Ubuntu 12.10 to 13.04 Server Upgrade Error

Are you Googl’ing around trying to figure out why you’re getting this error when trying to `do-release-upgrade’ your Ubuntu 12.10 system, even though you’re pretty much up to date?

root@mia:~# do-release-upgrade
Checking for a new Ubuntu release
Traceback (most recent call last):
File “/usr/bin/do-release-upgrade”, line 145, in <module>
fetcher.run_options += [“–mode=%s” % options.mode,
AttributeError: type object ‘DistUpgradeFetcherCore’ has no attribute ‘run_options’
Error in sys.excepthook:
Traceback (most recent call last):
File “/usr/lib/python3/dist-packages/”, line 137, in apport_excepthook
os.O_WRONLY | os.O_CREAT | os.O_EXCL, 0o640), ‘wb’) as f:
OSError: [Errno 2] No such file or directory: ‘/var/crash/_usr_bin_do-release-upgrade.0.crash’

Original exception was:
Traceback (most recent call last):
File “/usr/bin/do-release-upgrade”, line 145, in <module>
fetcher.run_options += [“–mode=%s” % options.mode,
AttributeError: type object ‘DistUpgradeFetcherCore’ has no attribute ‘run_options’
deb quantal-updates main restricted
deb-src quantal-updates main restricted

I just burned a couple hours trying to figure out why I only got this error on one specific server. It turns out that it’s a bug in the version of  the ubuntu-release-upgrader-core package, and you must be pulling updates from a “quantal-updates” repository to get the fixed package when you `apt-get upgrade’. To fix this, edit your /etc/apt/sources.list and make sure you have the following two lines:

deb quantal-updates main restricted
deb-src quantal-updates main restricted

After making sure you have these lines, get yourself updated again and re-try the release upgrade script:

apt-get update
apt-get upgrade

…and you should be rollin’ towards Raring!


Proxy Authentication Against Devise-Based Ruby Applications

(Quick GitHub link!)

My team at TGen has a Rails application using a typical devise + cancan installation for authentication and authorization, respectively, and a related Apache HTTPD proxy server we needed to authenticate against active accounts in the webapp before passing traffic to their destination, which is a single host. We tried mod_authn_dbd for a while, but the combination of Devise’s default adapive bcrypt password encryption that is not supported by mod_authn_dbd by default, a complex set of SQL statements to process the authorization directly, and that none of the existing modules seem to be able to do what we want, made it a messy ordeal.

Instead, we created devise-proxy: a simple proxy server written as Rack Middleware that you can deploy using Passenger within Apache or nginx. You simply provide devise-proxy with a config.yml file defining the hostname and port of the devise webapp to use as an authentication web service, and hostname and port of a single server to use as a forwarding target.

Clients connecting to the proxy use the email/password for their proxy username/password credentials. All authenticated clients will be forwarded to your provided host/port, but using the path in the client’s original HTTP request. Clients failing to authenticate will receive a 403 and the forwarding host will never be hit.

gem install devise-proxy # to install

git clone git:// # to clone!

devise-proxy is released under a BSD license via the GitHub project, here. Good luck!

computer Uncategorized

How To Custom Brand The OpenStack “Horizon” Dashboard

I’m deploying OpenStack “Essex” on Ubuntu Server 12.04, and have the openstack-dashboard package installed to provide the web-based “Horizon” GUI component newly added for the Essex release. Canonical also provides an openstack-dashboard-ubuntu-theme package that brands the Python-based Django GUI. Despite that the last major Canonical-maintained packages based on the OpenStack “Diablo” release in Ubuntu 11.10 did not include an administrative GUI, Horizon — as a standalone component — has been very stable for a mainstream debut. In the future, though, I’d like to see a quick and easy way to change the default branding to use your own logo, colors, and titles using only the GUI’s administrative screens.

