This page describes how to handle data stored on our mass storage system.
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.
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> Fill in you username and the experiment you are affiliated with accordingly.
On the M machines /pnfs is mounted read-only. This to protect to inadvertently remove a large portion of your files. As it is a mass storage system, you can easily delete sevela TBs of data. Therefore, writing and deleting files is done via only via grid enable command (see next section). These commands are mostly done via scripts, so the probability of an error is lessened.
However, we have seen the need for a more simple read-write access to /pnfs. Therefore, a dedicated machine was instantiated:
You can log into this machine like any other M-machine, and now 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.
In what follows, all 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'
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)
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.
There are 2 types of file url:
- Distant files: their url is of the type srm://<name_of_server>:<port>/some/path, eg for IIHE:
- Local files: their url is of the type file://path_of_the_file, eg for IIHE:
- To get a list of all distant urls for all the Storage Elements, one can do:
lcg-infosites --vo cms se
- To list the contents of a directory /pnfs/iihe/cms :
- To create a directory:
- 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
- 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/$USER/NewDir
Bulk file transfers
There is an elegant way to run gfal-copy through several files. This is done using the --from-file option.
gfal-copy -f --from-file files.txt file://$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
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 :
setenv DCACHE_RAHEAD 1 setenv DCACHE_RA_BUFFER 50000000
export DCACHE_RAHEAD=true export DCACHE_RA_BUFFER=50000000
- Via the 'curl' command over https
As seen in the last example in the previous section, dCache files are now seen over https. This means that they are also browsable via any web browser that support x509 certificates (like firefox, chrome and safari).
The part of dCache that implements this functionality is called dCache View and can be seen via the following url: