ComputingTutorials

Introduction

This page is intended for physicists who are just starting to work in the mu2e computing environment. The following is a broad overview of the major components, their terminology, and how you might use them. Following each into paragraph, here are links into more specific tutorials and the rest of the mu2e documentation which is more terse and is intended as a reference once you get through the introductory material.

You probably don't have to work through this entire page and you can stop and any point, please talk to you adviser or mentor to see what's appropriate. The material you are most likely need to use comes first, followed by more in-depth tutorials for people who will be spending years on mu2e and learn to do more complex work.

Prerequisites

In this tutorial we will assume you are familiar with the following topics

• the mu2e detector, the parts, what they do, and how they work
• the basic bash shell commands on a linux system
• c++ code concepts and syntax
• HEP offline concepts

Authentication

You login to the mu2e interactive machines with kerberos authentication. You will need a permanent ID called a kerberos "principal" which is looks like "your_username@FNAL.GOV". (You will have one username for all computing purposes at Fermilab.) You will have a password associated with your principal. You will use this principal and password to log into the various personal linux desktops located at Fermilab or to ssh into the collaboration interactive machines from your home institution. You typically re-enter your kerberos authentication every day.

The second identity you will need is the services principal, which looks like your_username@services.fnal.gov, or often just your_username, and also has a password (different from your kerberos password). You will need this identity to log into Fermilab email, the servicedesk web site and some other services based at the lab. You would typically only use this authentication at the point you log into the service.

The third identity you will need is a CILogin certificate. This "cert" is the basis of authentication to the mu2e documents database, the computing farms, and a few other services. You will use this cert in two ways. The first way is to load it into your browser, which then gives you access to web pages and web services. The second is by using your kerberos authentication to access a copy of your certificate maintained in a remote database. You get this certificate once and then renew it only once a year.

hypernews is an archived blog and email list - for access here, you will need both a hypernews password and your services password!

Finally, the mu2e internal web pages require a collaboration username and password, please ask your mu2e mentor.

Try:

• ComputingAccounts create your accounts and authentication if you are joining mu2e

Become familiar with these references:

• ComputingHelp

Interactive logins

Collaborators can do interactive computing work in several places. Probably the best place to start is the collaboration's interactive linux machines at Fermilab. The disks that the user sees are located on specialized disk server hardware and the same disks are mounted by all the interactive machines. There are five quad-core machines named mu2egpvm01.fnal.gov through mu2egpvm05.fnal.gov. You will have an account and a home area here (the same home area is on all machines) and some disk space for data. We prefer using the bash shell for all purposes. Collaborators can also compile and run mu2e code on their linux desktops or laptops.

Try:

• LoginTutorial checking your access

Become familiar with these references:

• ComputingLogin
• disks
• bash shell

Ntuple

The data from the detector, and the reconstructed data, is stored in files in art format. Accessing this data generally requires compiling code and learning a special configuration language, so we will save that for a later tutorial. To simplify, and speed up access to the data, we often run a program to copy a small part of the data in the art file into a convenient format call a root ntuple (pronounced "en-tuple"). This format is easy to browser interactively and make histograms. The ntuple file may contain histograms that were already made, or a list of the tracks in each event along with interesting quantities, such as the number of hits on the track or its reconstructed momentum.

Useful pages:

• NtupleTutorial will guide you through making plots with one of the Mu2e-specific ntuples that can be generated.
• ROOT is a very useful resource. In particular: getting started and code reference
• Overview of existing mu2e ntuples

Geometry Browser

It is often useful to look at the detector as it is implemented in the simulation either to debug (e.g. double-check the geometry is as you expect) or to get images for presentations.

Useful pages:

• Rob's demo from 2016 shows how to visualise the geometry with ROOT by reading a GDML file

Code, art and fcl

The main program that is used for simulation, reconstruction and analysis is Mu2e Offline. This is an art-based framework in which the data passes through a series of modules to perform a variety of tasks. Sometimes you will need to have the full Mu2e Offline framework (e.g. if you are a developer) but in other cases you might only need a partial build (which we call a Satellite release) or use an already existing build.

Useful pages:

• CodeRecipe runs you through setting up the environment, checking out a full or Satellite release and building Mu2e Offline.
• SatelliteRelease has more information on Satellite releases
• ReleaseList gives the list of releases that are available on cvmfs
• More tutorials to come...

Event Display

Not only is it useful to look at the geometry but it is also useful to look at specific events in the simulation to see what is happening.

Useful pages:

• EventDisplays shows the current possible ways to display events
• Tutorials to come...

Art Data Products

All objects (e.g. straw hits, calorimeter clusters) are stored in the art event as art data products. These are accessed and created in Offline modules.

Useful pages:

• ReadProducts gives information on reading products
• MakeProducts gives information on creating products
• Tutorials to come...

Checkout and build code

scons, satellite releases, warning about changing include files

Modules

example module code. access a product, make histograms, write a product(?) access geometry and config

Geometry and Config

alter a geometry file, examine a generator config file

Staging and Mixing Concepts

run multi-stage, run mixing, make fcl changes and re-run

dCache

explain dCache, write to scratch dcache, use ifdh, intro to upload?

Grids

build and submit a mu2eprodsys job, second tutorial to monitor the job

Git commits

provide a scratch repo that they can checkout and commit to randomly. Walk through both commit patterns

Code standards

code style, art standards, random numbers, CLHEP, boost, magic numbers

References and resources

discuss when and how to get help, maybe tour the wiki?

Random Links (scratch)

latest meeting

Sarah's google doc on clickable status and intro paragraphs

Rob's 10/26/17 talk on intro to computing plan

clickable detector

Overview

Build recipe

Rob's first geant run for new users

art workbook

test root

test display

Summer 2016 SCD workshops (includes geometry tutorial)

Summer 2016 mu2e tutorials

setup root by itself

c++

linux

root

July 2016 intro talks

Software tutorial

Practicalities of MC

Hits and Mixing

Tutorials (scratch)

• Testing the ROOT display
• Testing the Geant4 based event display
• Notes on dynamic libraries
• The First Step: the art workbook
• Running G4 within art: The first examples.
• Mu2e maintained FAQs: C++ FAQ, Unix/Linux FAQ, ROOT FAQ, Geant4 Notes