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The Square Wheel September 19, 2011

Posted by gordonwatts in Analysis, computers, LINQToTTree, ROOT.
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Another geek post, I’m afraid. Last week I posted about some general difficulties I was having with doing analysis at the LHC. I actually got a fair amount of response – but all of it was people talking to me here at CERN rather than comments on the blog. So to summarize before moving on…

The biggest thing I got back was that as the corrections become well known, they get automated – so there is no need for this two step process I outlined before – running on MC and data, deriving a correction, and then running a third time to do the actual work, taking the correction into account. Rather, the ROOT files are centrally produced and the correction is applied there by the group. So the individual doesn’t have to worry. Sweet! That definitely improves life! However, the problem remains (i.e. when you are trying to derive a new correction).

I made three attempts before finally finding an analysis framework that worked (well, four if you count the traditional approach of C++, python, bash, and duct tape!). As you can tell – what I wanted was something that would correctly glue several phases of the analysis together. The example from last time:

  1. Correct the jet pT spectra in Monte Carlo (MC) to data
    1. Run on the full dataset and get the jetPt spectra.
    2. Do the same for MC
    3. Divide the two to get the ratio/correction.
  2. Run over the data and reweight my plot of jet variables by the above correction.

There are basically 4 steps in this: run on the data, run on the MC, divide the results, run on the data. Ding! This looks like workflow! My firs two attempts were based around this idea.

Workflow has a long tradition in particle physics. Many of our computing tasks require multiple steps and careful accounting every step of the way. We have lots of workflow systems that allow you to assemble a task from smaller tasks and keep careful track of everything that you do along the way. Indeed, all of our data processing and MC generation has been controlled by home-rolled workflow systems at ATLAS and DZERO. I would assume at every other experiment as well – it is the only way.

This approach appealed to me: I can build all the steps out of small tasks. One task that runs on data and one that runs on MC. And then add the “plot the jet pT” sub-task to each of those two, take the outputs, and then have a small generic tasks that would calculate a rate, and then another task that would weight the events and finally make the plots. Easy peasy!

So, first I tried Trident, something that came out of Microsoft Research. An open source system, it was designed to work with a number of scientists with large datasets that required frequent processing (NOAA related, I think). It had an attractive UW, and arbitrary data could be passed between the tasks, and the code interface for writing the tasks was pretty simple.


I managed to get some small things working with it – but there were two big things that caused it to fail. First, the way you pass around data was painful. I wanted to pass around a list of files to run on – and then from that I needed to pass around histograms. I wanted fine grained tasks that would manipulate histograms (dividing the plots) and the same time other tasks would be manipulating whole files (making the plots). Ugh! It was a lot of work just to do something simple! The second thing that killed it was that this particular tool – at the time – didn’t have sub-jobs. You couldn’t build a workflow, and then use it in other workflows. It was my fault that I missed that fact when I was choosing the tool.

So, I moved onto a second attempt. Since my biggest problem had been hooking everything up I decided to write my own. Instead of a GUI interface, I had an XML interface. And I did what is known as “coding-by-convention.” The idea is that I’d set a number of defaults into the design so that it “just worked” as long as the individual components obeyed the conventions. Since this was my own private framework there was no worry that this wouldn’t happen. The framework knew how to automatically combine similar histograms, for example, or if it was presented with multiple input datasets it knew how to combine those as well – something that would have required a another step in the Trident solution.

This solution went much better – I was able to do more than just do my demo – I tried moving beyond the reweighting example above and tried to do something more complex. And here is where, I think, I hit on the real reason that workflow doesn’t work for analysis (or at least for me): you are having to switch between various environments too often. The framework was written in XML. If I wanted a new task, then I had to write C++, or C# (depending). Then there was the code that ran the framework – I’d have to upgrade that periodically.

Really, all I wanted to do was make a stupid plot on two datasets, divide it, and then make a third plot using the first as a weight. Why did I need different languages and files to do that – why couldn’t I write that in a few lines??

