This lesson is still being designed and assembled (Pre-Alpha version)

Computing Basics for DUNE - Late 2024 edition: Mission Setup

Objectives

Requirements

You must be on the DUNE Collaboration member list and have a valid FNAL or CERN account.

You should join the DUNE Slack instance and look in #computing-training-basics (see Mission Setup below) for help with this tutorial

Windows users are invited to review the Windows Setup page.

Step 1: DUNE membership

To follow most of this training, you must be on the DUNE Collaboration member list. If you are not, talk to your supervisor or representative to get on it.

Note: Other experiments may find the setup and first few modules useful.

The first few modules on access and disk spaces should work for other Fermilab experiments if you substitute dune --> other.

Step 2: Getting accounts

With FNAL

If you have a valid FNAL computing account with DUNE, go to step 3.

If you have a valid FNAL computing account but not on DUNE yet (say you have access to another experiment’s resources), you can ask for a DUNE-specific account using the Service Now Update my Affiliation/Experiment/Collaboration membership Request form.

If you do not have any FNAL accounts yet, you need to contact your supervisor and/or Institutional Board representative to obtain a Fermilab User Account. More info: https://get-connected.fnal.gov/users/access/. This can take several weeks the first time.

With CERN

If you have a valid CERN account and access to CERN machines, you will be able to do many of the exercises as some data is available at CERN. The LArSoft tutorial has been designed to work from CERN. We strongly advise pursuing the FNAL computing account though.

If you have trouble getting access, please reach out to the training team several days ahead of time. Some issues take some time to resolve. Please do not put this off. We cannot help you the day of the tutorial as we are busy doing the tutorial.

Step 3: Mission setup (rest of this page)

We ask that you have completed the setup work to verify your access to the DUNE servers. It is not complicated, and should take 10 - 20 min.

If you are not familiar with Unix shell commands, here is a tutorial you can do on your own to be ready: The Unix Shell

If you have any questions, contact us at dune-computing-training@fnal.gov or on DUNE Slack #computing_training_basics.

You should join the DUNE Slack instance and look in #computing-training-basics for help with this tutorial

go to https://atwork.dunescience.org/tools/ scroll down to Slack and request an invite. Please do not do this if you are already in DUNE Slack.

Also check out our Computing FAQ for help with connection and account issues.

0. Basic setup on your computer.

Computer Setup goes through how to find a terminal and set up xwindows on MacOS and Windows. You can skip this if already familiar with doing that.

Note

The instructions directly below are for FNAL accounts. If you do not have a valid FNAL account but a CERN one, go at the bottom of this page to the Setup on CERN machines.

1. Kerberos business

If you already are a Kerberos aficionado, go to the next section. If not, we give you a little tour of it below.

What is it? Kerberos is a computer-network authentication protocol that works on the basis of tickets.

Why does FNAL use Kerberos? Fermilab uses Kerberos to implement strong authentication, so that no passwords go over the internet (if a hacker steals a ticket, it is only valid for a day).

How does it work? Kerberos uses tickets to authenticate users. Tickets are made by the kinit command, which asks for your kerberos password (info on kerberos password here). The kinit command reads the password, encrypts it and sends it to the Key Distribution Centre (KDC) at FNAL. The Kerberos configuration file, which lists the KDCs, is stored in a file named krb5.conf. On Linux and Mac, it is located here:

/etc/krb5.conf

If you do not have it, create it. A FNAL template is available here for each OS (Linux, Mac, Windows). More explanations on this config file are available here if you’re curious.

To log in to a machine, you need to have a valid kerberos ticket. You don’t need to do this every time you login, only when your ticket is expired. Kerberos tickets last for 26 hours. To create your ticket:

kinit -f username@FNAL.GOV

The -f option means your ticket is forwardable. A forwardable ticket is one that originated on computer A, but can be forwarded to computer B and will remain valid on computer B. Careful: you need to write FNAL.GOV in uppercase.

To know if you have a valid ticket, type:

klist

Typical output of klist on macOS looks like this:

Mac-124243:~ trj$ klist
Ticket cache: FILE:/tmp/krb5cc_10143_xSCwboGiuY
Default principal: trj@FNAL.GOV

Valid starting     Expires            Service principal
05/18/23 12:43:23  05/19/23 11:41:42  krbtgt/FNAL.GOV@FNAL.GOV
	renew until 05/25/23 12:41:42
05/18/23 15:13:22  05/19/23 11:41:42  nfs/homesrv01.fnal.gov@FNAL.GOV

Tickets are stored in /tmp and have file permissions so that only you can read and write them. If your ticket has not expired yet but will soon, you can refresh it for another 26 hours by typing:

kinit -R

Refreshing a ticket can be done for up to one week after it was initially issued.

