LoginTutorial: Difference between revisions
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==Setup Code== | ==Setup Code== | ||
Please make sure your bash login scripts follow the recommendations in [[Shells]], in particular, your <code>.bash_profile</code> executes | |||
source /cvmfs/fermilab.opensciencegrid.org/products/common/etc/setups.sh | |||
You can see that this worked if you get the following | |||
> printenv PRODUCTS | |||
/cvmfs/fermilab.opensciencegrid.org/products/common/db | |||
You now have the [[UPS]] system ready to use. UPS is a Fermilab package which allows you to access other UPS products in the UPS system. UPS commands do things like put executables in your path, and set environmental variables. The available products include code tools, analysis products, and access to grid computing. | |||
The next step is to execute a UPS command to set the Mu2e environment. | |||
setup mu2e | |||
The main effect is to define PRODUCTS environmental variable: | The main effect is to define PRODUCTS environmental variable: | ||
<pre> | <pre> | ||
Line 152: | Line 161: | ||
/cvmfs/fermilab.opensciencegrid.org/products/common/db | /cvmfs/fermilab.opensciencegrid.org/products/common/db | ||
</pre> | </pre> | ||
all the | all the UPS products are under these directories and further setup commands can add them to your environment. | ||
In addition, the <code>setup mu2e</code> command has set a few environmental variables for you | |||
> printenv MU2E | |||
/cvmfs/mu2e.opensciencegrid.org | |||
> printenv MU2E_DATA_PATH | |||
/cvmfs/mu2e.opensciencegrid.org/DataFiles | |||
and setup two more UPS products: | |||
# a modern version of git | |||
# the Mu2e code build scripts, called [[Muse]] | |||
you can see this with | |||
> ups active | |||
Active ups products: | |||
git v2_31_1 -f Linux64bit+3.10-2.17 -z /cvmfs/mu2e.opensciencegrid.org/artexternals | |||
muse v2_07_00 -f NULL -z /cvmfs/mu2e.opensciencegrid.org/artexternals | |||
ups v6_0_8 -f Linux64bit+3.10-2.17 -z /cvmfs/mu2e.opensciencegrid.org/artexternals | |||
The exact versions you see will probably be different, since new versions come out fairly regularly. | |||
[[Category:Computing]] | [[Category:Computing]] | ||
[[Category:Tutorial]] | [[Category:Tutorial]] |
Revision as of 21:54, 20 September 2021
Authentication and First Login
To login to the central machines at Fermilab, you will need first need your accounts created. This process may take up to one month; so start early. This process will create three ways to authenticate to different types of Fermilab resources:
- kerberos used for loggins into central machines, among others
- a services account for email, servicedesk and other uses
- certificate authentication, for submitting jobs, transferring and uploading data
You can read more about this at Authentication, which you should at least scan before continuing.
If you are sitting at a Fermilab linux computer, you can use your kerberos login at the login screen. If you are at a university computer with kerberos installed, you may or may not be able to obtain your kerberos authentication. If you are already on a Fermilab desktop or a Mu2e central computer, you can get this authentication with:
kinit <your user name>@FNAL.GOV
If that is successful, you can login to the central systems:
ssh <username>@mu2egpvm01.fnal.gov
If you have problems, please look through Authentication and the links it points to, in particular, if you are on a University machine, you might need to configure kerberos with a new krb5.conf file.
If you are on a windows laptop, you will want to install Putty and xming. PuTTy allows you to login in a terminal window on the central machines, and xming allows you to display xwindows back on your laptop. If you are on a Mac, see Mac's.
You probably want to try out your email, by going to email.fnal.gov and putting in your services password. Some official communications are sent only to this address so check it regularly or forward it to a preferred account.
OK, from here on we will assume you are on a central machine.
You can see your ticket with the klist command:
> klist Ticket cache: FILE:/tmp/krb5cc_1311_xShHU10541 Default principal: rlc@FNAL.GOV Valid starting Expires Service principal 06/18/19 12:58:54 06/19/19 14:58:50 krbtgt/FNAL.GOV@FNAL.GOV renew until 06/25/19 12:58:50
If you stay logged on overnight, it will expire and you will need to renew it with kinit.
