Neutrino Platform Storage at CERN

Introduction

This page describes how to access data at CERN in different locations, explaining the different commands and tools to be used and the access policy to the storage. Neutrino Platform at CERN mostly relies now on EOS for disk only space.
xrootd is used and works with EOS technology.
All commands and examples are thought to be issued on neutplatform nodes inside the CERN network. Most of them work anyway as well from outside CERN.

CASTOR tape storage system

CASTOR is the acronym for CERN Advanced STORage manager, a data storage system used at CERN, more on cern.ch/castor. CASTOR should not be used as a backup service, as suggested here.

CASTOR is meant for storing large volumes of physics data. CASTOR is inefficient for small files, both for writing data to tape (migration) and getting data from tape (recall): the optimal file size for CASTOR is 1GB and larger.

CASTOR doesn’t know about e-groups at all, just UNIX-like permissions (user::groups), so much simpler than EOS.

In order to access CASTOR service, one needs to set some variables. In bash:

export RFIO_USE_CASTOR_V2=YES
export STAGE_HOST=castorpublic
export STAGE_SVCCLASS=default

Neutrino Platform CASTOR tape area

NP base directories are:

/castor/cern.ch/neutplatform/protodune
/castor/cern.ch/neutplatform/dune

Experimental area is granted to np-comp UNIX group, so be aware you have to belong to this UNIX computing group.

copying single files

Remember to set proper variables for CASTOR. You can use now rfcp command to copy file:

rfcp /castor/cern.ch/neutplatform/protodune/.../somefile.root /home/user/workspace

Or new XROOT protocol (might be faster, no need to setup variables for CASTOR):

xrdcp root://castorpublic//castor/cern.ch/neutplatform/protodune/.../somedir/somefile.root /home/user/workspace/ -OSsvcClass=default 
xrdcp /home/user/workspace/somefile.root root://castorpublic//castor/cern.ch/neutplatform/protodune/.../somedir/ -ODsvcClass=default

If some of these commands hangs - read next section of this page.

Long waiting time with rfcp

To check status of file, use stager_qry command:
stager_qry -M /castor/cern.ch/neutplatform/protodune/.../somefile.root

In most cases, as an result you can get one of following answers:

  • STAGED
  • STAGEIN
  • Error 2/No such file


STAGED means that means "file on disk matrix (fast access)", so you should obtain it quickly with rfcp command.
Received 1 responses
/castor/cern.ch/neutplatform/protodune/.../somefile.root
312327210@castorns STAGED


STAGEIN means that "file is on a tape" and need to be transferred to the disk matrix, which takes some time. You need to wait for the result of rfcp command.
Received 1 responses
/castor/cern.ch/neutplatform/protodune/.../somefile.root
386766073@castorns STAGEIN


"Error 2/No such file" also means that "file is on a tape" and need to be transferred to the disk matrix, which takes some time. You need to wait for the result of rfcp command.
Error 2/No such file or directory (File /castor/cern.ch/neutplatform/protodune/.../somefile.root not on this service class)
This error is very similar to the one that you obtain when asking about not existing file. In such case (file really missing) you will see:
Error 2/No such file or directory (Filename /castor/cern.ch/neutplatform/protodune/.../somefile.root)
You can check is file is existing with nsls command.


In second and third case you can ask stager directly to move files to the "disk matrix" by issuing following command:
stager_get -S default -M /castor/cern.ch/neutplatform/protodune/.../somefile.root

More on this topic - read this

Reporting errors

Switch on debugging for rfcp (bash/zsh):

export RFIO_TRACE=3
export STAGER_TRACE=3
or for tcsh/csh
setenv RFIO_TRACE 3
setenv STAGER_TRACE 3

To switch debugging for xrdcp, use -d switch (i.e. -d 1, -d 2, -d 3)

Permissions

To set permission we use nssetacl, to get them nsgetacl.

Removing permissions

Remove ACL entry:

nssetacl -d u:'_username_':rwx /castor/cern.ch/neutplatform/protodune/offline/test

Changing permissions

Modify default ACLs to 775 (will be propagated).

nssetacl -m u::7,g::7,o::5 /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m d:u::7,d:g::7,d:o::5 /castor/cern.ch/neutplatform/protodune/offline/test
For every directory (or file) created under /castor/cern.ch/neutplatform/protodune/offline/test owner will be set up to the person who created it, but permissions of all directories will be set to 775. This way everybody in np-comp group will be able to write to any of subdirectories (whoever will create it).

