GridStorageAccess

This page describes how to handle data stored on our mass storage system.

Introduction

T2B has an ever increasing amount of mass storage available. This system hosts both the centrally produced datasets as well as the user produced data.
The mass storage is managed by a software called dCache. As this software is in full development, new features are added continuously. This page contains an overview of the most used features of the software.

General info

As dcache was designed for precious data, the files are immutable. This means that once they are written, they cannot be changed any more. So, if you want to make changes to a file on dcache, you need to first erase it and then write it anew. Our dCache instance is mounted on all the M machines and can be browsed via the /pnfs directory. If you want to find your personal directory, the structure is the following:

/pnfs/iihe/<Experiment>/store/user/<Username>     <-- Replace <Username> and <Experiment> accordingly.

On the M machines as well as the whole cluster, /pnfs is now mounted read-write (this is new!). Please be aware that you can now inadvertently remove a large portion of your files. As it is a mass storage system, you can easily delete several TBs of data.

Writing and deleting files can still be done via via grid enable commands (see next section). These should still provide the best read/write speeds compared to nfs access. These commands are mostly done via scripts, so the probability of an error is lessened.

There is a dedicated machine for file copying to /pnfs:

rw.iihe.ac.be 

You can log into this machine like any other M-machine, and use the regular 'cp' and 'rm' commands. However, this machine is not like the other M-machines. Its sole purpose is to access /pnfs via the regular posix commands, so code development and job submission is prohibited.

Before starting

In what follows, most of the commands will require some type of authentication to access /pnfs. This is because these commands can be executed over WAN and your location is irrelevant.
The way authentication is done on our mass storage instance is via an x509 proxy. This proxy is made through your grid certificate. If you do not have a grid certificate, see this page on how to get one.
The command to make a grid proxy is:

voms-proxy-init --voms <MYEXPERIMENT>

Where <MYEXPERIMENT> is one of 'cms, icecube, beapps'

Browser access

dCache now exposes files using the WebDav protocol. This means that the files are accessible to browse over https.
For this, you need to have your certificate in your browser (to import your .p12 certificate, google is your friend).
Then just point your browser to:

https://maite.iihe.ac.be:2880/pnfs/iihe/cms/store/user/

To be able to see and download your files.

dCache has an even more powerful web interface. It is called dCache View and can be accessed via:

https://maite.iihe.ac.be:3880/

Work is still in progress to make all actions work (12/2021).

Access via GFAL

GFAL is a wrapper around the latest grid commands. Learning to use it means that whatever middleware requires to be used in the future, you don't need to learn new commands (like srm, lcg, etc)

gfal-commands

If you want more information on the options that can be used, please use man gfal-command !

Here are all the commands that can be used:

• gfal-ls: get information on a file
• gfal-mkdir: remove a directory
• gfal-rm: removes a file. To remove an entire directory, use -r
• gfal-copy: copy files.

Usage

There are 2 types of file url:

• Distant files: their url is of the type <protocol>://<name_of_server>:<port>/some/path, eg for IIHE:

davs://maite.iihe.ac.be:2880/pnfs/iihe/

• Local files: their url is of the type file://path_of_the_file, eg for IIHE:

file:///user/$USER/MyFile.root

Be careful, the number of / is very -very- important

• To get a list of all distant urls for all the Storage Elements, one can do:

 lcg-infosites --is grid-bdii.desy.de --vo cms se 

Protocols

• https/WebDavs [preferred]

gfal-ls davs://maite.iihe.ac.be:2880/pnfs/iihe/cms/store/user/

• xrootd [preferred]

gfal-ls root://maite.iihe.ac.be:1094/pnfs/iihe/cms/store/user/

• srm [deprecated]

gfal-ls srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/

• nfs {local-only | no-cert}

gfal-ls /pnfs/iihe/cms/store/user/

• dcap {local-only | no-cert}

gfal-ls dcap://maite.iihe.ac.be/pnfs/iihe/cms/store/user

Examples

• To list the contents of a directory /pnfs/iihe/cms :

 gfal-ls srm://maite.iihe.ac.be:8443/pnfs/iihe/cms 

• To create a directory:

 gfal-mkdir srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/$USER/NewDir 

• copy file from local disk to remote server

 gfal-copy file:///user/$USER/MyFile.root srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/$USER/ 