The horizon documents briefly mention branding customization to give you a head start, but you probably want more specific steps. Here’s my custom-branded Horizon dashboard with custom colors, logo, and site title:

Once you know where to make the appropriate changes, it’s super simple. Step-by-step:

  1. Create a graphical logo with a transparent background. The text “TGen Cloud” in this example is actually rendered via .png files of multiple sizes I created with a graphics program. I used a 200×27 for the logged-in banner graphic, and 365×50 for the login screen graphic.
  2. Set the HTML title (shown at the top of the browser window) by adding the following line to /etc/openstack-dashboard/
    SITE_BRANDING = "Example, Inc. Cloud"
  3. Upload your new graphic files to:
  4. Create a new CSS stylesheet — we’ll call ours custom.css — in the directory:
  5. Edit your CSS file using the following as a starting point for customization, which simply overrides the Ubuntu customizations made in the ubuntu.css file. Change the colors and image file names as appropriate, though the relative directory paths should be the same.
    * New theme colors for dashboard that override the defaults:
    *  dark blue: #355796 / rgb(53, 87, 150)
    *  light blue: #BAD3E1 / rgb(186, 211, 225)
    * By Preston Lee <>
    h1.brand {
    background: #355796 repeat-x top left;
    border-bottom: 2px solid #BAD3E1;
    h1.brand a {
    background: url(../img/my_cloud_logo_small.png) top left no-repeat;
    #splash .login {
    background: #355796 url(../img/my_cloud_logo_medium.png) no-repeat center 35px;
    #splash .login .modal-header {
    border-top: 1px solid #BAD3E1;
    .btn-primary {
    background-image: none !important;
    background-color: #355796 !important;
    border: none !important;
    box-shadow: none;
    .btn-primary:active {
    border: none;
    box-shadow: none;
    background-color: #BAD3E1 !important;
    text-decoration: none;
  6. Open the following HTML template in an editor:
  7. Add a line to include your new stylesheet: (I’ve highlighted the new line in bold.)
     <link href='{{ STATIC_URL }}bootstrap/css/bootstrap.min.css' media='screen' rel='stylesheet' />
     <link href='{{ STATIC_URL }}dashboard/css/{% choose_css %}' media='screen' rel='stylesheet' />
     <link href='{{ STATIC_URL }}dashboard/css/custom.css' media='screen' rel='stylesheet' />
  8. Restart apache just for good measure:
     sudo service apache2 restart
  9. Reload the dashboard in your browser and fine tune your CSS appropriate.

You’re done!


computer Uncategorized

OpenStack Nova Essex MySQL Database Schema Diagram and SQL

I’m in the process of setting up an OpenStack Essex installation on a small cluster of Ubuntu 12.04 servers using the Canonical-supplied and supported packages. I innocently and unfortunately ended up with a state corruption issue causing nova-compute to crash on startup, and found it necessary to dive into the schema as a troubleshooting aid. I used MySQL workbench to reverse-engineer the schema into an EER diagram as well as raw SQL. I’m sure others will find this useful as the OpenStack community slowly upgrades to Essex. Hope it helps!

[Download diagram, SQL, and MySQL workbench file]


OpenStack Diablo on Ubuntu 11.10 w/MySQL

If you’re installing the OpenStack cloud computing platform “Diablo” release on Ubuntu 11.10 server using the official guide and are using MySQL, don’t forget to:

sudo apt-get install python-mysqldb

The “glance” package (and probably others) are configured to use SQLite by default and do not automatically install this dependency by default. Unfortunately, the November 2011 version of the manual also fails to mention this and the log file (/var/log/glance/registry.log) prints a variety of “INFO [sqlalchemy.engine.base.Engine…” messages but no warnings or errors. I assume a corresponding comment applies to PostgreSQL as well but have not confirmed.


Quick FASTQ File Parsing Via Memory Mapping In C/C++

I recently had a need to speedily parse through 8GiB+ .fastq text files to calculate a simple statistic of genomic data. My initial “pfastqcount” implementation in Ruby worked fine, but with many files to process took longer than I had hoped in addition to consuming an alarming amount of CPU. I ended up reimplementing the pfastqcount command-line program in C, which takes one or more .fastq files, memory maps them, and creates the statistic. Simply dropping my algorithm down to raw C significantly sped up the process and reduced CPU usage, especially coming from an interpreted language. If any of you bioinformaticians find the need to implement a FASTQ data processing algorithm in C, I encourage you to fork the project and use it as a template. The project is Apache 2.0 licensed for your convenience and publicly available on GitHub.