Running into issues? Users logging in from outside the Fermilab network may be behind Network Address Translation (NAT) routers. If so, you may need an “addressless” ticket. For this, add the option -A:

kinit -A -f username@FNAL.GOV

Some users have reported problems with the Kerberos utilities provided by Macports and Anaconda. Macintosh users should use the system-provided Kerberos utilities – such as /usr/bin/kinit. Use the command

which kinit

to report the path of the kinit that’s first in your $PATH search list. If you have another, non-working one, a suggestion is to make an alias like this one:

alias mykinit="/usr/bin/kinit -A -f myusername@FNAL.GOV"

Then you can simply use:

mykinit

If you need to remove a ticket (for example, you are logged in at CERN with one Kerberos account but want to log in to a Fermilab machine with your Fermilab account), you can use the command

kdestroy

After executing this command, you will have to use kinit again to get a new ticket. If you have tickets from a non-working kinit, be sure to use the corresponding kdestroy to remove them. klist should return an empty list to make sure you have a clean setup before running the system-provided kinit.

Some users have reported that an installation of Anaconda interferes with the use of the system kinit. If you must use the kinit supplied with Anaconda, see these instructions.

Check out the DUNE FAQ for a long list of possible error messages and suggested solutions.

DUNE FAQ

2. ssh-in

What is it? SSH stands for Secure SHell. It uses an encrypted protocol used for connecting to remote machines and it works with Kerberos tickets when configured to do so. The configuration is done in your local file in your home directory:

cat ~/.ssh/config

If it does not exist, create it. A minimum working example to connect to FNAL machines is as follows:

Host *.fnal.gov
ForwardAgent yes
ForwardX11 yes
ForwardX11Trusted yes
GSSAPIAuthentication yes
GSSAPIDelegateCredentials yes

Now you can try to log into a machine at Fermilab. There are now 15 different machines you can login to: from dunegpvm01 to dunegpvm15 (gpvm stands for ‘general purpose virtual machine’ because these servers run on virtual machines and not dedicated hardware, others nodes which are indented for building code run on dedicated hardware). The dunegpvm machines run Scientific Linux Fermi 7 (SLF7). To know the load on the machines, use this monitoring link: dunegpvm status.

How to connect? The ssh command does the job. The -Y option turns on the xwindow protocol so that you can have graphical display and keyboard/mouse handling (quite useful). But if you have the line “ForwardX11Trusted yes” in your ssh config file, this will do the -Y option. For connecting to e.g. dunegpvm07, the command is:

ssh username@dunegpvmXX.fnal.gov

where XX is a number from 01 to 15. If you experience long delays in loading programs or graphical output, you can try connecting with VNC. More info: Using VNC Connections on the dunegpvms.

3. Get a clean shell

To run DUNE software, it is necessary to have a ‘clean login’. What is meant by clean here? If you work on other experiment(s), you may have some environment variables defined (for NOvA, MINERvA, MicroBooNE). Theses may conflict with the DUNE environment ones.

Two ways to clean your shell once on a DUNE machine:

Cleanup option 1: Manual check and cleanup of your custom environment variables To list all of your environment variables:

env

The list may be long. If you want to know what is already setup (potentially conflicting later with DUNE), you can grep the environment variables for a specific experiment (here the -i option is ‘case insensitive’). Here is an example to list all NOvA-specific variables:

env | grep -i nova

Another useful command that will detect UPS products that have been set up is

ups active

A “clean” response to the above command is:

bash: ups: command not found...

and if your environment has UPS products set up, the above command will list the ones you have.

Once you identify environment variables that might conflict with your DUNE work, you can tweak your login scripts, like .bashrc, .profile, .shrc, .login etc., to temporarily comment out those (the “export” commands that are setting custom environment variables, or UPS’s setup command). Note: files with names that begin with . are “hidden” in that they do not show up with a simple ls command. To see them, type ls -a which lists all files.

