Project

General

Profile

exercises » History » Version 42

Kolahal Bhattacharya, 03/03/2017 06:54 PM

1 7 Eric Church
h1.  LArSoft Exercises
2 1 Eric Church
3 16 Eric Church
{{>toc}}
4 16 Eric Church
5 5 Eric Church
h2. Run a simple lar job to create mu-'s of momentum 1.5 GeV/c from a point source.
6 1 Eric Church
7 40 Kolahal Bhattacharya
We will create a file containing events that each have a single muon using the code in a public place. That means you will not need to build any code at this stage. So, go to your test release, that is your working directory. You made this in the guide. Set yourself up to run there with an appropriate mrb working directory, which we call @lgm@ here. All this is explained at  https://cdcvs.fnal.gov/redmine/projects/uboonecode/wiki/Uboone_guide. In this first exercise you are going to run from fcl files and .so libraries -- files that form the heart of the framework -- that live in the official places. You will setup to run against uboonecode v06_26_02. *It is not obvious we're still using nightly in the modern era. If this is broken, use the latest vX__YY_ZZ instead!* Namely, you are not using your own code. So, let's first show the setup, which we urge you perform via an alias, like the following. Have a line like the below line starting @alias@ in your ~/.bashrc. (Use an alias and hand-execute the alias each login; *do not execute this stuff in your shell-initiated start up scripts* like ~/.profile or ~/.bashrc.)
8 7 Eric Church
9 5 Eric Church
<pre>
10 41 Kolahal Bhattacharya
<uboonegpvm02.fnal.gov> alias ulgmr='source /grid/fermiapp/products/uboone/setup_uboone.sh; cd /uboone/app/users/username/lgm/build; setup uboonecode v6_26_02 -qe10:prof; mrbslp;'  # a potential setup alias
11 6 Eric Church
<uboonegpvm02.fnal.gov> ulgmr # actually execute the commands in the alias
12 5 Eric Church
</pre>
13 4 Eric Church
14 5 Eric Church
And now, run the executable on this canned fcl job script file.
15 4 Eric Church
<pre>
16 1 Eric Church
lar -c prodsingle_uboone.fcl
17 1 Eric Church
</pre>
18 4 Eric Church
19 5 Eric Church
This fcl file will produce 5 muons through the set of modules SingleGen, LArG4, and DetSim. That's pretty cool. But where did it find prodsingle_uboone.fcl? How do I know it will run 5 events? 
20 19 Eric Church
The answer comes from looking at our job script fcl file. We find our fcl files from sleuthing in directories whose names we know from the key environment variable $FHICL_FILE_PATH.
21 1 Eric Church
22 33 Eric Church
Here's a handy code chunk for looking for parameter sets. e
23 33 Eric Church
24 5 Eric Church
<pre>
25 33 Eric Church
echo $FHICL_FILE_PATH | sed "s/:/\n/g" | less
26 33 Eric Church
</pre>
27 33 Eric Church
28 33 Eric Church
It displays each individual path on it's own line, make it much easier
29 33 Eric Church
to figure out what's going on.
30 33 Eric Church
31 33 Eric Church
<pre>
32 1 Eric Church
<uboonegpvm02.fnal.gov> echo $FHICL_FILE_PATH 
33 38 Eric Church
.:./job:/grid/fermiapp/products/uboone/uboonecode/nightly/job:.:./job:/grid/fermiapp/products/larsoft/larpandora/nightly/job:/grid/fermiapp/products/larsoft/larana/nightly/job:/grid/fermiapp/products/larsoft/larreco/nightly/job:/grid/fermiapp/products/larsoft/larexamples/nightly/job:/grid/fermiapp/products/larsoft/lareventdisplay/nightly/job:/grid/fermiapp/products/larsoft/larsim/nightly/job:/grid/fermiapp/products/larsoft/larevt/nightly/job:/grid/fermiapp/products/larsoft/lardata/nightly/job:/grid/fermiapp/products/larsoft/nutools/v1_01_04/fcl:/grid/fermiapp/products/larsoft/larcore/nightly/job:/grid/fermiapp/products/larsoft/art/v1_08_10/fcl
34 37 Eric Church
<uboonegpvm02.fnal.gov> more /grid/fermiapp/products/uboone/uboonecode/nightly/job/prodsingle_uboone.fcl 
35 1 Eric Church
</pre>
36 1 Eric Church
37 25 Eric Church
The job starts each event with a clean slate as indicated by the EmptyEvent key word. Note that in prodsingle_uboone.fcl maxEvents is 5.  Note the output root file full of histograms (that we declared and filled in the source code) is specified to be at @single_hist_uboone.root@ and the output ART root file (which serves as the one that we'll pass onto any further modules in subsequent @lar@ jobs) is to be called @single_gen_uboone.root@. Note, that these did indeed appear in your directory! 