Let us do the same as above, but not for group np-comp, but for list of users.

nssetacl -m d:u::7,d:g::5,d:o::5 /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m u::7,g::5,o::5 /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m default:group:np-comp:rx,default:other:-,default:mask:rwx /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m default:user:_username_:rwx,default:mask:rwx /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m user:_username_:rwx,mask:rwx /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m d:u:_username1_:7,d:m:7 /castor/cern.ch/neutplatform/protodune/offline/test
nssetacl -m u:_username1_:7,m:7 /castor/cern.ch/neutplatform/protodune/offline/test 
For every directory (or file) created under /castor/cern.ch/neutplatform/protodune/offline/test owner will be set up to the person who created it, but permissions of all directories will be set to 755. This way everybody in np-comp group will be able just to read from any of subdirectories (whoever will create it). Only users from the list can write to subdirectories.

If after some time, new user needs to be added to the list, then we shall add him permissions to write to existing files. Following command will work only with bash.

nsfind /castor/cern.ch/neutplatform/protodune/offline/test  -type f > filechecklist.txt
cat filechecklist.txt | xargs nssetacl -m u:_username2_:rw,m:rw
nsfind /castor/cern.ch/neutplatform/protodune/offline/test -type d > dirchecklist.txt
cat dirchecklist.txt | xargs nssetacl -m d:u:_username2_:rwx,d:m:rwx
cat dirchecklist.txt | xargs nssetacl -m u:_username2_:rwx,m:rwx

Changing ownership

If recursive method for applying access rights was applied as it is described above, it might happen that newly created directories might have different owner as their parent directories. To change it one may use recursive version of nschown command, i.e:.

nschown -R _username3_ /castor/cern.ch/neutplatform/protodune/offline/test

IMPORTANT: such command might disable effective access rights. To bring them back, read from output of nsgetacl commands who has for example read access and grant again such access for one user. This will make effective access rights correct, i.e:.

nsfind /castor/cern.ch/neutplatform/protodune/offline/test -type d > dirchecklist.txt
cat dirchecklist.txt | xargs nssetacl -m d:u:_username_:rx,d:m:rx
cat dirchecklist.txt | xargs nssetacl -m u:_username_:rx,m:rx

How to use Personal CASTOR storage area?

Every user with CERN account has a directory in CASTOR. To list the files in your directory, type:

  • rfdir /castor/cern.ch/user/initial/username/ to list the files in your directory, where initial is the first letter of your user name.
  • nsls - list home CASTOR directory
  • nsls /castor....
  • nsls -l - long listing
  • rfmkdir /castor/cern.ch/user/initial/username/dir to create directories
  • rfcp filename /castor/cern.ch/user/initial/username/dir copy files to a CASTOR directory
  • nsrm /castor/cern.ch/user/initial/username/dir - remove dir directory

Other useful commands:

  • xrdcp
  • nsgetacl , nssetacl
  • stager_qry
  • stager_get

Documentation

*CASTOR quick tutorial for beginners *CASTOR Knowledge Base Articles/FAQ

EOS storage system

Pools usually accessed directly by the users exploit the EOS technology. They can be accessed through the eospublic.cern.ch xrootd redirector using the xrootd tools and commands.
This section will briefly explain the easiest way to perform usual operations on EOS (i.e., listing directories, writing and reading files).
For more actions, you can open an interactive shell on eospublic by simply typing eos.
From within the EOS shell, type help for a full list of commands you can perform on EOS (most of them mimic the common unix commands, like ls, mkdir, rm, ...).
Similarly, from your linux shell you can also type xrd eospublic to open a xrootd interactive session on eospublic. Typing help from within the interactive shell will give you the list of xrd actions you can perform on EOS.

How to access personal EOS space

The initial and mandatory step to using your CERNBox is to create it.  
Use any Web browser to go to 'https://cernbox.cern.ch' 
and login via the CERN Single Sign-On page with your username and password (NICE or lxplus).

This first connection creates your CERNBox storage space (1 TB, up to 1 million files), hosted in the CERN Data Centre.

To activate the corresponding service go to:
https://resources.web.cern.ch/resources/Manage/EOS/Default.aspx?login=YOUR_UNIX_LOGIN

You must set up your environment before starting:

export EOS_MGM_URL=root://eosuser.cern.ch

and your user directories are under /eos/user/<initial>/<userid>

*Please take into account*, personal EOS space (/eos/user/<firstletter_login_name>/<login_name>) has nothing to do with experimental 
EOS space (/eos/experiment/neutplatform/...). 

How to best access EOS from central services (LXPLUS and LXBATCH)

If you still have problems you can get help through the CERN Service Portal.

If you have questions, you might also have a look at the cernbox FAQ

Web browser supported platforms.

How to access Neutrino Platform experimental EOS either form lxplus or from neutplatform computing cluster

Neutrino Platform experimental EOS space  is located at /eos/experiment/neutplatform/.
A user to have access needs to be a member of the np-comp UNIX group.
Ensure that the users who will access the space have the correct primary UNIX group.
Otherwise get them to change it in the accounts setting page
https://resources.web.cern.ch/resources/Manage/Linux/Settings.aspx?login=YOUR_UNIX_LOGIN
 
If for any reason you can't have access to the !EOS space from our cluster please take into consideration the following:
   * check if you are a member of the appropriate e-group
   * check if you have a valid kerberos certificate

Setting up Neutrino Platform EOS

  • If you want to make use of most recent features mentioned in this FAQ you have to pick the 'client' version of EOS using a bash or tcsh setup script:
// How to setup neutplatform EOS space
  // Verify first that you are connecting to 'your' experiment dedicated EOS instance
ssh neutplatform
source /afs/cern.ch/project/eos/installation/0.3.121-aquamarine.public/etc/setup.sh
mkdir <folder_name>
eosmount <folder_name>
ls <folder_name>/experiment/neutplatform

//unmount the folder
In order to unmount the folder you can either disconnect from the machine you are connected to or
eosumount  <folder_name>

The automatic EOS endpoint setting use your group membership to sort you into an experiment. 
If this does not work for you, you can just specify your endpoint via an environment variable: 
export EOS_MGM_URL=root://eospublic.cern.ch

Using EOS

  • The 'eos' CLI (Command Line Interface) supports most of the standard filesystem commands like:
  • ls, cd, mkdir, rm, rmdir, find, cp ...
  • 'eos help' shows all available commands, 'eos --help' explains each command

The 'eos' CLI can be used as an interactive shell with history

as a busy-box command
bash$ eos whoami

bash$ eos
EOS console [root://eospublic.cern.ch] |/> whoami
to quit from the EOS console
EOS console [root://eospublic.cern.ch] |/>.q
 
# check eos version
bash$ eos version
EOS_INSTANCE=eospublic
EOS_SERVER_VERSION=0.3.226 EOS_SERVER_RELEASE=1
EOS_CLIENT_VERSION=0.3.121 EOS_CLIENT_RELEASE=aquamarine

# check eos help
bash$ eos help

Proposal for a new structure in NP-EOS

Please see here the structure it self and the assigned rights to corresponding e-groups.

Proposal NP02/NP04

**current situation**. You could start using it and let neutplatform computing supportMicrosoft Outlook e-mail file know.

purpose EOS path e-groups (ACLs) quotas Notes
For both protoDUNEs (np02/np04) common path: /eos/experiment/neutplatform/protodune   Total :500 TB  
For NP02 RAW data /eos/experiment/neutplatform/protodune/rawdata/np02 eos-experiment-cenf-np02-readers (rx)    
For NP04 RAW data /eos/experiment/neutplatform/protodune/rawdata/np04 eos-experiment-cenf-np04-readers (rx)    
NP02/NP04 MCC files : detector performance, reconstruction, calibration, physics, cross-section, measurements /eos/experiment/neutplatform/protodune/npmcproddisk/dragroupdisk eos-experiment-cenf-np02-readers (rx)   TODO
eos-experiment-cenf-np04-readers (rx)
eos-experiment-cenf-np02-writers (rwx)
eos-experiment-cenf-np04-writers (rwx)
NP02/NP04 physics area: output from various subgroups analyses output , ROOT files mainly /eos/experiment/neutplatform/protodune/physgroupdisk eos-experiment-cenf-np02-readers   TODO
eos-experiment-cenf-np04-readers (rx)
eos-experiment-cenf-np02-writers (rwx)
eos-experiment-cenf-np04-writers (rwx)
NP04 beamgroup : studies on particle composition of the hadron beam at the entrance of the cryostat /eos/experiment/neutplatform/protodune/npmcproddisk/beamgroupdisk eos-experiment-cenf-np04-readers (rx)   TODO
eos-experiment-cenf-np04-writers (rwx)

-->

Proposal for DUNE

**NOT READY**

Accessing an EOS file from ROOT

  • You have to use URLs as file names which are built in this way: root://eospublic.cern.ch//eos/experiment/neutplatform/... e.g.
  • root://eospublic.cern.ch//eos/experiment/neutplatform/.../histo.root
  • root [0]: TFile::Open("root://eospublic.cern.ch//eos/experiment/neutplatform/.../histo.root");