Cleanup option 2: Back up your login scripts and go minimal at login (recommended)

A simpler solution would be to rename your login scripts (for instance .bashrc as .bashrc_save and/or .profile as .profile_bkp) so that your setup at login will be minimal and you will get the cleanest shell. For this to take into effect, you will need to exit and reconnect through ssh.

Note: Avoid putting experiment specific setups in .bashrc or .profile

You are going to be doing some setup for dune, which you will also need to do when you submit batch jobs. It is much easier to make a script setup_dune.sh which you execute every time you log in. Then you can duplicate the contents of that script in the script you use to run batch jobs on remote machines. It also makes it much easier for people to help you debug your setup.

4.1 Setting up DUNE software - Scientific Linux 7 version

See SL7_to_Alma9 for more information

To set up your environment in SL7, the commands are:

Log into a DUNE machine running Alma9

Launch an SL7 container

/cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --shell=/bin/bash \
-B /cvmfs,/exp,/nashome,/pnfs/dune,/opt,/run/user,/etc/hostname,/etc/hosts,/etc/krb5.conf --ipc --pid \
/cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest

You will then be in a container which looks like:

Apptainer>

You can then set up DUNE’s code

export UPS_OVERRIDE="-H Linux64bit+3.10-2.17" # makes certain you get the right UPS
source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh

You should see in your terminal the following output:

Setting up larsoft UPS area... /cvmfs/larsoft.opensciencegrid.org/products/
Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/

Optional

See how you can make an alias so you don’t have to type everything

You can store this in your (minimal) .bashrc or .profile if you want this alias to be available in all sessions. The alias will be defined but not executed. Only if you type the command dune_setup yourself.> Not familiar with aliases? Read below.

To create unix custom commands for yourself, we use ‘aliases’:

alias my_custom_commmand='the_long_command_you_want_to_alias_in_a_shorter_custom_name'

For DUNE setup, you can type for instance:

alias dune_setup='source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh'

So next time you type:

dune_setup

Your terminal will execute the long command. This will work for your current session (if you disconnect, the alias won’t exist anymore).

Optional

See if ROOT works

Try testing ROOT to make certain things are working

setup root v6_28_12 -q e26:p3915:prof # sets up root for you  
root -l -q $ROOTSYS/tutorials/dataframe/df013_InspectAnalysis.C

You should see a plot that updates and then terminates. You may need to export DISPLAY=0:0.

Caveats for later

Note: You cannot submit jobs from the Container

You cannot submit jobs from the Container - you need to open a separate window. In that window do the minimal Alma9 setup below and submit your jobs from that window.

You may need to print your submit command to the screen or a file to do so if your submission is done from a script that uses ups.

4.2 Setting up DUNE software - Alma9 version

======= Try testing ROOT to make certain things are working

setup root -v v6_28_12 -q e26:p3915:prof # sets up root for you  

#  right now setup seems to spew out 1000's of lines of verbose output just doing its job. 

root -l -q $ROOTSYS/tutorials/dataframe/df013_InspectAnalysis.C

You should see a plot that updates and then terminates. You may need to export DISPLAY=0:0 .

Caveats for later

You cannot submit jobs from the Container - you need to open a separate window, not do the apptainer and submit your jobs from that window.

4.2 Setting up DUNE software - Alma9 version

We are moving to the Alma9 version of unix. Not all DUNE code has been ported yet but if you are doing basic analysis work, try it out.

Here is how you set up basic DUNE software on Alma 9. We are now using the super-computer packaging system Spack to give versioned access to code.

  1. login into a unix machine at FNAL or CERN

  2. Log into a gpvm or lxplus

source /cvmfs/larsoft.opensciencegrid.org/spack-packages/setup-env.sh 

# get some basic things - 
# use the command spack find to find packages you might want
# If you just type spack load ... you may be presented with a choice and will need to choose. 
#
spack load root@6.28.12
spack load cmake@3.27.7
spack load gcc@12.2.0
spack load fife-utils@3.7.0
spack load metacat@4.0.0
spack load rucio-clients@33.3.0
spack load sam-web-client@3.4%gcc@12.2.0 
spack load kx509

# config for dune
spack load r-m-dd-config experiment=dune
export SAM_EXPERIMENT=dune

Optional

See if ROOT works

Try testing ROOT to make certain things are working

root -l -q $ROOTSYS/tutorials/dataframe/df013_InspectAnalysis.C

You should see a plot that updates and then terminates.

