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newcomers:gettingstarted

Getting started

This page aims to give an overview of the necessary steps and links to get started relatively quickly in the UZH's CMS group.

Registrations

If you are a Bachelor's or Master's student, you can best get an external CERN account, a CMS account and an account at PSI's Tier3.

If you already have a CERN account, you can change your status and home institute as described here.

External CERN collaborator

It is possible to register as an external CERN collaborator if you only require a computing account (lxplus) and other electronic services. With such an external CERN account you do not need to go to CERN, but you do need a CMS registration.

  1. Please fill out this form.
  2. Please contact the CMS secretariat by e-mail to request a CERN ID and lxplus account, mentioning your affiliation to this group.

You will receive a reply outlining the next steps for CMS registration which are also described in the section about CMS below.

Full CERN member

Follow these steps of CERN's User Office to register as a full CERN member. You will need to

  1. make a scan of your identity card or passport,
  2. fill out a Home Institution Declaration (at time of writing, Monika Röllin (Y36 J 80​) can sign and stamp this) and make a scan,
  3. ask your Professor to add you with the pre-registration tool. They will need your contact information (there may be an option to forward a link to the form) and the scans from steps 1 and 2.

After this, you will receive a confirmation e-mail with an attestation of pre-registration. To complete the registration, go to the CERN Users' Office in Geneva. You will need to bring your identity card or passport, Home Institution Declaration, attestation of pre-registration and if you are staying in Switzerland a visa or residence permit (Ausländerausweis / Livret pour étrangers).

When this is completed you will get more instructions (cyber-security exam, emergency contacts form, …), but most of all a CERN e-mail address and a CERN computing account at the CERN lxplus cluster!

More information on

  • how to get there (you can use the shuttle service from Geneva airport with CERN card or a print-out of the attestation of pre-registration),
  • the CERN hotel for overnight stays.

CMS

You can request CMS registration by filling in this form. (For the “Main project at CMS” field, choose “Tracker”.) Upon submission, you will receive an e-mail with a link to upload a scan of an identity card or passport, and a link to a registration form. After submitting all of that, ask the team leader of our CMS group (Florencia at the moment of writing) to confirm your CMS registration. Then you will get information on how to activate your account.

VOMS and GRID certificates

After all that, you should register with VOMS, get and install GRID certificates on your local computer and computing accounts. These certificates give you authorized acces to a number of grid computing services. Follow the steps lined out here and here, in summary:

  1. install a GRID user certificate on you local computer, see the CERN Certification Authority (use of Mozilla Firefox highly recommended, Safari highly discouraged),
  2. register with VO CMS here or here (might take a few days to come through),
  3. export the certificate (presumably from FireFox) to cert.p12, from which you create .pem files to install them on the computing account:
    1. for lxplus, see this page,
    2. for PSI T3, see this page and the next section.

To create the .pem files from the .p12 certicicate, and set the correct permissions:

mkdir $HOME/.globus
openssl pkcs12 -in cert.p12 -clcerts -nokeys -out $HOME/.globus/usercert.pem
openssl pkcs12 -in cert.p12 -nocerts -out $HOME/.globus/userkey.pem
chmod go-rw $HOME/.globus/userkey.pem

Test with

voms-proxy-init -voms cms

This will also create a file like /tmp/x509up.u<user-id>, where <user-id> is your user ID, found with the id -u command. You can specify the proxy's location by including the following in your .bashrc:

export X509_USER_PROXY=~/.x509up_u`id -u`

PSI - CMS Tier 3

Our UZH group uses PSI's servers for computing (since it has more storage space than CERN's lxplus). To get a computing account at Tier3, you first need a CERN lxplus account. Please follow these steps to get an PSI T3 account. You will need to send a formatted e-mail, for example:

User's first name: John
User's last name: Doe
Institute/group: Physik-Institute/Kilminster
Institution: UniZ
group leader: Ben Kilminster
CMS hypernews name: jdoe
physics group: uniz-higgs
Grid cert subject: /DC=ch/DC=cern/OU=Organic Units/OU=Users/CN=jdoe/CN=137035/CN=john doe
User's phone number: +41 7 13 70 35 99
PSI AFS account (if existing):
login shell: /bin/bash
mail: john.doe@uzh.ch
secondary mail address: john137@hotmail.com
leaving date: -1
  • physics group: you should choose uniz-higgs.
  • login shell: your personal choice, when in doubt choose bash (which is also standard on Mac OS. Z shell zsh is more customizable and interactive and so a bit more complicated for beginners.)
  • Grid cert subject: leave empty if you do not have a GRID certificate (usercert.pem) installed yet, and share it with the T3 admins later. Until then, you will not be able to make use of certain services such as acces to T3's storage element (/pnfs). Otherwise, use one of the following commands on your lxplus or local certificate file usercert.pem:
openssl x509 -subject -dates -noout -in ~/.globus/usercert.pem
voms-proxy-info --subject

CMS Hypernews

CMS Hypernews is used as a mailing list for CMS groups, a discussion forum for review (approval) of CMS papers and a inbox spamming device. You can create an account and password in the lxplus command line:

ssh hypernews.cern.ch

and voluntarily sign up for several forums (your favorite analyses, CMS groups, etc.)

