How to work with Storage Element

SE clients

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://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]  

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
[::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

$ 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.

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/  
  

$ 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	
...

$ 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
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

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

data_replica.py