38 1 Eric Church
39 25 Eric Church
How did I make 1.5GeV/c muons and not, say, Higgsinos? The answer comes from drilling down into the included fcl files. From the job script we note that for the generator we need the fcl parameter set called @microboone_singlep@. fcl parameter sets are in fcl files in the same places as the job script fcl files: at all possible directories in $FHICL_FILE_PATH. So, let's search ...
40 1 Eric Church
41 37 Eric Church
@<uboonegpvm02.fnal.gov> grep microboone_singlep  /grid/fermiapp/uboone/products/uboone/uboonecode/nightly/job/* @
42 21 Eric Church
@<uboonegpvm02.fnal.gov> grep microboone_singlep  /grid/fermiapp/products/larsoft/lar*/nightly/job/* @
43 7 Eric Church
The relevant return line is from the second effort: @/grid/fermiapp/products/larsoft/larsim/nightly/job/singles.fcl:microboone_singlep: @local::standard_singlep@. That's the only place where microboone_singlep appears on the left hand side of a colon, and that's where the parameter set is defined. Although, what we've learned is that this parameter set is equated to @standard_singlep@, which we must now hunt down, in turn. Note that the return from the greps shows us that after defining microboone_singlep to be standard_singlep, we then proceed to over-write some parameters like X0 and Z0, meaning we force the particles to be generated from a particular point in the TPC. We will return to this idea. We grep the lar* job areas again for singlep and discover the motherlode at @/grid/fermiapp/products/larsoft/larsim/nightly/job/singles.fcl@, which upon investigation shows the full single particle parameter set, including  the line @PDG: [13]@. Hence, we have generated mu-s.
44 6 Eric Church
45 24 Eric Church
h2. Reconstruct your muons
46 1 Eric Church
47 42 Kolahal Bhattacharya
Go run @lar -c standard_reco_uboone_2D_noopt.fcl -s single_gen_uboone.root@.
48 1 Eric Church
49 25 Eric Church
Note that this fcl script is magically just found in some other job/ directory. (Homework: which one?) The -s flag above tells @lar@ to read up the outputted ART root file of our previous job. Also, note this fcl file uses a rather bland series of reconstruction modules: calwire, which you absolutely must perform, then ffthitfinder, then dbcluster.
50 24 Eric Church
51 25 Eric Church
Now that we're running a job with recon modules in it @source:{ module_type }@ says RootInput, as we're sucking up an already-written root file in a previous job. 
52 25 Eric Church
53 24 Eric Church
What would it take to make this fcl script use gaushitfinder (sic) and fuzzycluster instead of ffthitfinder and dbcluster? What would be required to make it also create spacepoints and run track3dkalmansps on those spacepoints? We leave that as an exercise to the reader. (A suggested starting point is to just copy down this fcl script to some local area and edit it, as before with prodsingle_uboone.fcl.)
54 1 Eric Church
55 26 Eric Church
h2. Eventdisplay your recon'd muons
56 26 Eric Church
57 26 Eric Church
Go run @lar -c evd_ub.fcl -s standard_reco_uboone.root@.
58 26 Eric Church
59 26 Eric Church
Note that you can turn on/off the viewing of Hits/Clusters. This may motivate you to tack on 3D recon modules -- spacepointfinder, track3dkalmansps, showerfinder -- and re-recon your muons and then go see if you can view the 3D objects. 
60 26 Eric Church
61 26 Eric Church
Try out our other event viewer, argo at http://argo-microboone.fnal.gov/. Note that you can browse to your just-produced ART root files and view events.
62 26 Eric Church
63 24 Eric Church
h2. Change the mu-'s to K+'s of lower momentum, originating throughout the TPC.
64 1 Eric Church
65 7 Eric Church
Here we want to still use canned code: stuff from the nightly's or the vX_YY_ZZ's.