Hacking Your Own Genome

Many thanks to everyone that participated in my Hacking Your Own Genome session at today’s Desert Code Camp 2011.2 event in Chandler, Arizona! I’m very passionate about the topic area, and hope the session was both entertaining and useful. Here are the presentation materials, source code for the “youandme” application, and a few other links you might find useful. Thanks again for the opportunity and don’t hesitate to reach out and stay connected!


Additional Links:

Have fun!



Amazon Finally Adds Lending Library

Late is better than never! (From the press release. Customer details here.)

With an Amazon Prime membership, Kindle owners can now choose from thousands of books to borrow for free - including over 100 current and former New York Times Bestsellers - as frequently as a book a month, with no due dates
Books can be borrowed and read on all Kindle E Ink devices and Kindle Fire

Not exactly the most giving of terms, but it’s a start. Thanks to the Kindle team!

personal Uncategorized

10 Universal Weight Loss Tips For Men

I’ve spent the majority of my adult life in the “obese” clinical strata, and have only in recent years taken to caring about maintaining a reasonable weight. I am an American male, 5’10”, with Koren-Caucation ancestry and have ranged between 149 and 172 pounds in the past year. My bodies individual natural comfort zone seems to be in the 150-155 range. At my heaviest I capped out in the 200-210 range. In other words, my physical stature and default dietary habits are spectacularly unspectacular for an American, and I consider myself fairly representative of the “average American male”. I lost most of those excess pounds (180+) in a fairly short amount of time. Everyone is unique in many ways, but from my own research and personal experimentation I believe these points to be largely universal for adult men.

Weight And Health

Weight loss does not necessarily correlate to health gain. It’s possible to lose weight on a diet of Twinkies, but you would be seriously lacking in dietary components despite being lighter, and most likely put yourself at higher risk of heart disease and diabetes. Assuming that part of your motivation for weight loss comes from a desire for better health and longevity, remember to see the forest through the trees. It’s great to look healthy, and better to be healthy.

As a general guidelines, stick to eating actual foods. (Edible substances like high fructose corn syrup should not be considered “food”.) If you couldn’t produce the ingredient if you really wanted to, you probably don’t want to eat it. You have tons of zero-calorie sugar replacements–Splenda, Nutrasweet etc.–but these are not magic bullets and generally should be avoided as “crutch” substances. See Michael Pollan’s excellent Food Rules for guidelines.

10 Tips

  1. Weight yourself daily at a consistent time with no excuses. It’s especially important to continue weighting yourself when you’re struggling to hold yourself accountable and to prevent prolonged lapses of judgement.
  2. Treat weight management as a lifestyle, not a program. Programs are things you do for a short period of time before going back to the status quo. Lifestyle changes are long-term investments made for the benefit of yourself and those you love.
  3. Drink water and tea when you are thirsty. Have other tasty beverages for enjoyment, not to quench thirst. Beer and other alcoholic drinks are unfortunately high in calories, as are many sodas and even fruit juices. Water first.
  4. Shop when you’re full. Plowing through the aisles on an omg-I-have-nothing-to-eat rampage is going to result in a cabinet full of snacks. You body evolved to crave certain foods to compensate for natural rarity. When you’re hungry, reason goes out the door, and satisfying cravings for those foods that are now readily available becomes the easiest fix.
  5. Visit only upper-tier merchants such as Whole Foods and Trader Joe’s when at all possible. In addition to higher quality foods, they do a much better job than conventional grocery stores of not barraging you with excess junk. Fruits and vegetables are also of notably higher quality and tastiness.
  6. Maintain the lifestyle because “nothing tastes as good as fit feels”, not to punish or deprive yourself.
  7. Talk about solutions with others doing the same. Being around others taking action is extremely encouraging and motivating. Keep in mind the exact opposite also applies.
  8. Focus more on diet than exercise. Both are necessary, but you’d be better served with a good diet and only 30 minutes of exercise per week than horrible diet and 4 hours of exercise per week. Many weight loss systems prescribe disciplined physical regiments, but remember that diet matters more.
  9. Weight train for weight loss. Additional muscle mass allows you to burn calories faster, even when you’re not exercising. Cardiovascular exercise is great for your heart and blood pressure, but doesn’t build the calorie burning, protein-consuming muscle like weight training does. Also remember that you cannot control where you lose weight: only where you build muscle. No one is going to see your rock hard abdominal muscles if your mouth can’t trade in the cheese sandwiches.
  10. Know when to break the rules. If you use a formal system such as Paleo or Atkins you may have strict guidelines. At some point, however, most foods are going to be ok in moderation so long as you can control yourself. It’s ok to not be perfect!








