ComputingTutorials: Difference between revisions
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* [[NtupleTutorial]] will guide you through making plots with one of the Mu2e-specific ntuples that can be generated. | * [[NtupleTutorial]] will guide you through making plots with one of the Mu2e-specific ntuples that can be generated. | ||
* [https://root.cern.ch/ ROOT] is a very useful resource. In particular: [https://root.cern.ch/getting-started getting started] and [https://root.cern.ch/guides/reference-guide code reference] | * [https://root.cern.ch/ ROOT] is a very useful resource. In particular: [https://root.cern.ch/getting-started getting started] and [https://root.cern.ch/guides/reference-guide code reference] | ||
* Overview of existing [[Ntuples|mu2e ntuples]] | |||
==Geometry Browser== | ==Geometry Browser== |
Revision as of 19:02, 2 August 2018
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 topic
- the mu2e detector, the parts, what they do, and how they work
- the basics bash shell commands on a linux system
- familiar with c++ code concepts and syntax
- familiar with HEP offline concepts
provide links to external references
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:
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.
When ready, you can read more about the , the disks, bash shell, and how to get the code distribution from the code disk, or copied to a desktop, laptop or remote institution.
Try:
- LoginTutorial checking your access
Become familiar with these references:
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
where is the code (do not run git yet tho), intro to releases, cvmfs, run genReco, set output file names and Nevents intro to fcl, paths and filters. maybe a couple of tutorials?
Event Display
run EventDisplay
Products
print and dump files, list products, write input tags. Maybe look at RecoDataProducts
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)
Sarah's google doc on clickable status and intro paragraphs
Rob's 10/26/17 talk on intro to computing plan
Rob's first geant run for new users
Summer 2016 SCD workshops (includes geometry tutorial)
July 2016 intro talks
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