Notebook Entry

Today's task list:

  • [x] Write up findings on cost of Matlab and use with AWS
  • [x] Talk to Patsy about purchasing our stuff and the AWS account
  • [x] Order computers
  • Install Matlab
  • Run structural identifications for Dr. Hess
  • [x] Read and do exercises in Chapter of Professional Plone Development
  • Reply to Open Science email
  • Review the todo items on the Yeadon paper
  • Work on parsing the walking data

Matlab Purchasing Options

The following is a copy of the email I sent to my PI and the lab about purchasing Matlab licenses:

I spoke with our Mathworks rep yesterday about purchasing Matlab licenses for the lab and the ability to use Amazon AWS with Matlab for parallel computing needs.

Basic Matlab

We have two licensing options from Mathworks:

Academic License

Matlab plus all desired tool boxes are purchased for each computer we need it for. This allows you to install the software on a machine for perpetual use, but only on one machine. This is the ideal situation as but there is another potentially cheaper option below.

Concurrent License

The concurrent license scheme allows you to install software on a personal server that allows people to checkout a license to Matlab. So Matlab is installed on as many machines as you want, but you can't use it unless you are connected to the server and a license is available. If you want to use Matlab while you are away from the lab you would need to have a VPN type of IP routing so that you can checkout a license when you are not in the lab. Going this route could potentially allow you to purchase fewer copies of Matlab and fewer copies of toolboxes because everyone isn't actually using all of these at the same time as each other. This will require us to run and manage a local server and probably setup this VPN thing.

Cost of core Matlab (no toolboxes):

  • 1 license: $500
  • 5-9 license: $300 each
  • 10-?: $220 each

Cost of toolboxes:

  • 1 general toolbox: $200
  • 2-4 general toolboxes: $158 each
  • 5-? general toolboxes: $105 each
  • Simulink 5-?: $150

This includes 1 year of tech support and 1 year of upgrades (Matlab releases twice a year).

Additional years of tech support and upgrades cost 20% of total license cost (including toolbox costs) per year per license.

There is also a Student Version of Matlab that students can purchase for $99 for their personal machines. These technically can't be installed on University owned computers. But our grad students can run this on their own machines if they want.

The wish list of toolboxes we may use:

  • Optimization Toolbox
  • Global Optimization Toolbox
  • Control System Toolbox
  • System Identification Toolbox
  • Signal Processing Toolbox
  • Data Acquisition Toolbox
  • SimMechanics
  • Simulink
  • Parallel Computing Toolbox

Let me know if you have any other favorites!

We can probably get away without buying all these depending on what we use. It sounds like Sandy and Obinna only use simulink and the sys id toolboxes.

Ok, drum roll ....

If we assume we need 5 licenses available for simultaneous use and we get all the tool boxes then the expensive cost (academic licenses) is something like:

5*$300 + 5*8*$105 + 5*$150 = $6450

plus a $1290 per year tech support/upgrade fee

If we got the cheaper route and get 5 licenses in the concurrent scheme, purchase 2 of each toolbox, and buy a cheap low power server then we would spend something like:

5*$300 + 2*8*$105 + 2*$150 = $3480

plus a $696 per year tech support/upgrade fee

If we go really cheap and I give you all a 2-3 workshop on Octave, Scilab, GSL, and/or SciPy, etc then we can get "most" of this for:

$0

:)

Parallel Computing

Matlab has a parallel toolbox that helps you parallelize your code from up to 12 cores per license. It offer's some basic function for writing parallel code and you have access to many functions that we may normally use that have being parallelized by Mathworks engineers. If you want to send jobs from this tool box to higher core systems or clusters, then you need to buy the Distributed Computing Server from Matlab. Dawei, in Dr. Simon's lab, somehow uses 2 licenses to run on 24 cores with simultaneous Matlab instances which is some sort of hack, but can save you lots of money. The Distributed Computing server also has facilities to send jobs to Amazon Web Services Ec2 instances for multicore runs (this is relatively new).

The Distrubuted Computer Server has some steep costs:

  • up to 16 cores is $1650
  • up to 32 cores is $2950

Plus if you want to use AWS instead of us buying and maintaining our own hardware you pay these fees:

  • Matlab usage fee: $0.16 per core per hour
  • AWS Ec2 $0.06 to $4.60 per hour depending on size of machine/cluster (they have up to 32 core machines and I think you can cluster instances too, maybe up to 8).

So for 1 32 core machine on AWS with Matlab for an hour computation you may spend $5-$10. And for a AWS cluster of 32 core machines you may spend $40-$50 per hour.

