with little to no leftover grit.

Invented in Germany in the 1830s, the Coffee Syphon, also known as the vacuum pot, is one of the older methods of producing coffee. It was actually quite popular in most households up until the 1960s, when more convenient coffee machines and instant coffee appeared on the market. They normally consist of two parts made from heat-resistant glass – a lower flask and an upper chamber with a long glass tube and a rubber seal. When placed together, a seal is created allowing a vacuum to be formed. A filter made from metal or cloth is placed between the upper and lower chambers.

The principle of the device is pretty straightforward. Heat some water in the flask, the water expands up the glass tube into the upper chamber where the coffee grounds reside, allow the brew to steep for a minute or two and remove the heat. The liquid then contracts as it cools and moves back down to the lower chamber, getting filtered on the way.

The setup

The particular syphon that I have is a TCA-5 made by Hario of Japan, where these things still seem to be reasonably popular. There are many different possible heat sources, stove-top models also exist, but this particular syphon comes supplied with an alcohol burner that sits below the flask. It consist of a cotton wick and alcohol container, the wick is immersed in the alcohol a few minutes before use. Clean-burning alcohol such as methylated spirits should be used, which can be obtained from most chemists.

The alcohol burner.

The TCA-5 comes with a cotton filter secured to a metal disk. The disk also has a spring-loaded chain that you attach to the bottom of the glass tube of the upper chamber. It’s important not to let the cotton filter dry out after use, otherwise stale coffee flavours will stick around, so I keep it stored in a small lunch box filled with water.

Cotton filter stored in water.

A small clip holds the spring loaded chain to the glass tube. I always try to center the filter in the upper chamber as much as possible, this ensures that no grinds can bypass the filter.

Attaching the filter.

The best grind size for the syphon seems to be something between filter and espresso. Not too fine but not overly coarse either.

Adding the coffe grinds.

I always boil up some water beforehand, you can use the burner to do this but I’d imagine it would take a very long time. The burner is then lit and the upper chamber is placed onto the flask.

Lighting the burner

Once the flame looks clean (more blue than orange), it’s placed under the flask and the whole apparatus is sealed by pressing the upper chamber and the flask together.

Soon after, the water will quickly shoot up into the upper chamber, creating bubbles and a nice coffee aroma.

Bubbling coffee.

Once most of the water is gone from the flask, a very small amount will be left in the bottom, allow the coffee to steep in the upper chamber for a minute and stir it. Then the heat is removed and the vacuum takes over.

Heat removed.

Going..

..going

..gone.

Pouring out the coffee.

There’s very little left in the bottom of the cup once the coffee is drunk, especially if you compare this to what’s left after a cup of french press coffee.

Clean!

flickr
P1010985

jcftang posted a photo:

P1010985

Got a bottle capper and I was bottling my own kombucha. This was my batch of mango and passion fruit flavoured kombucha, it was surprisingly good.

Posted
linuxjunk
Sum weights
I have a file with a bunch of sequences and some weights at the top of the file:

>WEIGHTS 0.926434 1.000000 1.000000 0.926434 1.000000 0.892712 1.000000 1.000000 1.000000 1.000000 1.000000 0.892712 
>CRTC_EUGGR__Q9ZNY3 Calreticulin precursor.
XRKELWXXXXXXXXXXXXXXXXXXXXXXXXXTRWTHSTXXSDYXKFKLTSGKFYGDKAKDAGIQTSQDAKFYAISSPIASXXSXEXXXLVLQFSVKHXXXXXXGXGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKXEPRCEXDTLSHTYXAXXXXDXXXEVLVDQVKKESGTLEEDWEILKPKTIPDPEDKKPADWVDEPDMVDPEDKKPEDWDKEPAQIPDPDATQPDDWDEEEDGKWEAPMISNPKYKGEWKAKKIPNPAYKGVWKPRDIPNPEYEADDKVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFYDQTNGATKDAEKKAFDSAEADKRKKEEDERKKQEEEEKKTAEEDEXXXDEXXXEDDKKDEL
>HSP47_RAT__P29457 47 kDa heat shock protein precursor (Collagen-binding protein 1) (GP46).
XRSLXXXXXXXXXXXXXXXXXXXXEAAAPGTAEKLSSKATTLAEXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKXXXXSQAKAVLSAEKLRDEEVHTGLGELVRSLSNXTARNVTWKLGSXXXXXXXXSFADDFVRSSKQHYNCEHSKINFRDKRSALQSINEWASQTTDGKLPEVTKDVERTDXXLLXXAMXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYXYXXXXXXXXQXVEMXXXXXXXXXXXXXXXXXXXXXRLEKXXTKXQLKTWMGKMQKKAXXISLPXGVVXVTHDLQKXXAGLGLTEAIXKNKADLSXXSGXXXXXXXXXXXXXXXEWDTEGNPFDQDIYGRXXXRSXXXXXXXXXXXXXXXXXXXXXXXXIGRLXXXXGDKMRDEL
>ENPL_PIG__Q29092 Endoplasmin precursor (94 kDa glucose-regulated protein) (GRP94) (GP96 homolog) (98 kDa protein kinase) (PPK 98) (ppk98).
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
>CRTC_HUMAN__P27797 Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) (grp60).
XLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTSXXIESXXXSDFXXFVLSSGKFYGDEEKDKGLQTSQDARFYALSASFEXXSXXXXXLVVXFXXKHXXXXXXGGGYVKLFPNSLDQTDMHGDSEYNIMFGPDIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTYEVKIDNSQVESGSLEDDWDFLPPKKIKDPDASKPEDWDERAKIDDPTDSKPEDWDKPEHIPDPDAKKPEDWDEEMDGEWEPPVIQNPEYKGEWKPRQIDNPDYKGTWIHPEIDNPEYSPDPSIYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAYAEEFGNETWGVTKAAEKQMKDKQDEEQRLKEEEEDKKRKEXXXAXDKEDXEXKXEDXXDXXDKXXDXXEDVPGQAKDEL


I want to sum the weights which is fine for this example with like 12 sequences. However, some of the files have a couple of hundred entries. Step in Bash:

 head -n 1 filename.txt | awk '{for (i=1; i<=NF; i++) s=s+$i}; END{print s}'

Giving me the sum of the weights! Woohoo.
Posted

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Just a few rss feeds

Here lies some RSS feeds of blogs of colleagues, friends and stuff.

  • frau-klein-blog: Cannot detect feed type (0 posts)
  • linuxjunk: last checked (27 posts)
  • spoofedpacket: last checked (18 posts)
  • irishbornchinese: last checked (10 posts)
  • last.fm: last checked (6941 posts)
  • googlereader: last checked (2016 posts)
  • flickr: last checked (309 posts)
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