Difference: TimothyBrooks (1 vs. 55)

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Tim Brooks

Third Year PhD Student - Supervised by Glen Cowan
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FORM FIELD FirstName FirstName Timothy
FORM FIELD LastName LastName Brooks
FORM FIELD OrganisationName OrganisationName RHUL
FORM FIELD OrganisationURL OrganisationURL www.pp.rhul.ac.uk
FORM FIELD OfficeLocation OfficeLocation RHUL
FORM FIELD OfficeRoom OfficeRoom W263
FORM FIELD OfficePhone OfficePhone +44 (0)1784 276467 (Internal: 6467)
FORM FIELD Position Position PhD student
FORM FIELD Country Country UK
FORM FIELD State State
FORM FIELD Address Address
FORM FIELD Location Location Egham
FORM FIELD Telephone Telephone 07716159534
FORM FIELD VoIP VoIP
FORM FIELD InstantMessaging (IM) InstantMessagingIM
FORM FIELD Email Email timothy.brooks.2009@live.rhul.ac.uk
FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
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FORM FIELD First Name FirstName Timothy
FORM FIELD Last Name LastName Brooks
FORM FIELD Loginname Loginname puap062
FORM FIELD Wikiname Wikiname TimBrooks
FORM FIELD Titles Titles Mr
FORM FIELD Email Email timothy.brooks.2009@live.rhul.ac.uk
FORM FIELD Telephone Telephone
FORM FIELD Mobile Mobile
FORM FIELD Skype ID SkypeID
FORM FIELD Department Department BL4S
FORM FIELD Room Room
FORM FIELD Organization Organization CERN
FORM FIELD URL URL
FORM FIELD Location Location 4 R-021
FORM FIELD Region Region Geneva
FORM FIELD Country Country Switzerland
FORM FIELD Image Image
FORM FIELD Status Update StatusUpdate
FORM FIELD Information Information ?
FORM FIELD WorkStatus WorkStatus
 
META FILEATTACHMENT attachment="Tadpole.png" attr="h" comment="" date="1276023500" name="Tadpole.png" path="Tadpole.png" size="12830" stream="Tadpole.png" user="Public.TimothyBrooks" version="1"
META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283514271" name="poster.pdf" path="poster.pdf" size="510756" stream="poster.pdf" user="Public.TimothyBrooks" version="13"
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Tim Brooks

Second Year PhD Student - Supervised by Glen Cowan
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ATLAS Links

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Revision 5213 Jun 2012 - TimothyBrooks

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

Second Year PhD Student - Supervised by Glen Cowan
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  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }

Programming Tips

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Command line-fu

The command line is very powerful: There are a few tools to learn that do very simple jobs, but piping their output to each other allows you to get things done without scripting. Here's an example for downloading specific files in a dataset.
dataset="user.brooks.mc11_7TeV.555555.Dataset.NTUP_SUSY/"
dq2-ls -f $dataset | cut -f 2 | grep root | tr "\\n" "," | xargs -i dq2-get -f {} $dataset
The dq2-ls -f command gives me a list of all files in a dataset in a pretty format. I just want filenames, which happens to be the 2nd column. The cut command slices out columns of text in its input. The -f switch counts whitespace delimited fields. I then decide to select lines contating root filenames; grep does this nicely. Unfortunatly dq2-get isn't very clever, and can't pick filenames from stdin. It doesn't need to though, as we can massage the command line arguments and use xargs to pipe them to dq2-get. First off, we need to turn the newline separated filenames into a comma separated list. This is exactly what tr (translate) does. The -i switch tells xargs to replace {} with arguments from stdin. So dq2-get sees the -f switch (to pick individual files in a dataset) followed by the filenames we selected with grep, separated by commas, followed by the dataset name.

