(r142) HowToAccessSe < CmsTier3

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---+!! How to work with Storage Element

%TOC%   

---++ SE clients
Storage data (based on dCache) located under directory   /pnfs/psi.ch/cms/trivcat/store/user/%BLUE%username%ENDCOLOR% . </br>
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). </br>

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

---+++ XROOTD  examples
 
   *  *The T3 Xrootd LAN* 

[[http://xrootd.org/doc/man/xrdfs.1.html][xrdfs]] executed on a UI in the Xrootd LAN service case :
<pre>
$ 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/%BLUE%ZllH.DiJetPt.Mar1.DY1JetsToLL_M-50_TuneZ2Star_8TeV-madgraph_procV2_mergeV1V2.root%ENDCOLOR%
...
</pre>
 
[[http://xrootd.org/doc/man/xrdcp.1.html][xrdcp]] executed on a UI in the Xrootd LAN service case :
<pre>
$ xrdcp -d 1 root://t3dcachedb.psi.ch:1094///pnfs/psi.ch/cms/trivcat/store/user/$USER/%BLUE%ZllH.DiJetPt.Mar1.DY1JetsToLL_M-50_TuneZ2Star_8TeV-madgraph_procV2_mergeV1V2.root%ENDCOLOR% /dev/null -f 
[1.472GB/1.472GB][100%][==================================================][94.18MB/s]  
</pre>

   *  *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 [[https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookXrootdService][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 [[https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookXrootdService][CMS AAA]] policy to =cms-xrd-transit.cern.ch= as shown by the following example :
<pre>
$ 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]  
</pre>


---+++ ROOT examples

   *   *Reading a file in ROOT by xrootd*
https://confluence.slac.stanford.edu/display/ds/Using+Xrootd+from+root
<pre>
$ root -l
$ root [1] TFile *_file0 = TFile::Open("root://%BLUE%t3dcachedb03.psi.ch%ENDCOLOR%:1094//pnfs/psi.ch/cms/trivcat/store/user/leo/whatever.root") 
</pre>
   * *Reading a file in ROOT by dcap* 
<pre>
$ root -l
$ root [1] TFile *_file0 = TFile::Open("dcap://%BLUE%t3se01.psi.ch%ENDCOLOR%:22125//pnfs/psi.ch/cms/trivcat/store/user/leo/whatever.root") 
</pre>
   * *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=:</br>
%TWISTY%
<pre>
$ 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 %ORANGE%-f0%ENDCOLOR%
%GREEN%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root%ENDCOLOR%
%BLUE%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_12.root%ENDCOLOR%
%BLUE%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_13.root%ENDCOLOR%
hadd %ORANGE%Target%ENDCOLOR% file:
%GREEN%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/merged.root%ENDCOLOR%
hadd %ORANGE%Source%ENDCOLOR% file 1:
%BLUE%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_12.root%ENDCOLOR%
hadd %ORANGE%Source%ENDCOLOR% file 2:
%BLUE%gsidcap://t3se01:22128/pnfs/psi.ch/cms/trivcat/store/user/at3user/babies/QCD-Pt300to475/QCD_Pt300to470_PU_S14_POSTLS170/treeProducerSusyFullHad_tree_13.root%ENDCOLOR%
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
</pre>%ENDTWISTY%
 
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 =%BLUE%root%ENDCOLOR%://t3dcachedb03.psi.ch=  to  upload/download a file:
<pre>
$ gfal-copy --force %BLUE%root%ENDCOLOR%://t3dcachedb03.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/  
  </pre>
Some other protocols options:
<pre>
$ gfal-copy --force %BLUE%gsiftp%ENDCOLOR%://t3se01.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/
<!--$ gfal-copy --force %BLUE%srm%ENDCOLOR%://t3se01.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/ -->
$ gfal-copy --force %BLUE%gsidcap%ENDCOLOR%://t3se01.psi.ch/pnfs/psi.ch/cms/t3-nagios/1MB-test-file_pool_t3fs14_cms_11 file:////$PWD/ 
</pre>

Further examples :

<pre>
$ %BLUE%gfal-mkdir%ENDCOLOR%  root://t3dcachedb03.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/user_id/testdir
</pre>
<pre>
$ %BLUE%gfal-copy%ENDCOLOR% 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 

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

Erasing a remote whole (non-empty) dir with all content:
<pre>$ %BLUE%gfal-rm -r %ENDCOLOR% root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/%GREEN%dir-name%ENDCOLOR% </pre>

Action of the =%BLUE%gfal-save%ENDCOLOR%= and =%BLUE%gfal-cat%ENDCOLOR%= commands :
<pre>$ cat %GREEN%myfile%ENDCOLOR%
%ORANGE%Hello T3%ENDCOLOR%
$ cat %GREEN%myfile%ENDCOLOR% | %BLUE%gfal-save%ENDCOLOR% root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/%GREEN%myfile%ENDCOLOR%
$ %BLUE%gfal-cat%ENDCOLOR% root://t3dcachedb03.psi.ch//pnfs/psi.ch/cms/trivcat/store/user/auser/%GREEN%myfile%ENDCOLOR%
%ORANGE%Hello T3%ENDCOLOR%
</pre>

---+++ 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. </br>These tools  are blocked towards the outside, so you cannot use them from a machine outside of PSI  like =lxplus=  for downloading files.