66 1 Eric Church
67 37 Eric Church
But we have to get ahold of the prodsingle_uboone.fcl to alter a couple parameters to do what we want to do in this exercise. For now, let's just grab a copy and put it in our local area and use that. (We know this will work, cuz the very first item in $FHICL_FILE_PATH is "."). So, in your working area go @cp /grid/fermiapp/products/uboone/uboonecode/nightly/job/prodsingle_uboone.fcl .@
68 7 Eric Church
69 14 Eric Church
We'll show it here, as we'll refer to it a lot.
70 13 Eric Church
71 13 Eric Church
<pre>
72 13 Eric Church
#include "services.fcl"
73 13 Eric Church
#include "singles.fcl"
74 13 Eric Church
#include "largeantmodules.fcl"
75 13 Eric Church
#include "detsimmodules.fcl"
76 13 Eric Church
#include "mccheatermodules.fcl"
77 13 Eric Church
78 13 Eric Church
process_name: SinglesGen
79 13 Eric Church
80 13 Eric Church
services:
81 13 Eric Church
{
82 13 Eric Church
  # Load the service that manages root files for histograms.
83 13 Eric Church
  TFileService: { fileName: "single_hist_uboone.root" }
84 13 Eric Church
  Timing:       {}
85 13 Eric Church
  RandomNumberGenerator: {} #ART native random number generator
86 13 Eric Church
  user:         @local::microboone_simulation_services
87 13 Eric Church
}
88 13 Eric Church
89 13 Eric Church
90 13 Eric Church
#Start each new event with an empty event.
91 13 Eric Church
source:
92 13 Eric Church
{
93 13 Eric Church
  module_type: EmptyEvent
94 13 Eric Church
  maxEvents:   5        # Number of events to create
95 13 Eric Church
  firstRun:    1           # Run number to use for this file
96 13 Eric Church
  firstEvent:  1           # number of first event in the file
97 13 Eric Church
}
98 13 Eric Church
99 13 Eric Church
# Define and configure some modules to do work on each event.
100 13 Eric Church
# First modules are defined; they are scheduled later.
101 13 Eric Church
# Modules are grouped by type.
102 13 Eric Church
physics:
103 13 Eric Church
{
104 13 Eric Church
105 13 Eric Church
 producers:
106 13 Eric Church
 {
107 13 Eric Church
   generator: @local::microboone_singlep	  
108 13 Eric Church
   largeant:  @local::microboone_largeant	  
109 13 Eric Church
   daq:       @local::microboone_simwire  
110 13 Eric Church
   backtrack: @local::standard_backtrackerloader
111 13 Eric Church
 }
112 13 Eric Church
113 13 Eric Church
 analyzers:
114 13 Eric Church
 {
115 13 Eric Church
   largana:   @local::microboone_largeantana
116 13 Eric Church
 }
117 13 Eric Church
118 13 Eric Church
 #define the producer and filter modules for this path, order matters, 
119 13 Eric Church
 #filters reject all following items.  see lines starting physics.producers below
120 13 Eric Church
 simulate: [ generator, largeant, daq, backtrack ] 
121 13 Eric Church
 analyzeIt:  [ largana ]
122 13 Eric Church
 #define the output stream, there could be more than one if using filters 
123 13 Eric Church
 stream1:  [ out1 ]
124 13 Eric Church
125 13 Eric Church
 #trigger_paths is a keyword and contains the paths that modify the art::event, 
126 13 Eric Church
 #ie filters and producers
127 13 Eric Church
 trigger_paths: [simulate] 
128 13 Eric Church
129 13 Eric Church
 #end_paths is a keyword and contains the paths that do not modify the art::Event, 
130 13 Eric Church
 #ie analyzers and output streams.  these all run simultaneously
131 13 Eric Church
 end_paths:     [analyzeIt, stream1]  
132 13 Eric Church
}
133 13 Eric Church
134 13 Eric Church
#block to define where the output goes.  if you defined a filter in the physics
135 13 Eric Church
#block and put it in the trigger_paths then you need to put a SelectEvents: {SelectEvents: [XXX]}
136 13 Eric Church
#entry in the output stream you want those to go to, where XXX is the label of the filter module(s)
137 13 Eric Church
outputs:
138 13 Eric Church
{
139 13 Eric Church
 out1:
140 13 Eric Church
 {
141 13 Eric Church
   module_type: RootOutput
142 13 Eric Church
   fileName:    "single_gen_uboone.root" #default file name, can override from command line with -o or --output
143 13 Eric Church
 }
144 13 Eric Church