Of course, all that's kind of long to type, so you might want a script for that anyway. wink

 

Bash Basics

It's handy to have a /bin folder in your home area. This can be added to your path in your bash start script: export PATH=~/bin:$PATH

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Tim Brooks

Second Year PhD Student - Supervised by Glen Cowan
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My Research

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Second Year PhD Student - Supervised by Glen Cowan
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My Research

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Tim Brooks

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Second Year PhD Student - Supervised by Glen Cowan
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Second Year Trash.PhD Student - Supervised by Glen Cowan
 
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FORM FIELD OfficeLocation OfficeLocation RHUL
FORM FIELD OfficeRoom OfficeRoom W263
FORM FIELD OfficePhone OfficePhone +44 (0)1784 276467 (Internal: 6467)
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Tim Brooks

Second Year PhD Student - Supervised by Glen Cowan
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My Research

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My Research

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First Year PhD Student - Supervised by Glen Cowan
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My Research

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Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for identification of supersymmetry via profile likelyhood fits.
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See my research page in the ATLAS web. Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for characterization of top events.
 ATLAS SUSY points:
  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }

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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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  h->GetXaxis()->SetNdivisions(105) -Sets tick number. Format is minor ticks per major one * 100 + major ticks in the axis, i.e. to divide into 13 major ticks with 5 minors each; use 500 + 13 = 513.
Added:
>
>

Getting reasonable colour palettes

To get a colour palette (for 2D plots etc.) that goes from red to blue, set;
gStyle->SetPallette(1,0);
 

Adding multiple files with hadd

hadd usage:

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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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 Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for identification of supersymmetry via profile likelyhood fits. ATLAS SUSY points:
  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }
Deleted:
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Use simplifiedRefFinal for EtMiss
 

Programming Tips

Bash Basics

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TMVA

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In booking a tree the option Boost_AdaBoostBeta (Default=1) is "The ADA boost parameter that sets the effect of every boost step on the events’ weights"
>
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In booking a tree the option Boost_AdaBoostBeta (Default=1) is "The ADA boost parameter that sets the effect of every boost step on the event weights"
 

Bugs

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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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 Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for identification of supersymmetry via profile likelyhood fits. ATLAS SUSY points:
  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }
Added:
>
>
Use simplifiedRefFinal for EtMiss
 

Programming Tips

Bash Basics

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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
META FILEATTACHMENT attachment="Tadpole.png" attr="h" comment="" date="1276023500" name="Tadpole.png" path="Tadpole.png" size="12830" stream="Tadpole.png" user="Public.TimothyBrooks" version="1"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283502622" name="poster.pdf" path="poster.pdf" size="510755" stream="poster.pdf" user="Public.TimothyBrooks" version="11"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283514271" name="poster.pdf" path="poster.pdf" size="510756" stream="poster.pdf" user="Public.TimothyBrooks" version="13"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283451394" name="poster.pdf" path="poster.pdf" size="490742" stream="poster.pdf" user="Public.TimothyBrooks" version="10"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283502622" name="poster.pdf" path="poster.pdf" size="510755" stream="poster.pdf" user="Public.TimothyBrooks" version="11"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283435700" name="poster.pdf" path="poster.pdf" size="486662" stream="poster.pdf" user="Public.TimothyBrooks" version="8"
>
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283451394" name="poster.pdf" path="poster.pdf" size="490742" stream="poster.pdf" user="Public.TimothyBrooks" version="10"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283426796" name="poster.pdf" path="poster.pdf" size="463630" stream="poster.pdf" user="Public.TimothyBrooks" version="5"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283435700" name="poster.pdf" path="poster.pdf" size="486662" stream="poster.pdf" user="Public.TimothyBrooks" version="8"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
META FILEATTACHMENT attachment="Tadpole.png" attr="h" comment="" date="1276023500" name="Tadpole.png" path="Tadpole.png" size="12830" stream="Tadpole.png" user="Public.TimothyBrooks" version="1"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283368738" name="poster.pdf" path="poster.pdf" size="465832" stream="poster.pdf" user="Public.TimothyBrooks" version="4"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283426796" name="poster.pdf" path="poster.pdf" size="463630" stream="poster.pdf" user="Public.TimothyBrooks" version="5"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
META FILEATTACHMENT attachment="Tadpole.png" attr="h" comment="" date="1276023500" name="Tadpole.png" path="Tadpole.png" size="12830" stream="Tadpole.png" user="Public.TimothyBrooks" version="1"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283362647" name="poster.pdf" path="poster.pdf" size="465253" stream="poster.pdf" user="Public.TimothyBrooks" version="3"
>
>
META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283368738" name="poster.pdf" path="poster.pdf" size="465832" stream="poster.pdf" user="Public.TimothyBrooks" version="4"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan

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From Wikipedia's Tadpole article:
Tadpole.png
"The physics of tadpoles and the word tadpole was invented by Sidney Coleman. The editor was not satisfied, but he changed his mind once Sidney Coleman proposed spermion instead. [citation needed]"
 

My Links

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 Application servers are listed here: Application servers. For external use, linappserv1 acts as a gateway to the network, and is reasonably fast. Internally, linappserv0 is the fastest machine we have. linappserv3 & 4 are usually quiet, so good for running jobs that may take some time to complete. 1, 3, & 4 use 'Linux based on Scientific Linux CERN SLC release 4.8 (Beryllium)' while linappserv0 uses 'Linux based on Scientific Linux CERN SLC release 5.4 (Boron)'. All machine names can be accessed locally (e.g. ssh user@linappserv0) and those accessable outside can be found as X.pp.rhul.ac.uk (e.g. ssh user@linappserv1.pp.rhul.ac.uk).
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The faraday cluster is controlled via machine ui1. Instructions for using the cluster are here: How to use the cluster. The cluster uses 'Linux based on RedHat Scientific Linux CERN Release 3.0.5 (SL)' which does not support current ATLAS software.
>
>
The faraday cluster is controlled via linappserv0. Instructions for using the cluster are here: How to use the cluster. The cluster can be used for ATLAS production. See my event generation page.

 
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FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
META FILEATTACHMENT attachment="Tadpole.png" attr="h" comment="" date="1276023500" name="Tadpole.png" path="Tadpole.png" size="12830" stream="Tadpole.png" user="Public.TimothyBrooks" version="1"
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META FILEATTACHMENT attachment="poster.pdf" attr="h" comment="RAL Summer School Poster" date="1283362647" name="poster.pdf" path="poster.pdf" size="465253" stream="poster.pdf" user="Public.TimothyBrooks" version="3"
 
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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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  h->GetXaxis()->SetNdivisions(105) -Sets tick number. Format is minor ticks per major one * 100 + major ticks in the axis, i.e. to divide into 13 major ticks with 5 minors each; use 500 + 13 = 513.
Added:
>
>

Adding multiple files with hadd

hadd usage:

Usage: hadd [-f] [-T] targetfile source1 [source2 source3 ...]
This program will add histograms from a list of root files and write them
to a target root file. The target file is newly created and must not 
exist, or if -f ("force") is given, must not be one of the source files.
Supply at least two source files for this to make sense... ;-)
If the first argument is -T, Trees are not merged
When -the -f option is specified, one can also specify the compression
level of the target file. By default the compression level is 1, but
if "-f0" is specified, the target file will not be compressed.
if "-f6" is specified, the compression level 6 will be used.
if Target and source files have different compression levels
 a slower method is used

 

TMVA

In booking a tree the option Boost_AdaBoostBeta (Default=1) is "The ADA boost parameter that sets the effect of every boost step on the events’ weights"

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Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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My Links

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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My Research

Added:
>
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Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for identification of supersymmetry via profile likelyhood fits.
 ATLAS SUSY points:
  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }

Revision 3006 Aug 2010 - TimothyBrooks

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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Added:
>
>

My Research

ATLAS SUSY points:

  • SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }
 

Programming Tips

Bash Basics

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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My Links

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Added:
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Changed:
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ATLAS Links

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  • GridView - Nice visualisation of what the grid is doing (Watch ATLAS hit 100TB/day)
 
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Programming Tips

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Bash Basics

It's handy to have a /bin folder in your home area. This can be added to your path in your bash start script: export PATH=~/bin:$PATH
Placing scripts here can make mindless tasks much easier.
e.g. To rename a bunch of files that are called xxxthisxxx to xxxthatxxx, I have a bash script called mvls that is run like: mvls this that and changes every file in the pwd that contains 'this' in the name to have 'that' instead.
Here's the script

#!/bin/bash
for file in *;do
newfile=$(echo $file | sed s/$1/$2/g)
test "$file" != "$newfile" && mv "$file" $newfile
done

JaxoDraw needs to be run in it's home directory for axoDraw.sty else it can't export to .eps
A quick script switches the wd, and returns it to how it was:

#!/bin/bash
export jaxodrawdir=/scratch0/brooks/tools/JaxoDraw-2.0-1/
export OWD=$PWD
cd $jaxodrawdir
java -jar ${jaxodrawdir}jaxodraw-2.0-1.jar
cd $OWD
 

