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• Configuration management in support of scientific computing

  - by Sharpie

  For the past few years I have been involved with developing and maintaining a system for forecasting near-shore waves. Our team has just received a significant grant for further development and as a result we are taking the opportunity to refactor many components of the old system. We will also be receiving a new server to run the model and so I am taking this opportunity to consider how we set up the system. Basically, the steps that need to happen are: Some standard packages and libraries such as compilers and databases need to be downloaded and installed. Some custom scientific models need to be downloaded and compiled from source as they are not commonly provided as packages. New users need to be created to manage the databases and run the models. A suite of scripts that manage model-database interaction needs to be checked out from source code control and installed. Crontabs need to be set up to run the scripts at regular intervals in order to generate forecasts. I have been pondering applying tools such as Puppet, Capistrano or Fabric to automate the above steps. It seems perfectly possible to implement most of the above functionality except there are a couple usage cases that I am wondering about: During my preliminary research, I have found few examples and little discussion on how to use these systems to abstract and automate the process of building custom components from source. We may have to deploy on machines that are isolated from the Internet- i.e. all configuration and set up files will have to come in on a USB key that can be inserted into a terminal that can connect to the server that will run the models. I see this as an opportunity to learn a new tool that will help me automate my workflow, but I am unsure which tool I should start with. If any member of the community could suggest a tool that would support the above workflow and the issues specific to scientific computing, I would be very grateful. Our production server will be running Linux, but support for OS X would be a bonus as it would allow the development team to setup test installations outside of VirtualBox.

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• Configuration management in support of scientific computing

  - by Sharpie

  For the past few years I have been involved with developing and maintaining a system for forecasting near-shore waves. Our team has just received a significant grant for further development and as a result we are taking the opportunity to refactor many components of the old system. We will also be receiving a new server to run the model and so I am taking this opportunity to consider how we set up the system. Basically, the steps that need to happen are: Some standard packages and libraries such as compilers and databases need to be downloaded and installed. Some custom scientific models need to be downloaded and compiled from source as they are not commonly provided as packages. New users need to be created to manage the databases and run the models. A suite of scripts that manage model-database interaction needs to be checked out from source code control and installed. Crontabs need to be set up to run the scripts at regular intervals in order to generate forecasts. I have been pondering applying tools such as Puppet, Capistrano or Fabric to automate the above steps. It seems perfectly possible to implement most of the above functionality except there are a couple usage cases that I am wondering about: During my preliminary research, I have found few examples and little discussion on how to use these systems to abstract and automate the process of building custom components from source. We may have to deploy on machines that are isolated from the Internet- i.e. all configuration and set up files will have to come in on a USB key that can be inserted into a terminal that can connect to the server that will run the models. I see this as an opportunity to learn a new tool that will help me automate my workflow, but I am unsure which tool I should start with. If any member of the community could suggest a tool that would support the above workflow and the issues specific to scientific computing, I would be very grateful. Our production server will be running Linux, but support for OS X would be a bonus as it would allow the development team to setup test installations outside of VirtualBox.

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• Throttling outbound API calls generated by a Rails app

  - by Sharpie

  I am not a professional web developer, but I like to wrench on websites as a hobby. Recently, I have been playing with developing a Rails app as a project to help me learn the framework. The goal of my toy app is to harvest data from another service through their API and make it available for me to query using a search function. However, the service I want to pull data from imposes a rate limit on the number of API calls that may be executed per minute. I plan on having my app run a daily update which may generate a burst of API calls that far exceeds the limit provided by the external service. I wish to respect the performance of the external site and so would like to throttle the rate at which my app executes the calls. I have done a little bit of searching and the overwhelming amount of tutorial material and pre-built libraries I have found cover throttling inbound API calls to a web app and I can find little discussion of controlling the flow of outbound calls. Being both an amateur web developer and a rails newbie, it is entirely possible that I have been executing the wrong searches in the wrong places. Therefore my questions are: Is there a nice website out there aggregating Rails tutorials that has material related to throttling outbound API requests? Are there any ruby gems or other libraries that would help me throttle the requests? I have some ideas of how I might go about writing a throttling system using a queue-based worker like DelayedJob or Resque to manage the API calls, but I would rather spend my weekends building the rest of the site if there is a good pre-built solution out there already.

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• .Net Rocks Visual Studio 2010 Road Trip coming to Raleigh, NC May 6th

  - by Jim Duffy

  Listen up .NET developers within 50 miles of Research Triangle Park, NC!  Take out that red, blue, green, black or any other color Sharpie marker you fancy and circle May 6th! Fellow Microsoft Regional Directors Carl Franklin and Richard Campbell are going to be bringing the .Net Rocks Visual Studio 2010 Road Trip to town. What’s that you say, you’ve never been to a .Net Rocks Road Trip event and don’t know what to expect? Let me help with that. I stol… uhhh… I mean I was “inspired” by some content I found on the event information page. “Carl and Richard are loading up the DotNetMobile (a 30 foot RV) and driving to your town again to show off their favorite bits of Visual Studio 2010 and .NET 4.0! Richard talks about Web load testing and Carl talks about Silverlight 4.0 and multimedia. And to make the night even more fun, we’re going to bring a mystery rock star from the Visual Studio world to the event and interview them for a special .NET Rocks Road Trip show series. Along the way we’ll be giving away some great prizes, showing off some awesome technology and having a ton of laughs. So come out to the most fun you can have in a geeky evening – and learn a few things along the way about web load testing and Silverlight 4!“   I know I’ll be there so what are you waiting for? Head over to the event registration page and sign up today! Have a day. :-|

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• What makes these two R data frames not identical?

  - by Matt Parker

  UPDATE: I remembered dput() about the time Sharpie mentioned it. It's probably the row names. Back in a moment with an answer. I have two small data frames, this_tx and last_tx. They are, in every way that I can tell, completely identical. this_tx == last_tx results in a frame of identical dimensions, all TRUE. this_tx %in% last_tx, two TRUEs. Inspected visually, clearly identical. But when I call identical(this_tx, last_tx) I get a FALSE. Hilariously, even identical(str(this_tx), str(last_tx)) will return a TRUE. If I set this_tx <- last_tx, I'll get a TRUE. What is going on? I don't have the deepest understanding of R's internal mechanics, but I can't find a single difference between the two data frames. If it's relevant, the two variables in the frames are both factors - same levels, same numeric coding for the levels, both just subsets of the same original data frame. Converting them to character vectors doesn't help. Background (because I wouldn't mind help on this, either): I have records of drug treatments given to patients. Each treatment record essentially specifies a person and a date. A second table has a record for each drug and dose given during a particular treatment (usually, a few drugs are given each treatment). I'm trying to identify contiguous periods during which the person was taking the same combinations of drugs at the same doses. The best plan I've come up with is to check the treatments chronologically. If the combination of drugs and doses for treatment[i] is identical to the combination at treatment[i-1], then treatment[i] is a part of the same phase as treatment[i-1]. Of course, if I can't compare drug/dose combinations, that's right out.

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