create new tag
view all tags

How to work with Storage Element

SE clients

Storage data (based on dCache) located under directory /pnfs/psi.ch/cms/trivcat/store/user/username .
Data are accessible by standard gfal2 (Grid File Access Library), xrdcp and dcap (obsolete) utilities.

On login and compute nodes /pnfs is mounted Read-Only. With /pnfs one can use the common Linux commands cd, ls, find, du, stat, i.e. meta-data based commands displaying the file list, size, last access time, etc, but not file-content commands (it is not possible to cat or grep a file).

Here are examples how to copy file from dCache to local machine and vice versa:

XROOTD LAN (local area network, for local access from UI and worker nodes)

xrdfs executed on a UI in the Xrootd LAN service case :

$ xrdfs t3dcachedb03.psi.ch ls -l -u //pnfs/psi.ch/cms/trivcat/store/user/$USER/
-rw- 2015-03-15 22:03:41  5356235878 root://
-rw- 2015-03-15 22:06:04      131870 root://
-rw- 2015-03-15 22:06:45  1580023632 root://

xrdcp executed on a UI in the Xrootd LAN service case :

$ xrdcp -d 1 root://t3dcachedb.psi.ch:1094///pnfs/psi.ch/cms/trivcat/store/user/$USER/ZllH.DiJetPt.Mar1.DY1JetsToLL_M-50_TuneZ2Star_8TeV-madgraph_procV2_mergeV1V2.root /dev/null -f 

XROOTD WAN (wide area network, access from outside of Tier-3, stage-in / stage-out)

The Read-Write Xrootd service reachable by root://t3se01.psi.ch:1094//

Do NOT use this service for local analysis jobs. We limit the number of parallel transfers through this door, since it usually should only be used by efficient WAN copies, i.e. transfers of large files with high bandwidths, because too many of these transfers could harm the availability of the tier-3's small number of storage servers. If you use this door for your analysis jobs you will find that many of them will get queued.

$ xrdfs cms-xrd-transit.cern.ch locate /store/mc/RunIIFall15MiniAODv2/ZprimeToWW_narrow_M-3500_13TeV-madgraph/MINIAODSIM/PU25nsData2015v1_76X_mcRun2_asymptotic_v12-v1/00000/86A261F4-3BB8-E511-88EE-C81F66B73F37.root
[::]:1095 Server Read

$ host domain name pointer t3se01.psi.ch.

$ xrdcp --force  root://cms-xrd-transit.cern.ch//store/mc/RunIIFall15MiniAODv2/ZprimeToWW_narrow_M-3500_13TeV-madgraph/MINIAODSIM/PU25nsData2015v1_76X_mcRun2_asymptotic_v12-v1/00000/86A261F4-3BB8-E511-88EE-C81F66B73F37.root /dev/null   

ROOT examples

  • Reading a file in ROOT by xrootd
$ root -l
$ root [1] TFile *_file0 = TFile::Open("root://t3dcachedb03.psi.ch:1094//pnfs/psi.ch/cms/trivcat/store/user/leo/whatever.root") 
  • Reading a file in ROOT by dcap
$ root -l
$ root [1] TFile *_file0 = TFile::Open("dcap://t3se01.psi.ch:22125//pnfs/psi.ch/cms/trivcat/store/user/leo/whatever.root") 
  • Merging online two ROOT files by hadd and gsidcap
To merge online two ROOT files located at T3 you can use the ROOT tool hadd:
More... Close
$ source

$ which hadd

$ hadd -f0
hadd Target file:
hadd Source file 1:
hadd Source file 2:
hadd Target path:

$ ll /pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root
-rw-r--r-- 1 at3user ethz-susy 87M Oct  3 16:41

because of the gsidcap protocol that's usually just offered as a LAN protocol in a Tier 1/2/3, you're suppose to run hadd from a t3ui* server, not lxplus or some external UI, and you'll want to merge online two ROOT files that are necessarily stored at T3 with the final result again stored at T3.

GFAL2 examples

gfal2 is a CERN standard tools to interact with all the Grid SEs.

There are the following gfal2 tools are available gfal-cat, gfal-copy, gfal-ls, gfal-mkdir, gfal-rm, gfal-save, gfal-sum, gfal-xattr with corresponding manual page for each of them like $ man gfal-rm .

We recommend to use root://t3dcachedb03.psi.ch to upload/download a file:

$ gfal-copy --force root://t3dcachedb03.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/  
Some other protocols options:
$ gfal-copy --force gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/

$ gfal-copy --force gsidcap://t3se01.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/ 

Further examples :

$ gfal-mkdir  root://t3dcachedb03.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/user_id/testdir
$ gfal-copy root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:/dev/null -f
Copying root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11   [DONE]  after 0s 

$ gfal-ls -l root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user 
dr-xr-xr-x   0 0     0           512 Feb 21  2013 alschmid	
Remove a file from dCache:
$ gfal-rm root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/myfile

Erasing a remote whole (non-empty) dir with all content:

$ gfal-rm -r  root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/dir-name 

Action of the gfal-save and gfal-cat commands :

$ cat myfile
Hello T3
$ cat myfile | gfal-save root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/myfile
$ gfal-cat root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/myfile
Hello T3

DCAP examples

To copy a file from the SE to a local disk , for instance, on /scratch, use dcap (the only option to transfer data without grid certificate) and gsidcap protocols.
These tools are blocked towards the outside, so you cannot use them from a machine outside of PSI like lxplus for downloading files.

dccp dcap://t3se01.psi.ch:22125//pnfs/psi.ch/cms/testing/test100  /scratch/myfile

dccp gsidcap://t3se01.psi.ch:22128/pnfs/psi.ch/cms/testing/test100  /scratch/myfile

Setting data access permissions

Every user directory on T3 SE /pnfs/psi.ch/cms/trivcat/store/user/username is set with write permission just to owner; by default even your group members won't be able to alter your own SE dir like shown in the following example:

$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username
# file  : srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username
# owner : 2980
owner:2980:RWX    <---- 2980 is the UID
group:500:RX   <---- no group write ; 500 is the GID

if you need to create a /pnfs dir where also the group members can write and delete files do the following:

$ srmmkdir srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/TESTDIR
$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/TESTDIR

$ srm-set-permissions -type=ADD -group=RWX srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/TESTDIR

$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/TESTDIR
# file  : srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/TESTDIR
# owner : 2980
group:500:RWX   <---- now your group members can write files and dirs  

Getting data from remote SEs to the T3 SE

Official datasets

For official data sets/blocks that are registered in CMS DBS you must use the PhEDEx system.

Private datasets

The recommended way to transfer private datasets (non-CMSSW ntuples) between sites is the File Transfer System (FTS) documentation. In a nuthsell, you need to prepare a file that contains lines like protocol://source protocol://destination.

An example file is the following:

gsiftp://storage01.lcg.cscs.ch//pnfs/lcg.cscs.ch/cms/trivcat/store/user/jpata/tth/Sep29_v1/ttHTobb_M125_13TeV_powheg_pythia8/Sep29_v1/161003_055207/0000/tree_973.root gsiftp://t3se01.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/jpata/tth/Sep29_v1/ttHTobb_M125_13TeV_powheg_pythia8/Sep29_v1/161003_055207/0000/tree_973.root
gsiftp://storage01.lcg.cscs.ch//pnfs/lcg.cscs.ch/cms/trivcat/store/user/jpata/tth/Sep29_v1/ttHTobb_M125_13TeV_powheg_pythia8/Sep29_v1/161003_055207/0000/tree_981.root gsiftp://t3se01.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/jpata/tth/Sep29_v1/ttHTobb_M125_13TeV_powheg_pythia8/Sep29_v1/161003_055207/0000/tree_981.root

Then, you can submit the transfer with

$ fts-transfer-submit -s https://fts3-pilot.cern.ch:8446 -f files.txt

You will get back an ID string, which you can use to monitor your transfer on the site https://fts3-pilot.cern.ch:8449/fts3/ftsmon/#

The transfer will proceed in parallel, you can also specify resubmission options for failed jobs.

The site prefixes can typically be found out from existing transfer logs on the grid or by inspecting the files in


Some useful examples are below:


Job Stageout from other remote sites

You can try to stageout your CRAB3 Job outputs directly a T3_CH_PSI but if these transfers will get too slow and/or unreliable than stageout first at T2_CH_CSCS and afterwards copy your files at T3_CH_PSI by the Leonardo Sala's data_replica.py or whatever else Grid tool able to transfers files in parallel between 2 sites.

Topic attachments
I Attachment History Action Size Date Who Comment
Texttxt T2_Storage.py.txt r1 manage 1.6 K 2017-01-30 - 10:49 JoosepPata  
Edit | Attach | Watch | Print version | History: r144 < r143 < r142 < r141 < r140 | Backlinks | Raw View | Raw edit | More topic actions
Topic revision: r144 - 2023-06-09 - DerekFeichtinger
This site is powered by the TWiki collaboration platform Powered by Perl This site is powered by the TWiki collaboration platformCopyright © 2008-2024 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding TWiki? Send feedback