Caveats

We don’t have a full ability to rebuild DUNE Software packages yet. We will be adding more functionality here. Unless you are doing simple ROOT based analysis you will need to use the SL7 Container method for now.

5. Exercise! (it’s easy)

This exercise will help organizers see if you reached this step or need help.

1) Start in your home area cd ~ on the DUNE machine (normally CERN or FNAL) and create the file dune_presetup_2024.sh.

Launch the Apptainer as described above in the SL7 version

Write in it the following:

export DUNELAR_VERSION=v09_90_01d00
export DUNELAR_QUALIFIER=e26:prof

export UPS_OVERRIDE="-H Linux64bit+3.10-2.17"
setup dunesw $DUNELAR_VERSION -q $DUNELAR_QUALIFIER

alias dune_setup='source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh'

When you start the training, you will have to source this file:

source ~/dune_presetup_2024.sh

Then, to setup DUNE, use the created alias:

dune_setup

2) Create working directories in the dune/app and pnfs/dune areas (these will be explained during the training):

mkdir -p /exp/dune/app/users/${USER}
mkdir -p /pnfs/dune/scratch/users/${USER}
mkdir -p /pnfs/dune/persistent/users/${USER}

3) Print the date and add the output to a file named my_first_login.txt:

date >& /exp/dune/app/users/${USER}/my_first_login.txt

4) With the above, we will check if you reach this point. However we want to tailor this tutorial to your preferences as much as possible. We will let you decide which animals you would like to see in future material, between: “puppy”, “cat”, “squirrel”, “sloth”, “unicorn pegasus llama” (or “prefer not to say” of course). Write your desired option on the second line of the file you just created above.

Note

If you experience difficulties, please ask for help in the Slack channel #computing-training-basics. Please mention in your message this is about the Setup step 5. Thanks!

6. Getting setup for streaming and grid access

In addition to your kerberos access, you need to be in the DUNE VO (Virtual Organization) to access to global DUNE resources. This is necessary in particular to stream data and submit jobs to the grid. If you are on the DUNE collaboration list and have a Fermilab ID you should have been added automatically to the DUNE VO.

To check if you are on the VO, two commands. The kx509 gets a certificate from your kerberos ticket. On a DUNE machine, type:

kx509

Authorizing ...... authorized
Fetching certificate ..... fetched
Storing certificate in /tmp/x509up_u55793

Your certificate is valid until: Wed Jan 27 18:03:55 2021

To access the grid resources, you will need either need a proxy or a token. More information on proxy is available here.

How to authorize with the KX509/Proxy method

On Alma9 you may need to do this first

spack load kx509

This is to be done once every 24 hours per login machine you’re using to identify yourself:

kx509
export ROLE=Analysis
export X509_USER_PROXY=/tmp/x509up_dune_Analysis_`id -u`
voms-proxy-init -rfc -noregen -voms=dune:/dune/Role=$ROLE -valid 120:00

Your identity: /DC=org/DC=cilogon/C=US/O=Fermi National Accelerator Laboratory/ OU=People/CN=Claire David/CN=UID:cdavid
Contacting  voms1.fnal.gov:15042 [/DC=org/DC=incommon/C=US/ST=Illinois/L=Batavia/O=Fermi Research Alliance/OU=Fermilab/CN=voms1.fnal.gov] "dune" Done
Creating proxy .................................... Done

Your proxy is valid until Mon Jan 25 18:09:25 2021

You should be able to access files now

Report this by appending the output of voms-proxy-info to your first login file:

voms-proxy-info >> /exp/dune/app/users/${USER}/my_first_login.txt

With this done, you should be able to submit jobs and access remote DUNE storage systems via xroot.

Tokens method

We are moving from proxies to tokens - these are a bit different.

1. Get your token

 htgettoken -i dune --vaultserver htvaultprod.fnal.gov

the first time you do this (and once a month thereafter), it will ask you to open a web browser and

Attempting OIDC authentication with https://htvaultprod.fnal.gov:8200

Complete the authentication at:
    https://cilogon.org/device/?user_code=ABC-D1E-FGH
No web open command defined, please copy/paste the above to any web browser
Waiting for response in web browser

You will need to follow the instructions and copy and paste that link into your browser (can be any browser). There is a time limit on it so its best to do it right away. Choose Fermilab as the identity provider in the menu, even if your home institution is listed. After you hit log on with your service credentials, you’ll get a message saying you approved the access request, and then after a short delay (may be several seconds) in the terminal you will see.