Other EOS commands

# copy a single file
eos cp /eos/experiment/neutplatform/.../histo.root /tmp/
# using xrdcp
xrdcp histo.root root://eospublic.cern.ch//eos/experiment/neutplatform/../<destination_dir>
xrdcp root://eospublic.cern.ch//eos/experiment/neutplatform/../<destination_dir> /tmp/
   
# copy all files within a directory - no subdirectories
eos cp /eos/experiment/neutplatform/.../histodirectory/ /tmp/histodirectory 
 
# copy recursive the complete hierarchy in a directory
eos cp -r /eos/eos/experiment/neutplatform/.../histodirectory/ /tmp/histodirectory
# using xrdcp
xrdcp -f -R  root://eospublic.cern.ch//eos/experiment/neutplatform/../histodirectory/  /tmp/histodirectory/ 

# copy recursive the complete hierarchiy into the directory 'histordirectory' in the current local working directory
eos cp -r /eos/experiment/neutplatform/.../histodirectory/ histodirectory
# using xrdcp
xrdcp -f -R  root://eospublic.cern.ch//eos/experiment/neutplatform/../histodirectory/  histodirectory

# copy an WEB file [ currently the reported copy size is 0 ]
eos cp http://root.cern.ch/files/<file>.root /tmp/

  // If you just need to create an empty directory: 
eos mkdir /eos/experiment/neutplatform/../../dir1/dir2/..

How to list directories and files in EOS

// Verify first that you are connecting to 'your' experiment dedicated EOS instance
  // Creating file lists
You can run 'find' commands in EOS or XRootD storage like CASTOR using the 'eos' CLI. This command returns full pathnames!
# find all files under an EOS subdirectory (if you are an ordinary user, the file list is limited to 100k files and 50k directories)
eos find -f /eos/experiment/neutplatform/

# find all directories
eos find -d /eos/experiment/neutplatform/

# find all files in a CASTOR directory
eos find -f root://castorpublic//castor/cern.ch/user/<login_name/<dir_name>/

# find all files on a mounted file system
eos find -f file:/afs/cern.ch/user/<initial>/<login_name/<dir_name>/

  // Listing directories
# list files in eos
eos ls [-la] /eos/experiment/neutplatform/

# An alternative command is:
xrd eospublic dirlist /eos/experiment/neutplatform/

# list files in castor [ if you use '-la' be aware that the ownership and permissions shown are not correct ]
eos ls [-la] root://castorpublic//castor/cern.ch/user/<login_name/<dir_name>/

Writing and reading files on EOS

Files on EOS can also be accessed using xrootd, in particular the xrdcp command.
xrdcp can be used to copy a file to and from any EOS directory the user has reading/writing access to. The syntax is very simple and foresees a mandatory prefix that is composed of the protocol (root) and the name of the xrootd redirector (eospublic): root://eospublic/ (notice that from outside CERN you should include the domain part in the redirector name, i.e. root://eospublic.cern.ch/).
So, for example, suppose you want to copy in your current directory the file which resides at

/eos/experiment/neutplatform/dune/mcproddisk/mcc7/kaons/1GeV/reco/13301499_1X/mu_80_20160826T113204_gen_8c02e091-479d-4f2b-9af2-f0a782eb49af_g4_detsim_reco.root

Then what you should do is simply:

xrdcp root://eospublic//eos/experiment/neutplatform/dune/mcproddisk/mcc7/kaons/1GeV/reco/13301499_1X/mu_80_20160826T113204_gen_8c02e091-479d-4f2b-9af2-f0a782eb49af_g4_detsim_reco.root  .

Root files can also be accessed directly in ROOT using the root protocol:

TFile *file = TFile::Open("root://eospublic//eos/experiment/neutplatform/.../source_filename");

Deleting files and directories on EOS

// Files on !EOS can be deleted with the intuitive command :
eos rm /eos/experiment/neutplatform/.../filename=

  // The rm command accepts the option -r for recursive deletion. 
  // This will also delete the directory it's called on:
bash$ eos rm -r /eos/experiment/neutplatform/.../directory_to_remove

  // Don't use mv (move) on EOS. 
"Moving" files or directories on EOS is NOT supported.
You can copy from one plece to another, you can delete but you cannot move.
This is like this by design: moving would imply an actual recalculation of the accounting
(which is based on paths in EOS) and this would crash the system.

xrdcp man page

EOS Knowledge Based articles and documentation


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Major updates:
-- NectarB - 21-Sept-2016
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