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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 dcap, xrootd, gridftp (gsiftp) protocols as well as uberftp and gfal (Grid File Access Library) utilities.

On the t3ui* t3wn* servers /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:

dcap usage 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

XROOTD usage examples

  • The T3 Xrootd LAN

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://192.33.123.26:1094///pnfs/psi.ch/cms/trivcat/store/user/martinelli_f/xroot
-rw- 2015-03-15 22:06:04      131870 root://192.33.123.26:1094///pnfs/psi.ch/cms/trivcat/store/user/martinelli_f/xrootd.
-rw- 2015-03-15 22:06:45  1580023632 root://192.33.123.26:1094///pnfs/psi.ch/cms/trivcat/store/user/martinelli_f/ZllH.DiJetPt.Mar1.DY1JetsToLL_M-50_TuneZ2Star_8TeV-madgraph_procV2_mergeV1V2.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 
[1.472GB/1.472GB][100%][==================================================][94.18MB/s]  

  • The T3 Xrootd WAN

Read-Write Xrootd service exposed on Internet ( "WAN" ) is reachable by root://t3se01.psi.ch:1094//

This service is intentionally NOT connected to the CMS AAA cms-xrd-global.cern.ch service because of the 2016 CMS policy that excludes both permanently all the T3 sites and dynamically all the misbehaving T1/T2 sites ; root://t3se01.psi.ch:1094// is reachable from Internet because it's connected again by CMS AAA policy to cms-xrd-transit.cern.ch as shown by the following example :

$ 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
[::192.33.123.24]:1095 Server Read

$ host 192.33.123.24
24.123.33.192.in-addr.arpa 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   
[32MB/32MB][100%][==================================================][32MB/s]  

ROOT examples

  • Reading a file in ROOT by xrootd
https://confluence.slac.stanford.edu/display/ds/Using+Xrootd+from+root
$ 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
/swshare/ROOT/root_v5.34.18_slc6_amd64_py26_pythia6/bin/thisroot.sh

$ which hadd
/swshare/ROOT/root_v5.34.18_slc6_amd64_py26_pythia6/bin/hadd

$ hadd -f0
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_12.root
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_13.root
hadd Target file:
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root
hadd Source file 1:
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_12.root
hadd Source file 2:
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_13.root
hadd Target path:
gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root:/

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

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.

gfal-* tools

gfal-* is a CERN standard tools to interact with all the Grid SEs.

The following gfal-* tools are available both on the UIs and on the WNs servers:
gfal-cat, gfal-copy, gfal-ls, gfal-mkdir, gfal-rm, gfal-save, gfal-sum, gfal-xattr.

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/ 

A manual page is available for each of them like $ man gfal-rm

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	
...

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

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

uberftp examples

uberftp is a GridFTP interactive client.

  • Interactively accessing GridFTP server:
$ uberftp t3se01.psi.ch
220 GSI FTP door ready
200 User :globus-mapping: logged in
UberFTP (2.8)> cd /pnfs/psi.ch/cms/trivcat/store/user/martinelli_f
UberFTP (2.8)> ls
drwx------  1 martinelli_f martinelli_f          512 Nov 25  2014 sgejob-5939967
...
  • Listing remote directory or files:
$ uberftp t3se01.psi.ch 'ls /pnfs/psi.ch/cms/trivcat/store'  
$ uberftp  -ls gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username
  • Make a new direcory on dCache:
$ uberftp -mkdir gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/newdirectory
  • Copying file from dCache to local node:
$ uberftp t3se01.psi.ch 'get /pnfs/psi.ch/cms/testing/test100' 
$ uberftp gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms//trivcat/store/user/username/dir-name/somefile.root file:///t3home/username/local-dir/.
  • Copying file from local node to dCache:
$  uberftp  file://$PWD/uftp.root  gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/dir
  • Copying a remote dCache dir to local node:
Be aware that's a serial copy, not parallel :
$ uberftp t3se01.psi.ch 'get -r  /pnfs/psi.ch/cms/testing .

  • Remove a file from dCache:
$ uberftp -rm  gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms//trivcat/store/user/username/filelocation 
  • Erasing a remote whole (non-empty) dir with all content:
$ uberftp t3se01.psi.ch 'rm -r /pnfs/psi.ch/cms/trivcat/store/user/martinelli_f/VHBBHeppyV12'
$ uberftp -rm -r gsiftp://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/dir-with-content
or in debug mode :
$ uberftp  -debug 2 t3se01.psi.ch 'rm -r /pnfs/psi.ch/cms/trivcat/store/user/martinelli_f/VHBBHeppyV12'

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
user:2980:RWX
group:500:RX   <---- no group write ; 500 is the GID
other:RX        

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
owner:2980:RWX
user:2980:RWX
group:500:RWX   <---- now your group members can write files and dirs  
other:RX

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
a360e11e-ab3b-11e6-8fe7-02163e00a39b

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

/cvmfs/cms.cern.ch/SITECONF/T2_CH_CSCS/JobConfig/site-local-config.xml
/cvmfs/cms.cern.ch/SITECONF/T2_CH_CSCS/PhEDEx/storage.xml

Some useful examples are below:

gsiftp://storage01.lcg.cscs.ch//pnfs/lcg.cscs.ch/cms/trivcat
gsiftp://t3se01.psi.ch//pnfs/psi.ch/cms/trivcat
gsiftp://eoscmsftp.cern.ch//eos/cms/

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.

Understanding of dCache for advanced user

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