Indico

Indico is used by CERN for video conferences and meetings. Install Vidyo after singing up with your CERN account. Links to the UZH CMS Group meetings and other can be found here.

If you are a non-doctoral student you are likely not on the author list for CMS publications (yet). If you do not have access to CMS physics meetings on Indico with your CERN account, you might not be in the cms-physics-access e-group. You can verify by going to your CERN account page, to, “My Accounts” to “Check account status...”, under “E-Group membership”. If you are not part of cms-physics-access, ask you group leader to add you as an exception via http://cms.cern.ch/iCMS/admin/newexception.

Renewal

For renewal, please get a signed Home Institute Declaration (from Regina at the moment of writing), and fill out the this EDH form.

Setting up computing accounts

After registering you need to know how to acces and setup your account.

Connecting

To connect remotely to UZH's physics linux cluster, CERN's lxplus or PSI T3 servers, use the secure shell command ssh in a Terminal:

ssh <username>@linux.physik.uzh.ch
ssh <username>@lxplus.cern.ch
ssh <username>@t3ui03.psi.ch

Where <username> is you username. On a Mac OS, you should use ssh -Y and make sure that XQuartz is installed (this is a X Window System tool, formerly X11, allowing you to run remote linux applications with GUI's on your Mac OS). At the time of writing, UZH members should use T3's User Interface server ui03.

Protip: Connecting to the UZH or PSI T3 can be done passwordlessly (at your own risk). Follow these instruction. (CERN is more difficult; please let me know if you find a way.)

Copying stuff

From your local computer, you can copy stuff to a remote account or vice versa with secure copy scp, for example:

scp <username>@linux.physik.uzh.ch:~/somefile.txt ./  # UZH   to local
scp foo.txt <username>@linux.physik.uzh.ch:~/         # local to UZH
scp <username>@ineuteli@t3ui03.psi.ch:~/foo.txt ./    # PSI   to local
scp foo.txt <username>@ineuteli@t3ui03.psi.ch:~/      # local to PSI

Where <username> is your username. Use the recursive flag -r to copy directories like you would with the standard copy command cp. It will ask your password, unless you have setup a passwordless ssh login.

Setting up your PSI T3 account

Please read How to set up your account at PSI Tier-3 and make note of the PSI Tier-3 policies about disk quotas and more; at the moment:

  • /shome/$USER: 400 GB (current data, including past data saved in snapshots /shome/$USER/.zfs/snapshot)
  • /scratch: 4TB
  • RAM: 132GB
  • cores: 72

Check your currently used and available space here.

To use CMS-related commands and root at PSI T3, you will need to first run

source $VO_CMS_SW_DIR/cmsset_default.sh

at every login. The environmental variable VO_CMS_SW_DIR should be /cvmfs/cms.cern.ch.

If you want to use root, you first need to get a CMSSW release and run cmsenv in its src directory with every login. Check the next subsection. Furthermore, to make use of certain services such as acces to T3's storage element (/pnfs), you will need to initiate a VOMS proxy certificate every once in a while:

voms-proxy-init -voms cms -valid 200:0  # valid for 200 hours

Setting up your UZH account

To use root on the UZH cluster, first run these two commands:

cd /cern/root_v5.34.25
source bin/thisroot.sh

Beginner's tip: In any shell you can have user defined commands with alias and argument-taking functions using function. For example:

alias sshp='ssh <username>@t3ui03.psi.ch'
alias cdA='cd ~/analysis/'
function cppl { scp -r <username>@t3ui03.psi.ch:~/"$1" ./; } # copy first argument from PSI to local

These command line definitions and the root setup scripts above can be saved in the start-up file, which are located in your home directory ~/ and are run everytime you log into a new session. In a bash shell these are .bashrc and .bash_profile, in the Z shell zsh it is .zshrc. Check whether they exist with ls -a ~/ and use Google for more information.