Saving credkey to /nashome/u/username/.config/htgettoken/credkey-dune-default
Saving refresh token ... done
Attempting to get token from https://htvaultprod.fnal.gov:8200 ... succeeded
Storing bearer token in /tmp/bt_token_dune_Analysis_somenumber.othernumber
Storing condor credentials for dune

you only have to do the web thing once/month.

2. Tell the system where your token is

export BEARER_TOKEN_FILE=/run/user/`id -u`/bt_u`id -u`

the id -u just returns your numerical user ID

With this done, you should be able to submit jobs and access remote DUNE storage systems via xroot.

Issues

If you have issues here, please ask #computing-training-basics in Slack to get support. Please mention in your message it is the Step 6 of the setup. Thanks!

Success

If you obtain the message starting with Your proxy is valid until… Congratulations! You are ready to go!

Set up on CERN machines

Warning Some data access operations here still require a fermilab account. We are working on a solution.

See https://github.com/DUNE/data-mgmt-ops/wiki/Using-Rucio-to-find-Protodune-files-at-CERN for instructions on getting full access to DUNE data via metacat/rucio from lxplus.

1. Source the DUNE environment setup script

CERN access is mainly for ProtoDUNE collaborators. If you have a valid CERN ID and access to lxplus via ssh, you can setup your environment for this tutorial as follow:

log into lxplus.cern.ch

fire up the Apptainer as explained in SL7 Setup but with a slightly different version as mounts are different.

/cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --shell=/bin/bash\
-B /cvmfs,/afs,/opt,/run/user,/etc/hostname --ipc --pid \
/cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest

You may have to add some mounts - here I added /afs/ but removed /nashome/, /exp/, /etc/krb5.conf and /pnfs/.

You should then be able to proceed with much of the tutorial thanks to the wonder that is /cvmfs/.

Set up the DUNE software

export UPS_OVERRIDE="-H Linux64bit+3.10-2.17" # makes certain you get the right UPS
source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh
setup kx509

Setting up larsoft UPS area... /cvmfs/larsoft.opensciencegrid.org/products/
Setting up DUNE UPS area... /cvmfs/dune.opensciencegrid.org/products/dune/

If you have a Fermilab account already do this to get access the data catalog worldwide

kdestroy
kinit -f <fnalaccount>@FNAL.GOV
kx509
export ROLE=Analysis
voms-proxy-init -rfc -noregen -voms=dune:/dune/Role=$ROLE -valid 120:00

Checking if /tmp/x509up_u79129 can be reused ... yes
Your identity: /DC=org/DC=cilogon/C=US/O=Fermi National Accelerator Laboratory/OU=People/CN=Heidi <fnalusername>n/CN=UID:<fnalusername>
Contacting  voms1.fnal.gov:15042 [/DC=org/DC=incommon/C=US/ST=Illinois/O=Fermi Research Alliance/CN=voms1.fnal.gov] "dune" Done
Creating proxy .......................................................................................... Done

Your proxy is valid until Sat Aug 24 17:11:41 2024

2. Access tutorial datasets

Normally, the datasets are accessible through the grid resource. But with your CERN account, you may not be part of the DUNE VO yet (more on this during the tutorial). We found a workaround: some datasets have been copied locally for you. You can check them here:

ls /afs/cern.ch/work/t/tjunk/public/may2023tutorialfiles/

np04_raw_run005387_0019_dl5_reco_12900894_0_20181102T023521.root
PDSPProd4_protoDUNE_sp_reco_stage1_p1GeV_35ms_sce_datadriven_41094796_0_20210121T214555Z.root

3. Notify us

You should be good to go, and you might revisit Indico event page. If however you are experiencing issues, please contact us as soon as possible. Be sure to mention “Setup on CERN machines” if that is the case, and we will do our best to assist you.

Success

If you can list the files above, you should be able to do most of the tutorial on LArSoft.

Warning

Connecting to CERN machines will not give you the best experience to understand storage spaces and data management. If you obtain a FNAL account in the future, you can however do the training through the recorded videos that will be made available after the event.

Issues

If you have issues here, please go to the #computing-training-basicsSlack channel to get support. Please note that you are on a CERN machine in your message. Thanks!

The DUNE FAQ on GitHub.

Wiki page on DUNE’s interactive computing resources, including tips on using Kerberos and VNC.

s