PyROOT

Basic script

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First Year PhD Student - Supervised by Glen Cowan
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 AddEntry takes the histogram handle, a title for that histogram, and an option that is either "f" for boxes or "l" for lines.
SetFillStyle(0) makes the legends background transparent and adds a border. Alternatively, you can SetFillColor(kWhite) for a white background with no border. (Make sure you don't lose any datapoints behind it!)
Changed:
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Setting up axis

>
>

Setting up an Axis

 
Changed:
<
<
h->GetXaxis()->SetNdivisions(105) -Sets ticks such that there is exactly one per bin.
>
>
h->GetXaxis()->SetNdivisions(105) -Sets tick number. Format is minor ticks per major one * 100 + major ticks in the axis, i.e. to divide into 13 major ticks with 5 minors each; use 500 + 13 = 513.

TMVA

In booking a tree the option Boost_AdaBoostBeta (Default=1) is "The ADA boost parameter that sets the effect of every boost step on the events’ weights"

Bugs

  • In TMVA Manual,
 

ATLAS Software Links

ATLAS software information in the wiki:

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Programming Tips

PyROOT

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First Year PhD Student - Supervised by Glen Cowan
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 leg->Draw("same") AddEntry takes the histogram handle, a title for that histogram, and an option that is either "f" for boxes or "l" for lines.
Changed:
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<
SetFillStyle(0) makes the legends background transparent and adds a border. Alternatively, you can SetFillColor(kWhite) for a white background with no border. (Make sure you don't lose and datapoints behind it!)
>
>
SetFillStyle(0) makes the legends background transparent and adds a border. Alternatively, you can SetFillColor(kWhite) for a white background with no border. (Make sure you don't lose any datapoints behind it!)
 

Setting up axis

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

First Year PhD Student - Supervised by Glen Cowan
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 AddEntry takes the histogram handle, a title for that histogram, and an option that is either "f" for boxes or "l" for lines.
SetFillStyle(0) makes the legends background transparent and adds a border. Alternatively, you can SetFillColor(kWhite) for a white background with no border. (Make sure you don't lose and datapoints behind it!)
Added:
>
>

Setting up axis

h->GetXaxis()->SetNdivisions(105) -Sets ticks such that there is exactly one per bin.

 

ATLAS Software Links

ATLAS software information in the wiki:

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META TOPICPARENT name="TWikiUsers"

Tim Brooks

First Year PhD Student - Supervised by Glen Cowan

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From Wikipedia's Tadpole article:
Tadpole.png
"The physics of tadpoles and the word tadpole was invented by Sidney Coleman. The editor was not satisfied, but he changed his mind once Sidney Coleman proposed spermion instead. [citation needed]"
 

My Links

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FORM FIELD Email Email timothy.brooks.2009@live.rhul.ac.uk
FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
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My Links

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  This switches off the toner wasting gray backgrounds on plots and the bizarre yellow borders.
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Adding Legends to Plots

leg = new TLegend(0.6,0.7,0.89,0.89);
leg->AddEntry(hist_A, "Sample A","f");
leg->AddEntry(hist_B, "Sample B","f");
leg->SetFillStyle(0)
leg->Draw("same") 
AddEntry takes the histogram handle, a title for that histogram, and an option that is either "f" for boxes or "l" for lines.
SetFillStyle(0) makes the legends background transparent and adds a border. Alternatively, you can SetFillColor(kWhite) for a white background with no border. (Make sure you don't lose and datapoints behind it!)
 

ATLAS Software Links

ATLAS software information in the wiki:

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My Links

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Programming Tips

PyROOT

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My Links

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ATLAS Links

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ATLAS Links

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My Links

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Installing Root from source

The Root source code can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
Changed:
<
<
Once that's done; untar the root package move the unzipped folder somewhere (e.g. /opt/root). Then, in the root folder, run ./configure --prefix=/opt/ then make (or, if you want; make -j n where n is the number of cores in your machine). This should leave you with a working root install, then set up your env variables to use it:
>
>
Once that's done; untar the root package move the unzipped folder somewhere (e.g. /opt/root). Then, in the root folder, run ./configure --prefix=/opt/root then make (or, if you want; make -j n where n is the number of cores in your machine). This should leave you with a working root install, then set up your env variables to use it:
 