CMSSW

CMSSW is a framework that is used for many different CMS related analyses. More information on the recommended version can be found here (existing releases are found with scram list -a). To get for example CMSSW 8.0.20 on lxplus or T3, use:

cmsrel CMSSW_8_0_20
cd CMSSW_8_0_20/src
cmsenv

After this you can run root. Every time you start a new session, you will need to run

cd CMSSW_8_0_20/src
cmsenv

When you use other packages, it can be installed in the CMSSW's src directory, after which you compile everything with scram:

cd CMSSW_8_0_20/src
scram b distclean
scram b -j8

Finding and writing publications

As a UZH member, you have acces to freely view article in large journals such as Physics Letters and APS from a UZH netwerk. When you are not connected to a UZH network, you can still get acces with a VPN proxy.

With CMS hypernews you can follow discussions on papers and much more.

Internal CMS documents can be found on iCMS under CMS Publications. Public articles such as Public Analysis Summaries (PAS) and much more can be found on the CERN Document Server (CDS).

On iCMS you can also request new Analysis Notes (AN). This TWiki page summarizes the procedure to request a CMS note or paper. This TWiki pages summarizes how to use Apache Subversion's svn (similar to git) and the Technical Document Register's tdr system. Guidelines for authors can be found here, here and here.

CERN members have access to professional accounts on the online LaTeX editor Overleaf, see here. With this editor, it is possible to edit LaTeX files simultaneously with other people. However, to compile CMS documents, a few steps are involved, see this or this TWiki page.

For approval, authors need to find a language editor themselves, see this TWiki page with CMS certified language editors

CMS style

CMS analysis and physics symmary notes automatically complies with the CMS house style when using the LaTeX template of the tdr system. For more info, see:

To make CMS plots, use the mentioned macros. You may have to update CMS_lumi.py for you needs and preferences. In python for example, use it like this:

import CMS_lumi, tdrstyle
CMS_lumi.cmsText = "CMS"
CMS_lumi.extraText = "Preliminary"
CMS_lumi.lumi_13TeV = "35.9 fb^{-1}"
tdrstyle.setTDRStyle()
# make TCanvas, TH1, ...
CMS_lumi.CMS_lumi(canvas,4,0) # (canvas,iPeriod,iPos)
                              # iPeriod = 1*(0/1 7 TeV) + 2*(0/1 8 TeV)  + 4*(0/1 13 TeV) 

CMS authorship & service work

Once you have started your position as a PhD student or higher, check if you are on the CMS author list.

To be include its members to the author list, the group needs to have enough EPR points. Each member can perform some service works to gain EPR. You can pledge for EPRs for tasks here. You can sign up for shifts on CMS online.

CERN courses & trainings

CMS induction courses

Every six months a CMS induction course is organized for new members. Here are the slides of the one in January of 2020.

Safety training

CERN provides several safety course, some of which are mandatory for beginners or for access to CMS. You can enroll on the Learning Hub. Other courses, including those for CMS underground guides, are provided.

CERN & CMS schools

Here is kept a list of CMS schools, and here is the CERN school.

UZH and Zurich

Once you are here, make sure you receive a key and a validated student/staff card (legi) to acces the building and get discount at lunch. Also ask Roland to put you on the e-mail lists for our UZH CMS group.

Internal information:

  • Internal information of UZH Physik-Institute contains notes on the printers, linux and batch systems (for some pages you need to be logged into the UZH linux cluster).
  • As a staff member (Mitarbeider), you can use the printing machines on campus for free via UZH-PrintPlus. Full instructions are here:
    1. Check with this link whether your shortname is associated with the Physik-Institute.
    2. Install UZH-PrintPlus (SecurePrint) on your computer.
  • Here is a list of UZH and CMS meetings.

Reimbursements

Each time you travel, you can get reimbursed with one of these forms (“Dienstreise-Abrechnung”).

  1. UZH does not pay for meals at UZH or Zürich. Likewise, in general, meals away from UZH are not covered. Almost every city in the world has meal costs less than Zürich, so there is no cost of living adjustment for traveling.
  2. However, when staying somewhere that does not have a cafeteria/mensa, a per diem can be requested. As of 2019 this is CHF 10 / breakfast, CHF 25 / lunch, CHF 25 / dinner.
  3. For instance, CERN, DESY, PSI, and any University are considered to have cafeterias, and so there are no reimbursements for meals there.
  4. If hotels provide breakfast, or conferences provide lunch or dinners, there is no reimbursement for these meals, since they are already included in hotel and conference fees.
  5. Breakfast (dinner) cannot be claimed on the morning (evening) of travel (return travel) since it can be arranged before leaving (upon returning).

PhD students

UZH style

Here are UZH Templates for presentations, publications, etc. (with UZH log-in). For Master's theses and PhD dissertations you can find LaTeX template here (may be outdated): clvorlage2014.tar.gz (by Computer Linguistics, 2014).

More information

newcomers/gettingstarted.txt · Last modified: 2021/03/11 12:02 by iwn