}
145 13 Eric Church
146 13 Eric Church
physics.producers.generator.SigmaThetaXZ: [ 5.0 ]
147 13 Eric Church
physics.producers.generator.SigmaThetaYZ: [ 5.0 ]
148 13 Eric Church
physics.producers.generator.X0: [ 100.0 ]
149 13 Eric Church
physics.producers.generator.Z0: [ 50.0 ]
150 13 Eric Church
physics.producers.generator.P0: [ 1.5 ]
151 13 Eric Church
152 13 Eric Church
</pre>
153 13 Eric Church
154 11 Eric Church
Remembering that we can overwrite parameters at this stage,  and that the generator module lives in the producers clause of the physics parameter set, open an editor on your new copy of prodsingle_uboone.fcl and put these lines at the bottom in order to run 0.2 GeV/c K+s generated throughout the TPC, and not 1.5 GeV/c mu-s from a fixed point:
155 7 Eric Church
156 7 Eric Church
<pre> 
157 7 Eric Church
physics.producers.generator.PDG: [321] # K+ 
158 7 Eric Church
physics.producers.generator.P0: [ 0.2 ]
159 7 Eric Church
physics.producers.generator.SigmaX: [ 125.0 ] # width of Gaussian distribution, in cm
160 7 Eric Church
physics.producers.generator.SigmaY: [ 125.0 ]
161 7 Eric Church
physics.producers.generator.SigmaZ: [ 500.0 ]
162 7 Eric Church
</pre>
163 7 Eric Church
164 22 Eric Church
Parameters in brackets are vectors. If instead we say 
165 7 Eric Church
166 12 Eric Church
<pre> physics.producers.generator.PDG: [321, 13, 22, 2112] # K+, mu-, gamma, n 
167 1 Eric Church
</pre>
168 1 Eric Church
169 8 Eric Church
we'll choose randomly (flat distribution) to generate any of those 4 particle types. However, if we do that, we should now go overwrite every possible parameter in that set, as inherited from standard_singlep and make sure all of them are 4-elements long.
170 1 Eric Church
171 8 Eric Church
Let's note one more thing we have done with our canned code. We have run the module we label @largana@ in prodsingle_microboone.fcl. It is an analyzer, meaning it puts nothing on the event. This is in contrast with the producers which _do_ put persistent data onto the event. largana runs after all the producers. The key word @trigger_paths@ runs the producers, which you'll note are all captured in the @simulate@ array of modules, and the key word @end_paths@ holds the analyzers (held in @analyzeIt@) and the output.  We remind you that you will always run producers or analyzers or filters in your fcl scripts. 
172 1 Eric Church
173 8 Eric Church
If we go open the output @single_hist_uboone.root@ file we'll find a directory corresponding to largana, in which its histograms and a TTree reside.
174 8 Eric Church
<pre>
175 8 Eric Church
root [0] TFile f("single_hist_uboone.root")
176 8 Eric Church
root [1] TDirectoryFile* l = f->Get("largana")
177 8 Eric Church
root [2] l->cd()
178 8 Eric Church
root [3] MCTTree->Show(0)
179 8 Eric Church
======> EVENT:0
180 8 Eric Church
 MCEvt           = 1
181 8 Eric Church
 MCSub           = 0
182 8 Eric Church
 MCRun           = 1
183 8 Eric Church
...
184 8 Eric Church
</pre>
185 8 Eric Church
186 11 Eric Church
The natural question that follows might be Do these module labels, @generator, largeant, daq@, etc, mean anything? In fact, they don't mean anything per se, but they do mean something in a relative sense. The data from one producer module might well be used in subsequent modules. And thus, among the parameter set information for a producer is generally a label, or series of labels, that specifies which previous modules are needed from which the current module will get data. Those labels then are the names of the previously-run modules _from this or a previous job_. So, yes, those module labels generally have meaning down the line. 
187 1 Eric Church
188 17 Eric Church
h3. Let us urge at this point that you go chase the @daq@ module's parameter set  @microboone_simwire@. 
189 18 Eric Church
190 1 Eric Church
*  Note that each module's parameter set, first and foremost, gives a @module_type@ field, which is the name of the @*_module.cc@ file that holds the producer/analyzer class whose main produce()/analyze() method is run each event-- finally, we make contact with the C++! 