Setting up root

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My Links

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Installing Root from source

The Root source code can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
Changed:
<
<
Once that's done; untar the root package move the unzipped folder somewhere (e.g. /opt/root). Then, in the root folder, run ./configure --prefix=/opt/ then make (or, if you want; make -j n where n is the number of cores in your machine). This should leave you with a working root install, then set up your env variables to use it:
>
>
Once that's done; untar the root package move the unzipped folder somewhere (e.g. /opt/root). Then, in the root folder, run ./configure --prefix=/opt/ then make (or, if you want; make -j n where n is the number of cores in your machine). This should leave you with a working root install, then set up your env variables to use it:
 

Setting up root

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My Links

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Installing Root from source

The Root source code can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
Changed:
<
<
Once that's done; untar the root package and in the unzipped folder run ./configure --prefix=/usr/local --enable-soversion then make (or, if you want; make -j n where j is the number of cores in your machine)
>
>
Once that's done; untar the root package move the unzipped folder somewhere (e.g. /opt/root). Then, in the root folder, run ./configure --prefix=/opt/ then make (or, if you want; make -j n where n is the number of cores in your machine). This should leave you with a working root install, then set up your env variables to use it:
 

Setting up root

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  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
export PATH=${PATH}:${ROOTSYS}/bin
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Where /usr/local/root/v5.22.00/slc5.gcc3.4/root is the path of the current stable build of root (ie. check this is correct!)
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Where /usr/local/root/v5.22.00/slc5.gcc3.4/root is the path of the current stable build of root (ie. check this is correct! /usr/local/root/v5.22.00/slc5.gcc3.4/root is ok for machines at RHUL)
  For example; here are my .bashrc and .bash_profile.

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Programming Tips

PyROOT

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  Save this as something like tutorial.py and run it using python -i tutorial.py
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Batching plots

Here's a quick bit of code to make a plot and save it straight to a file without making a window.
ROOT.gROOT.SetBatch(True)                  # Switch to batch mode
c1=ROOT.TCanvas( 'c1', 'Plot', 640, 480 )  # Make a canvas of size 640x480
c1.cd()                                    # Set the output canvas (lets us have several going at once)
tt.Draw("ElectronAODCollection.phi()")     # Draw the phi distribution of electrons in the AOD
c1.Print("plot.png")                       # Save the canvas as an image file (ROOT uses the extension given)
 

Some things to play around with

  • from PyAnalysisUtils import PDG Lets you use PDG. instead of remembering pdgIds. Cool feature -> PDG.root_names[-PDG.nu_mu] returns a string with the ROOT syntax for an anti-muon-neutrino.
  • import AthenaCommon.SystemOfUnits as Units Gives you a Units object with most units in the ATLAS base units. e.g. Units.TeV = 1000000.0

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Programming Tips

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PyROOT

Basic script

import user 
import ROOT
import PyCintex
import AthenaROOTAccess.transientTree

# a bit less ugly ROOT style...
ROOT.gROOT.SetStyle("Plain")

f = ROOT.TFile.Open('/scratch0/brooks/MC09/mc09_7TeV.105200.T1_McAtNlo_Jimmy.recon.AOD.e510_s765_s767_r1205_tid123042_00/AOD.123042._000001.pool.root.1')
tt = AthenaROOTAccess.transientTree.makeTree(f)

Save this as something like tutorial.py and run it using python -i tutorial.py

Some things to play around with

  • from PyAnalysisUtils import PDG Lets you use PDG. instead of remembering pdgIds. Cool feature -> PDG.root_names[-PDG.nu_mu] returns a string with the ROOT syntax for an anti-muon-neutrino.
  • import AthenaCommon.SystemOfUnits as Units Gives you a Units object with most units in the ATLAS base units. e.g. Units.TeV = 1000000.0
  • ROOT.gROOT.SetBatch(True) Switches Root to batch mode.
 

Root

Deleted:
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Installing Root

Changed:
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Root can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
>
>
The easiest method is if your distro has a root package. These don't seem to be kept very up-to-date, but I think Root is stable enough to use older versions for most features. On Ubuntu, there is a package called root-system so you can simply run:
sudo apt-get install root-system
This dumps the root binarys into /usr/bin and the libraries into /usr/lib/root, but I think the relevant paths get set up for you in the installation, so you needn't worry about the 'Setting up root' section below.