Good living and good luck. 🙂

computer personal

Preston And AT&T Give Each Other The Finger

I made the jump the last day before Verizon stopped offering unlimited data plans. The delay for switching to Verizon was not lack of motivation–AT&T service has always paled to Verizon in Arizona and is nearly nonexistent at my summer home–but in desperate procrastination of dealing with the migration process. My longest conversation (highly abbreviated) with AT&T on the matter took about an hour and was so traumatizing that I can’t see myself ever returning. As far as I’m concerned AT&T is dead and buried:

Coverage map showing AT&T's miraculous ability to provide "Best" service without operational towers.


Me: I’m not happy with my AT&T service and would like to cancel my service plan.

Customer Service Representative: I’m sorry to hear that, sir. May I ask why?

Me: I’m in an area with about 1-bar service about half the time, no 3G data (EDGE only), and constant dropped calls. I’m not really getting “service” per se.

Rep: I’m very sorry to hear that. We can cancel your plan for $<huge fee>.

Me: Well… I really don’t think that’s entirely fair. The issue isn’t really that I don’t WANT service, but AT&T isn’t providing what I’m already paying for. I’m paying about $100/month for unlimited 3G data, <list of other features>, and I only get a few of them some of the time. Check the coverage map.

Rep: Yes, sir! I can see you live in a “Best Coverage” area. That is very good!

Me: 1-bar signal 50% of the time, no 3G and dropped calls the other 50% is “Best Coverage”?

Rep: The map shows we have multiple towers in the area! You should be getting great service according to the map.

Me: I understand what the map says; I’ve seen it many times, trust me. The issue is not just me, though. No one else with AT&T seems to get usable service here, either.

Rep: I’m very sorry to hear that, sir. One of the towers is not operational. That may have something to do with it. Would you like us to send out an engineer to test your hardware?

Me: Wait… what? First, my hardware is fine. It works fine in <other cities with service>. No one else’s phone works well here on AT&T’s network, either. Second, if you’re dispatching an engineer wouldn’t it make sense to fix the tower instead? …You know, the NOT OPERATIONAL one that is currently providing “Best Coverage”?

Rep: Unfortunately we cannot do that, sir.

Me: It doesn’t make sense to charge me for a service you just admitted you can’t provide. I understand I’m under contract and don’t dispute that, but AT&T has obligations, too, and if AT&T can’t meet them it isn’t right to punish the customer.

Rep: Unfortunately, sir, it is your fault for choosing to live in an area without good service coverage.

Me: ARE YOU FUCKING SERIOUS??? I checked your goddamn map before, during and after moving here, and the fucking thing says “BEST COVERAGE” despite having a non-operational tower. I’ve been here for some time now and it’s never been any better.

Rep: Yes, sir! Coverage in that area is strong. Would you like us to send out an engineering to test your equipment?


Rep: Like I said, sir, it is AT&T’s policy to charge cancellation fees according to your contract. We cannot even consider overriding them in such a strong service area.

Me: <Infuriated abrupt disconnect.>

So, I’m now staring at a ridiculous cancelation bill. On the bright side, though, I sold my old AT&T iPhone the next week via eBay for over $200, which not only covered the new Verizon hardware cost but activation fees as well. I’m not getting great 4G on my Mifi (which was disclosed though), but at least I’m getting ok 3G and voice service on my iPhone for about the same price. AT&T? Please.