Those of you who are active in this biz, of course, know the answer: two different environments. One set of code deals with looping over, possibly, terrabytes of data. That is the loop that makes the plot. Then you need some procedural code to do the histogram division. When that is done, you need another loop of code to do the final plots and reweighting. Take a step back. That is a lot of support code that I have to write! Loading up the MC and data files, running the loop over them, saving the resulting histogram. The number of lines I actually need to create the plot and put the data into the plot? Probably about 2 line or 3. The number of lines I need to actually run that job start to finished and make that plot? Closer to 150 or so, and in several files, some compiled and some interpreted. Too much ceremony for that one or two lines of code: 150 lines of boilerplate for 3 or so lines of the physics interesting code.

So, I needed something better. More on that next week.

BTW, the best visual analysis workflow I’ve seen (but not used) is something called VISPA. Had I known about it when I started the above project I would have gone to it first – it is cross platform, has batch manager, etc., integrated in, etc. (a fairly extensive list). Looking in retrospect it looks like it could support most of what I need to do. I say this only having done a quick scan of its documentation pages. I suspect I would have run into the same problem: having to move between different environments to code up something “simple”.


Reinventing the wheel September 10, 2011

Posted by gordonwatts in Analysis, computers, LINQToTTree, ROOT.
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Last October (2010) my term came to and end running the ATLAS flavor-tagging group. It was time to get back to being a plot-making member of ATLAS. I don’t know how most people feel when they run a large group like this, but I start to feel separated from actually doing physics. You know a lot more about the physics, and your input affects a lot of people, but you are actually doing very little yourself.

But I had a problem. By the time I stepped down in order to even show a plot in ATLAS you had to apply multiple corrections: the z distribution of the vertex was incorrect, the transverse momentum spectrum of the jets in the Monte Carlo didn’t match, etc. Each of these corrections had to first be derived, and then applied before someone would believe your plot.

To make your one really great plot then, lets look at what you have to do:

  1. Run over the data to get the distributions of each thing you will be reweighting (jet pT, vertex z position, etc.).
  2. Run over the Monte Carlo samples to get the same thing
  3. Calculate the reweighting factors
  4. Apply the reweighting factors
  5. Make the plot you’d like to make.

If you are lucky then the various items you need to reweight are not correlated – so you can just run the one job on the Data and the one job on the Monte Carlo in steps one and two. Otherwise you’ll have to run multiple times. These jobs are either batch jobs that run on the GRID, or a local ROOT job you run on PROOF or something similar. The results of these jobs are typically small ROOT files.

In step three you have to author a small script that will extract the results from the two jobs in steps 1 and 2, and create the reweighting function. This is often no more difficult that dividing one histogram by another. One can do this at the start of the plotting job (the job you create for steps 4 and 5) or do ti at the command line and save the result in another ROOT file that serves as one of the inputs to the next step.

Steps 4 and 5 can normally be combined into one job. Take the results of step 3 and apply it as a weight to each event, and then plot whatever your variable of interest is, as a function of that weight. Save the result to another ROOT file and you are done!!


I don’t know about you, but this looked scary to me. I had several big issues with this. First, the LHC has been running gang-busters. This means having to constantly re-run all these steps. I’d better not be doing it by hand, especially as things get more complex, because I’m going to forget a step, or accidentally reuse an old result. Next, I was going back to be teaching a pretty difficult course – which means I was going to be distracted. So whatever I did was going to have to be able to survive me not looking at it for a week and then coming back to it… and me still being able to understand what I did! Mostly, the way I normally approach something like the above was going to lead to a mess of scripts and programs, etc., all floating around.

It took me three tries to come up with something that seems to work. It has some difficulties, and isn’t perfect in a number of respects, but it feels a lot better than what I’ve had to do in the past. Next post I’ll talk about my two failed attempts (it will be a week, but I promise it will be there!). After that I’ll discuss my 2011 Christmas project which lead to what I’m using this year.

I’m curious – what do others do to solve this? Mess of scripts and programs? Some sort of work flow? Makefiles?? What?? What I’ve outlined above doesn’t seem scalable!