Installing Root from source

The Root source code can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
 
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
Once that's done; untar the root package and in the unzipped folder run ./configure --prefix=/usr/local --enable-soversion then make (or, if you want; make -j n where j is the number of cores in your machine)

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Programming Tips

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ATLAS Links

 

Programming Tips

Root

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Root

Changed:
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Installing root

root can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page reccomends can be had using:
>
>

Installing Root

Root can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page recommends can be had using:
 
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
Changed:
<
<
If you have that, untar the root package, and in the unzipped folder, run ./configure --prefix=/usr/local --enable-soversion then make (or if you want; make -j n where j is the number of cores in your machine)
>
>
Once that's done; untar the root package and in the unzipped folder run ./configure --prefix=/usr/local --enable-soversion then make (or, if you want; make -j n where j is the number of cores in your machine)
 

Setting up root

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 For example; here are my .bashrc and .bash_profile.
Changed:
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Setting the plot style to plain

>
>

Setting the plot style to plain

 In your home directory, make a file called .rootrc containing the following line:
Rint.Logon: ~/rootlogon.C
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  This switches off the toner wasting gray backgrounds on plots and the bizarre yellow borders.
Changed:
<
<

ATLAS Software

ATLAS software tutorials in the wiki:
>
>

ATLAS Software Links

ATLAS software information in the wiki:
 
Added:
>
>
Good tutorial on running PowHeg for ATLAS.
 

Packages of note

  • Generators/EvgenJobTranforms

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Root

Added:
>
>

Installing root

root can be downloaded from root.cern.ch There are a few packages you will need on your system; on ubuntu 9.10, I needed libx11-dev, libxft-dev, libxpm-dev and libxext-dev. All the requirements the root page reccomends can be had using:
sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev
If you have that, untar the root package, and in the unzipped folder, run ./configure --prefix=/usr/local --enable-soversion then make (or if you want; make -j n where j is the number of cores in your machine)
 

Setting up root

To use root you need to add the environment variable $ROOTSYS and append locations to $PATH and $LD_LIBRARY_PATH. A good way to do this is add the following to your ~/.bash_profile:

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Packages of note

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  • Generators/EvgenJobTranforms
  • JobOptions - Set of standard JobOptions for many processes of importance. Standardized such that samples can be merged with production sets.
>
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  • Generators/EvgenJobTranforms
  • Generators/EvgenATLAS.JobOptions - Set of standard JobOptions for many processes of importance. Standardized such that samples can be merged with production sets.
 

Computing resources

Application servers are listed here: Application servers.
Changed:
<
<
For external use, linappserv1 acts as a gateway to the network, and is reasonably fast. Internally, linappserv0 is the fastest machine we have. linappserv3 & 4 are usually quiet, so good for running jobs that may take some time to complete. 1, 3, & 4 use 'Linux based on Scientific Linux CERN SLC release 4.8 (Beryllium)' while linappserv0 uses 'Linux based on Scientific Linux CERN SLC release 5.4 (Boron)'. All machine names can be accessed locally (e.g. ssh user@linappserv0) and those accessable outside can be found as X.pp.rhul.ac.uk (e.g. ssh user@linappserv1.pp.rhul.ac.uk).
>
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For external use, linappserv1 acts as a gateway to the network, and is reasonably fast. Internally, linappserv0 is the fastest machine we have. linappserv3 & 4 are usually quiet, so good for running jobs that may take some time to complete. 1, 3, & 4 use 'Linux based on Scientific Linux CERN SLC release 4.8 (Beryllium)' while linappserv0 uses 'Linux based on Scientific Linux CERN SLC release 5.4 (Boron)'. All machine names can be accessed locally (e.g. ssh user@linappserv0) and those accessable outside can be found as X.pp.rhul.ac.uk (e.g. ssh user@linappserv1.pp.rhul.ac.uk).
  The faraday cluster is controlled via machine ui1. Instructions for using the cluster are here: How to use the cluster.
Changed:
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The cluster uses 'Linux based on RedHat Scientific Linux CERN Release 3.0.5 (SL)' which does not support current ATLAS software.
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The cluster uses 'Linux based on RedHat Scientific Linux CERN Release 3.0.5 (SL)' which does not support current ATLAS software.
 