<pre>
dccp dcap://%BLUE%t3se01.psi.ch%ENDCOLOR%:22125//pnfs/psi.ch/cms/testing/test100  /scratch/myfile
</pre>

<pre>
dccp gsidcap://%BLUE%t3se01.psi.ch%ENDCOLOR%:22128/pnfs/psi.ch/cms/testing/test100  /scratch/myfile
</pre>



<!-- 
uberftp  examples
uberftp is a !GridFTP interactive client.

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

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

---++ Setting  data access permissions

Every user directory on T3 SE   /pnfs/psi.ch/cms/trivcat/store/user/%BLUE%username%ENDCOLOR%  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:
<pre>$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/%BLUE%username%ENDCOLOR%
# file  : srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/%BLUE%username%ENDCOLOR%
# owner : 2980
owner:2980:R%GREEN%W%ENDCOLOR%X    &lt;---- 2980 is the UID
user:2980:R%GREEN%W%ENDCOLOR%X
group:500:RX   &lt;---- no group write ; 500 is the GID
other:RX        
</pre>


if you need to create a =/pnfs= dir where also the group members can write and delete files do the following:
<pre>$ srmmkdir srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/%BLUE%TESTDIR%ENDCOLOR%
$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/%BLUE%TESTDIR%ENDCOLOR%

$ %RED%srm-set-permissions%ENDCOLOR% -type=ADD -group=R%GREEN%W%ENDCOLOR%X srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/%BLUE%TESTDIR%ENDCOLOR%

$ srm-get-permissions srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/%BLUE%TESTDIR%ENDCOLOR%
# file  : srm://t3se01.psi.ch/pnfs/psi.ch/cms/trivcat/store/user/username/%BLUE%TESTDIR%ENDCOLOR%
# owner : 2980
owner:2980:R%GREEN%W%ENDCOLOR%X
user:2980:R%GREEN%W%ENDCOLOR%X
group:500:R%GREEN%W%ENDCOLOR%X   &lt;---- now your group members can write files and dirs  
other:RX
</pre>


---++ 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 [[HowToOrderData][PhEDEx system]].

---+++ Private datasets

The recommended way to transfer private datasets (non-CMSSW ntuples) between sites is the File Transfer System (FTS) [[http://fts3-docs.web.cern.ch/fts3-docs/docs/cli/cli.html][documentation]]. In a nuthsell, you need to prepare a file that contains
lines like =protocol://source protocol://destination=.

An example file is the following:
<pre>
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
</pre>

Then, you can submit the transfer with
<pre>
$ fts-transfer-submit -s https://fts3-pilot.cern.ch:8446 -f files.txt
a360e11e-ab3b-11e6-8fe7-02163e00a39b
</pre>

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

Some useful examples are below:
<pre>
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/
</pre>

---++ 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 [[https://twiki.cern.ch/twiki/bin/view/Main/LSDataReplica][data_replica.py]] or whatever else Grid tool able to transfers files in parallel between 2 sites.


<!--   ---++ =/pnfs= dirs cleanup ---+++ T3_CH_PSI
Each T3 user *must* to remove his/her old dir from =/pnfs= ; in order to quickly select and delete the unnecessary dirs, login on a UI ( it's crucial for the correct $USER resolution ) and prepare the file =/scratch/$USER/recursive.rm.pnfs= :
<pre>
# Extract your /pnfs dirs and save them in /scratch/$USER/recursive.rm.pnfs
$ curl http://t3mon.psi.ch/PSIT3-custom/v_pnfs_top_dirs.txt 2> /dev/null | egrep $USER | awk {' print "uberftp t3se01.psi.ch \047rm -r "$15"\047"}' > /scratch/$USER/recursive.rm.pnfs

# Erase in /scratch/$USER/recursive.rm.pnfs all the /pnfs dirs that you want to PRESERVE !! All the remaining /pnfs dirs will be recursively DELETED !! There are NO backups for /pnfs files !!
$ vim /scratch/$USER/recursive.rm.pnfs

# Run the recursive deletions ; a CMS proxy is needed 
$ source /scratch/$USER/recursive.rm.pnfs
</pre>
You might start with a small fragment of /scratch/$USER/recursive.rm.pnfs and check how it behaves before to run a big deletions campaign.

 T2_CH_CSCS

Regularly monitor your disk usage

<pre>
curl http://ganglia.lcg.cscs.ch/ganglia/files_cms.html | grep $USER
</pre>
or using the [[https://wiki.chipp.ch/twiki/pub/CmsTier3/HowToAccessSe/T2_Storage.py.txt][T2_Storage.py]] notebook/python script.

In order to clean up, use uberftp as explained above.

-->
 
---++[[BasicUnderstandingOfTheDCacheForAdvancedUser][Understanding of dCache for advanced user]]
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
txt	T2_Storage.py.txt	r1	manage	1.6 K	2017-01-30 - 10:49	JoosepPata
Topic revision: r142 - 2019-09-05 - NinaLoktionova
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