You can use your kerberos identity to invoke your certificate identity with kx509.
> kx509 Authorizing ...... authorized Fetching certificate ..... fetched Storing certificate in /tmp/x509up_u1311 Your certificate is valid until: Tue Jun 25 13:18:18 2019
You can see your cert with voms-proxy-info --all:
> voms-proxy-info --all subject : /DC=org/DC=cilogon/C=US/O=Fermi National Accelerator Laboratory/OU=People/CN=Raymond Culbertson/CN=UID:rlc issuer : /DC=org/DC=cilogon/C=US/O=CILogon/CN=CILogon Basic CA 1 identity : /DC=org/DC=cilogon/C=US/O=CILogon/CN=CILogon Basic CA 1 type : unknown strength : 2048 bits path : /tmp/x509up_u1311 timeleft : 167:51:31 key usage : Digital Signature, Key Encipherment, Data Encipherment
Your certificate can be extended with information about your experiment and the roles you have access to. This can be done with a script
/cvmfs/mu2e.opensciencegrid.org/bin/vomsCert
If you then run voms-proxy-info --all you will see your cert has gotten longer.
You will want to bring your certificate into your browsers since a few web pages, notably the Mu2e doc-db, are authenticated with the certificate. Download your cert into your browsers.
You will want to create an account on hypernews and subscribe to forums that are relevant for you. If you are working on Mu2e software you should subscribe to the following forums: "Software and Simulation" and "Help! Is it me or a bug?". If you use STNTUPLE you will also want to sign up for that forum. Speak with your colleagues to learn what other forums are relevant for you work.
Mu2e Machines
There are several Mu2e dedicated machines (actually virtual machines).
- mu2egpvm01,2,3,4,5 general purpose machines with SL6 operating system
- mu2egpvm06 general purpose machines with SL7 operating system
- mu2ebuild01 machine to compile code
By "general purpose" we mean running executables for a short time, or making and viewing histograms, or writing notes. These machines have 4 cores. The build machine, mu2ebuild01 has 16 cores so it can compile the entire Mu2e code in a reasonable time, about 11 min.
Mu2e Disks
You can read more about the Disks, but in the tutorial, we give a quick tour.
home disk
When you log in, your default directory will be your home area, which is the same for all the Mu2e centrl machines. It may or may not be the same as a linux desktop you are sitting at, depending on how it was set up.
> pwd /nashome/r/rlc
We recommend you use the bash shell, which you should get by default:
> echo $SHELL /bin/bash
to do only minor configuration of your preferences, such and alias for convenience. We have some recommendations
This disk is backed up daily.
app disk
/mu2e/app is where you will put code that you checkout compile and develop. You can create you own area:
mkdir -p /mu2e/app/users/$USER
and you should be able to write there
touch /mu2e/app/users/$USER/test
Note that you will have a finite quota on this disk, so do not put data files here (see next).
This disk is not backed up.
data disk
/mu2e/data is where you can put data files and ntuples that you are using now. You can create you own area:
mkdir -p /mu2e/data/users/$USER
and you should be able to write there
touch /mu2e/data/users/$USER/test
This space is limited, so if you are using more than 500 GB or the files are sitting there for more than a few months, you should consider putting the files on tape or dCache (see next).
This disk is not backed up.
dCache
dCache is a system of software, databases, and disk servers that are design to present a huge amount of disk, spread over many machines, as a single simple disk system. We will cover these area in more depth in future tutorials, but as an overview, dCache has three main parts:
- tape-backed If files are written here, they are copied to tape. These file might disappear off disk if they are not used, and can be restored to disk from tape, as needed. You will only write here using specific tools.
> ls -l /pnfs/mu2e/tape/phy-sim/sim/mu2e/DS-beam/MDC2018a/art/ff/f7/sim.mu2e.DS-beam.MDC2018a.001002_00373598.art -rw-r--r-- 1 mu2epro mu2e 34186158 May 24 2018 /pnfs/mu2e/tape/phy-sim/sim/mu2e/DS-beam/MDC2018a/art/ff/f7/sim.mu2e.DS-beam.MDC2018a.001002_00373598.art
- persistant Files written here are not automatically purged and are not copied to tape, so the space must be managed. Currenlty we only allow writing here in specific cases.