191 17 Eric Church
*  Note also the @DriftEModuleLabel@ field. You'll find that this is @largeant@, by default. That means the daq module needs the data from @largeant@, which it happens is exactly the module that runs before it in our prodsingle_uboone.fcl. If we'd called that module @largeeeeeant@ in prodsingle_uboone.fcl instead, we'd need to overwrite the module name expected by @daq@, which is done by tacking on physics.producers.daq.DriftEModuleLabel: "@largeeeeeant@" at the bottom.
192 17 Eric Church
* Go try rerunning prodsingle_uboone.fcl, changing producer module names and, simultaneously, the expected module labels by downstream modules
193 10 Eric Church
194 27 Eric Church
h2. A more complex job script -- for Yale Workshop.
195 27 Eric Church
196 29 Eric Church
For the Yale Workshop we've produced a fcl script to walk you through a more elaborate set of modules. We'll let you go get it with the aid of the  instructions on our corresponding wiki setup page. (Basically, from your new srcs directory, say @mrb g uboonecode@ if you haven't done that already, and walk down into @uboone/YaleWork/larsoftdemo.fcl@. This is on the develop branch of git.)
197 28 Eric Church
198 32 Eric Church
This module runs a bunch of producers, 3 analyzers, and a filter. We won't say much here about the producers, but we want to comment on the analyzers. The analyzers are in many ways redundant with one another. We run them all here to demonstrate that it can be done, and each demonstrates something unique. One analyzer that we run is @larg4ana@, which produces a nice TTree and, further, shows you how to get the MC particles off the stack. @analysistree@ is another analyzer module which produces a big end-of-event DST, if you will. (Data Summary Tape, from pre-2005 HEP parlance.) Finally, @analysisexample@ is very nice, as it does some of the the things the other two analyzer modules do in finer grain detail, and, further, introduces cleanly the concept of @art::Associations@. This is the mechanism by which we save and read-back, say, the hits which constitute a cluster. And, last, we learn in this filter module how to write to two streams, with given cuts. The Filter we run demands particular particles are generated as primaries. This is a bit silly for generating single particles, as we've done here. The only primaries are those which, by fiat, we forced to appear, and so the filtered output root file is either entirely overlapping or empty with respect to the non-filtered version here. This particular filter makes more sense if the primary generator is, say, Genie.
199 33 Eric Church
200 33 Eric Church
One other thing you'll notice about this fcl script is that not all the modules get their parameter sets from the included fcl files. AnalysisExample and the filter module get theirs on-the-fly -- meaning, their needed parameters are within stanzas here in the job script. This demonstrates some fcl flexibility.
201 33 Eric Church
202 33 Eric Church
AnalysisExample is an involved exercise unto itself and is documented here: https://cdcvs.fnal.gov/redmine/projects/larsoft/wiki/_AnalysisExample_.
203 33 Eric Church
204 33 Eric Church
205 27 Eric Church
206 10 Eric Church
h2. Edit the module that captures the truth information into histograms and TTree branches.
207 8 Eric Church
208 15 Eric Church
Alright, we've gone as far as we can with the canned code. We need to edit some C++ now. We used above the module we labeled @largana@. That module is, after some exploration, LArG4Ana_module.cc.
209 15 Eric Church
210 15 Eric Church
So, we need to grab that up. How does that work? Well, it's not MicroBooNE specific code, so it's not in uboonecode. That means it's in one of the lar* repositories. I am not so savvy with the O(10) lar* repositories as to know immediately where that is. My approach is to @ls -lt /grid/fermiapp/products/larsoft/lar*/nightly/source/*/LArG4Ana*@. We learn it's in larsim. We no longer want the nightly version. We want our own version. So, go now to https://cdcvs.fnal.gov/redmine/projects/uboonecode/wiki/Uboone_guide and remind yourself how you git clone a repository into your srcs directory.
211 15 Eric Church
212 23 Eric Church
Once you have larsim, go to @srcs/larsim/LArG4/LArG4Ana_module.cc@ and open it in an editor. Note the TTree and Histograms. Add a branch, remove a histogram, whatever. For sure, for piece of mind and if you do nothing else, add a line like @std::cout << "This is my code!!" << std::endl;@ Now, from the guide, go build, install and setup against your installed version. Run your prodsingle_uboone.fcl again.
213 15 Eric Church
214 15 Eric Church
Look for your message that shows you you've really run your code! Open the output hist*.root file in ROOT and look for your changed histograms and TTrees.