My humble opinion on this is that if we really have some massive problems that we want to run on clusters and/or high core machines that we rewrite our Matlab code in other languages and deploy our problems to the cloud and we don't have to pay Matlab's overhead. The open source world has this problem figured out better than Matlab from what I can tell so far and there is little incentive to pay Matlab's fees for this kind of stuff.

Making Purchases at CSU

I spoke with Patsy, our secretary, about how to actually purchase stuff we want for the lab. For general lab equipment and such the process is:

  • Make sure the vendor can accept a purchase order
  • Go to online vendor's website
  • Select the items you want and put them in your shopping cart
  • Before you press "Buy", print out the itemize cost sheet
  • Take this printout to the ME office
  • Patsy's fills out a form and sends it to the PI and the Chair for approval
  • Then this goes to the Dean's office for approval
  • Then it comes back to our office
  • Then I go back on the website to my hopefully saved shopping cart and finish the order

I'm still not sure how this works and if the vendor's online websites will take a purchase order number instead of a credit card. This process seems like a nightmare and no fun to do. Why are University's such in the stone age about purchasing. Why can't I just have a debit card that is tied to our grant. I can order stuff at my leisure and the power-at-be can approve things as I buy them to finalize the deal. I don't even want to think about the number of hours I've wasted with this kind of stuff in the past. The other option would be to by anything less than $1500 or so with my personal debit/credit card and just turn in a reimbursement form. Which often seems so much easier than a PO. Patsy also wasn't sure how we can pay for online services that may or may not have a variable monthly bill (like AWS, Dropbox, etc). She's looking into that for me.

Matlab and the Structural Model Work

I had some issues installing Matlab as I lost my original disk. I'll have to figure something out soon to run my structural model system id. Postponed.

Lab Web Site

I thought I wouldn't ever deploy a Plone site again and would probably lean towards static site generators, Django, Flask, etc, but I feel pretty confident that this is a good solution for the Human Motion & Control's lab website. Plone offers an full featured solution to do the things we want to do:

  • Have public facing website
  • Have a collaborative work space for sharing our work both publically and privately within out group
  • Share our publications, data, source code
  • Have a lab member web page for each student
  • Have a lab blog

I purchased the better of the Plone books a year or so back http://www.packtpub.com/professional-plone-4-development/book and will go through several of the Chapters so I can setup a proper dev environment for a plone site and build our own theme with diazo.

User of the site

  • The public
  • Grad students in the lab
  • The PI
  • Post docs and other lab members

The PI, students, and other lab members should be able to edit the website content. Content should default to private when published.

Sandy, one of Ton's grad students, made a sweet prototype of the website design:

/media/images/hmc-prototype.png

Data backup

We are trying to think of a nice centralized way to backup our experimental data. We have two computers that are offline and networked together that run our data collection software (D-Flow and Cortex). They generate flat text files for each experiment. But because they are offline for no-virus reasons, we need a way to get the data from there to a backup destination and to our personal computers for data analysis. I thought that we may be able to utilize cloud data backup. Here's the email I sent out with a workflow idea:

I think this could be a solution for our data backup:

https://www.dropbox.com/business

But it does seem pricey. Basically about 100 bucks per user per year.

I chatted with a sales rep and it has many cool features that we can use.

I imagine this work flow:

  1. take data on the offline mocap computer
  2. plug in flash drive to mocap computer and run a simple program that synchronizes the flash drive to a folder(s) in the d-flow/mocap computer
  3. take the flash drive to a server we have connected to the net
  4. run a similar script that synchronizes the flash drive to the drop box folder on that machine
  5. then drop box automatically does its synchronization to put our data in the cloud
  6. at this point there are four copies of the data: one on mocap computer, one on flash drive, one on server, and one in the cloud (and the dropbox data is versioned)
  7. Now you go to your computer and select which folders you want to have synchronized to your machine on dropbox so you can access the data you need

So all data will be available to anyone with the our account (or we can even make files public in dropbox for easy wider sharing).

But I also realized we could skip the drop box thing and do the traditional method and just have this server so that we can ssh/ftp into it from anywhere to get a copy of data. We'd lose automatic versioning and easy dropbox interface, but it should effectively do the same thing.

I was also trying to imagine this workflow where we don't have the server mentioned in step 3 and simply bring the flash drive back to your personal computer. But we don't want to force our personal computers to have a full copy of all the data, we only want the data we want to use on our personal computers.

Thoughts?

I could also use our Amazon AWS server and an S3 bucket to run our own server backup. And the S3 pricing is much more favorable. Even with the 30% academic price reduction, drop box is super expensive.

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