> ls -l /pnfs/mu2e/persistent/datasets/phy-etc/cnf/mu2e/CeEndpoint/MDC2018b/fcl/00/04/cnf.mu2e.CeEndpoint.MDC2018b.001002_00000025.fcl -rw-r--r-- 1 mu2epro mu2e 690 Aug 27 2018 /pnfs/mu2e/persistent/datasets/phy-etc/cnf/mu2e/CeEndpoint/MDC2018b/fcl/00/04/cnf.mu2e.CeEndpoint.MDC2018b.001002_00000025.fcl
- scratch You can write as much data here as you would like. As space is needed, file that have not be recently accessed will be deleted to make room. You can expect untouched files to last a month, but we have seen shorter times, under special circumstances.
Create your scratch directory:
mkdir -p /pnfs/mu2e/scratch/users/$USER
and you should be able to write there
touch /pnfs/mu2e/scratch/users/$USER/test
and copy a file there:
cp /pnfs/mu2e/persistent/datasets/phy-etc/cnf/mu2e/CeEndpoint/MDC2018b/fcl/00/04/cnf.mu2e.CeEndpoint.MDC2018b.001002_00000025.fcl \ /pnfs/mu2e/scratch/users/$USER
There a are few important notes about dCache you should know right from the beginning.
- dCache is not a file system - it is an nfs server backed by a database. This means simple disk commands such as "find" can cause millions of database queries and try up resources for hours. Only explore one directory at a time. Even using "ls" and not "ls -l" can be much faster.
- You cannot modify files on dCache, only write and read them. If you open a dCache file with an editor, it will come up read-only. The system is designed to be a large data cache, not an interactive disk. All your code should be in your home area or /mu2e/app.
cvmfs
We store code on the cvmfs disk. software packages from outside Mu2e:
ls -l /cvmfs/mu2e.opensciencegrid.org/artexternals
and pre-built Mu2e code versions:
ls -l /cvmfs/mu2e.opensciencegrid.org/Offline
cvmfs acts like a ready-only disk. It is actually a set of clients, servers, and databases. Anywhere the client is run, the identical /cvmfs disk appears on the node and can be read by the users. So this is perfect for distributing code to interactive machines, grid worker nodes, and universities.
Setup Code
Please make sure your bash login scripts follow the recommendations in Shells, in particular, your .bash_profile
executes
source /cvmfs/fermilab.opensciencegrid.org/products/common/etc/setups.sh
You can see that this worked if you get the following
> printenv PRODUCTS /cvmfs/fermilab.opensciencegrid.org/products/common/db
You now have the UPS system ready to use. UPS is a Fermilab package which allows you to access other UPS products in the UPS system. UPS commands do things like put executables in your path, and set environmental variables. The available products include code tools, analysis products, and access to grid computing.
The next step is to execute a UPS command to set the Mu2e environment.
setup mu2e
The main effect is to define PRODUCTS environmental variable:
> printenv PRODUCTS | tr ":" "\n" /cvmfs/mu2e.opensciencegrid.org/artexternals /cvmfs/fermilab.opensciencegrid.org/products/common/db
all the UPS products are under these directories and further setup commands can add them to your environment.
In addition, the setup mu2e
command has set a few environmental variables for you
> printenv MU2E /cvmfs/mu2e.opensciencegrid.org > printenv MU2E_DATA_PATH /cvmfs/mu2e.opensciencegrid.org/DataFiles
and setup two more UPS products:
- a modern version of git
- the Mu2e code build scripts, called Muse
you can see this with
> ups active Active ups products: git v2_31_1 -f Linux64bit+3.10-2.17 -z /cvmfs/mu2e.opensciencegrid.org/artexternals muse v2_07_00 -f NULL -z /cvmfs/mu2e.opensciencegrid.org/artexternals ups v6_0_8 -f Linux64bit+3.10-2.17 -z /cvmfs/mu2e.opensciencegrid.org/artexternals
The exact versions you see will probably be different, since new versions come out fairly regularly.