META FORM name="%25MAINWEB%25.UserForm"
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 For example; here are my .bashrc and .bash_profile.
Added:
>
>

Setting the plot style to plain

In your home directory, make a file called .rootrc containing the following line:
Rint.Logon: ~/rootlogon.C
Next make that file and paste in the following code:
{
  gROOT->SetStyle("Plain");
  gStyle->SetCanvasBorderMode(0); // turn off canvas borders
  cout << "******************************" << endl; 
  cout << "* Welcome to ROOT v" << gROOT->GetVersion() << " *" << endl; 
  cout << "******************************" << endl; 
  cout << endl;
}
This switches off the toner wasting gray backgrounds on plots and the bizarre yellow borders.

ATLAS Software

ATLAS software tutorials in the wiki:

Packages of note

  • Generators/EvgenJobTranforms
  • JobOptions - Set of standard JobOptions for many processes of importance. Standardized such that samples can be merged with production sets.

Computing resources

Application servers are listed here: Application servers. For external use, linappserv1 acts as a gateway to the network, and is reasonably fast. Internally, linappserv0 is the fastest machine we have. linappserv3 & 4 are usually quiet, so good for running jobs that may take some time to complete. 1, 3, & 4 use 'Linux based on Scientific Linux CERN SLC release 4.8 (Beryllium)' while linappserv0 uses 'Linux based on Scientific Linux CERN SLC release 5.4 (Boron)'. All machine names can be accessed locally (e.g. ssh user@linappserv0) and those accessable outside can be found as X.pp.rhul.ac.uk (e.g. ssh user@linappserv1.pp.rhul.ac.uk).

The faraday cluster is controlled via machine ui1. Instructions for using the cluster are here: How to use the cluster. The cluster uses 'Linux based on RedHat Scientific Linux CERN Release 3.0.5 (SL)' which does not support current ATLAS software.

 
META FORM name="%25MAINWEB%25.UserForm"
FORM FIELD FirstName FirstName Timothy

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My Links

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My Personal Data

Note: if personal data is being stored using a secret database, then it is only visible to the user and to administrators.

E-mail  

My Personal Preferences

Uncomment preferences variables to activate them (remove the #-sign). Help and details on preferences variables are available in TWikiPreferences.

Related Topics

>
>
 
Added:
>
>

Programming Tips

Root

Setting up root

To use root you need to add the environment variable $ROOTSYS and append locations to $PATH and $LD_LIBRARY_PATH. A good way to do this is add the following to your ~/.bash_profile:

export ROOTSYS=/usr/local/root/v5.22.00/slc5.gcc3.4/root
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
export PATH=${PATH}:${ROOTSYS}/bin

Where /usr/local/root/v5.22.00/slc5.gcc3.4/root is the path of the current stable build of root (ie. check this is correct!)

For example; here are my .bashrc and .bash_profile.

 

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My Links

  • ATasteOfTWiki - view a short introductory presentation on TWiki for beginners
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  • Write protect your home page: (set it to your WikiName)
  • Read protect your home page:
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META TOPICPARENT name="TWikiUsers"

My Links

My Personal Data

Note: if personal data is being stored using a secret database, then it is only visible to the user and to administrators.

E-mail  

My Personal Preferences

Uncomment preferences variables to activate them (remove the #-sign). Help and details on preferences variables are available in TWikiPreferences.

Related Topics

META FORM name="%25MAINWEB%25.UserForm"
FORM FIELD FirstName FirstName Timothy
FORM FIELD LastName LastName Brooks
FORM FIELD OrganisationName OrganisationName
FORM FIELD OrganisationURL OrganisationURL
FORM FIELD OfficeLocation OfficeLocation RHUL
FORM FIELD OfficeRoom OfficeRoom 0000
FORM FIELD OfficePhone OfficePhone 0000
FORM FIELD Position Position PhD student
FORM FIELD Country Country Other Country
FORM FIELD State State
FORM FIELD Address Address
FORM FIELD Location Location
FORM FIELD Telephone Telephone
FORM FIELD VoIP VoIP
FORM FIELD InstantMessaging (IM) InstantMessagingIM
FORM FIELD Email Email
FORM FIELD HomePage HomePage
FORM FIELD Comment Comment
META PREFERENCE name="VIEW_TEMPLATE" title="VIEW_TEMPLATE" type="Local" value="UserView"
 
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