• To copy a file from remote server to our Storage Element:

 gfal-copy srm://srm-eoscms.cern.ch:8443/srm/v2/server?SFN=/eos/cms/store/group/comm_trigger/L1TrackTrigger/BE5D_620_SLHC6/singleMu/NoPU/reDIGI_SLHC6-TrackTrigger_muon_pgun-0499.root srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/odevroed/eosTransfer.root 

• To delete a file on remote server

 gfal-rm srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/$USER/MyFile.root 

• To remove a directory and its entire content on remote server ?!? not working for now ?):

 gfal-rm -r srm://maite.iihe.ac.be:8443/pnfs/iihe/cms/store/user/$USER/NewDir 

Bulk file transfers

There is an elegant way to run gfal-copy through several files. This is done using the --from-file option.

Syntax:

 gfal-copy -f --from-file files.txt file://$PWD 

where files.txt is a file where every line is a source in srm url syntax.

Make some tests with one line in datafile and make sure the srm url is OK for both source and destination before running over several files.

Copy directories from and to pnfs within the IIHE

A script to copy full directories to and from pnfs exists on the slc6 UI's:

copyDirectoryPnfs.py
Move all files in a directory to or from pnfs
This script assumes that you copy within the IIHE
The script does not do recursive copying
Make sure you have a valid proxy, made with voms-proxy-init --voms cms:/cms/becms

Mandatory options:
--in=                 : directory to copy from
--out=                : directory to copy to
Both directories need to be complete (i.e. including the /pnfs or /user part

example:
copyDirectoryPnfs.py --out=/user/odevroed/newfile --in=/pnfs/iihe/cms/store/user/odevroed/newdir

Optional:
-h, --help             : print this help message

Other ways to access the mass storage system

Read and copy access

As stated in the introduction, dCache is an immutable file system, therefore files cannot be changed once they are written. Furthermore, for data protection, files are only available in read mode from /pnfs.
Files can be accessed from pnfs in several ways.

• Via the regular 'cp' command

cp /pnfs/iihe/cms/store/user/odevroed/DQMfile_83_1_hF2.root /user/odevroed 

• Via the dcache copy command (dccp):

dccp dcap://maite.iihe.ac.be/pnfs/iihe/cms/store/user/odevroed/DQMfile_83_1_hF2.root ./ 

• To open files using root, use eg

root dcap://maite.iihe.ac.be/pnfs/iihe/some/file.root 

When reading out the rootfiles is rather slow or it doesn't work at all and nothing is wrong with the root file (e.g. in an interactive analysis on beo or msa) you can increase your dCache readahead buffer. Don't make the buffer larger than 50MB! To enlarge the buffer set this in you environment :
For csh:

setenv DCACHE_RAHEAD 1
setenv DCACHE_RA_BUFFER 50000000

For bash:

export DCACHE_RAHEAD=true
export DCACHE_RA_BUFFER=50000000

• Via the 'curl' command over https

Copy from /pnfs:
curl -L --cert $X509_USER_PROXY --key $X509_USER_PROXY --cacert $X509_USER_PROXY --capath $X509_CERT_DIR  -O https://maite.iihe.ac.be:2880/pnfs/iihe/cms/store/user/odevroed/testing_transfer

Copy to /pnfs
curl -L --cert $X509_USER_PROXY --key $X509_USER_PROXY --cacert $X509_USER_PROXY --capath $X509_CERT_DIR  -T testing_transfer  https://maite.iihe.ac.be:2880/pnfs/iihe/cms/store/user/odevroed/testing_transfer_2

This is equivalent to issuing the gfal-cp command via the https protocol:
gfal-copy https://maite.iihe.ac.be:2880/pnfs/iihe/cms/store/user/odevroed/testing_transfer ./