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| − | = National Storage using iRODS =
| + | #REDIRECT[[Swestore iRODS is decommissioned]] |
| − | [[Category:Storage]]
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| − | [[Category:iRODS]]
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| − | | |
| − | NOTA: THIS PAGE IS OUT OF DATE !
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| − | | |
| − | == Getting access ==
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| − | ; Apply for storage
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| − | : Please follow the instructions on the [[Apply for storage on SweStore]] page.
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| − | | |
| − | ;iRODS user authentication
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| − | :SweStore's iRODS system uses [http://www.yubico.com/products/yubikey-hardware/yubikey/ Yubikey] one-time passwords (OTP). With a simple touch of a button, a 44 character one-time password is generated and sent to the system. The user will be provided with a SweStore yubikey.
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| − | :Yubikey has a status as pilot now. It can be changed in the future.
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| − | | |
| − | ; iRODS usage <span style="color:#FF0000"> Pilot. </span><br> - How to acquire a SweStore yubikey
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| − | :Please send an email to [mailto:support@swestore.se?subject=Yubikey support@swestore.se] and provide the shipping address to where the yubikey should be sent.<br>
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| − | :Yubikey has a status as pilot now. It can be changed in the future.
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| − | | |
| − | == Support ==
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| − | | |
| − | If you have any issues using SweStore please do not hesitate to contact [mailto:support@swestore.se support@swestore.se].
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| − | | |
| − | <span style="color:#FF0000"> Better not to use filename with single quotes. (There were problems with these but they had been fixed.</span><br>
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| − | | |
| − | == Usage monitoring ==
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| − | * [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]
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| − | | |
| − | == Supported clients ==
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| − | | |
| − | : iDrop web - Point your Web browser to [https://iweb.swestore.se iweb.swestore.se]
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| − | : E-iRODS iCommands 3.0 - Command line client [ftp://ftp.renci.org/pub/irods/releases/3.0.1 Download E-iRODS icommands]
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| − | | |
| − | SweStore iRODS uses PAM authentication and SweStore yubikeys. With a simple touch of a button, a 44 character one-time password is generated and sent to the system.
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| − | | |
| − | | |
| − | === Web GUI (iDrop web) ===
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| − | Please see the specific documentation for [[iDrop web]].
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| − | | |
| − | === Community iRODS version 3.3 ===
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| − | The community iRODS client version 3.3 also should work, with PAM authentication.<br>
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| − | It is available from [http://irods.sdsc.edu/download.html SDSC].
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| − | Please install the OpenSSL include files and libraries:
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| − | <pre>
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| − | $ sudo apt-get install libssl-dev (debian based system)
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| − | # yum install openssl-devel (redhat-based systems)
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| − | </pre>
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| − | Download irods 3.3 from http://irods.sdsc.edu/download.html and unpack the tar.gz archive.
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| − | | |
| − | Please enable the following defines in the Makefile iRODS/config/config.mk.in
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| − | <pre>
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| − | PAM_AUTH = 1
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| − | PAM_AUTH_NO_EXTEND = 1
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| − | USE_SSL = 1
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| − | </pre>
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| − | Please run irodssetup to compile the irods community client with PAM authentication.
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| − | | |
| − | == SweStore iRODS usage documentation ==
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| − | | |
| − | To use the system you need to have the E-iRODS command line client installed or using iDROP web.
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| − | | |
| − | === Command line client ===
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| − | | |
| − | For Linux systems the iRODS command line client is available as an installable package for various
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| − | Linux platforms from the e-iRODS website downloads section.
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| − | | |
| − | The command line client is natural to use for Unix users.
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| − | There are versions of the usual ls, rm, mv, mkdir, pwd, rsync
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| − | commands prefixed with an i for iRODS, i.e. irm, imv, imkdir etc.
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| − | | |
| − | As expected iput and iget move files to and from the irods system.
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| − | All these commands print short help when using the -h option.
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| − | | |
| − | ==== iCommands environment file ====
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| − | | |
| − | There is an environment file .irodsEnv in the .irods subdirectory
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| − | of the home directory ($HOME/.irods/.irodsEnv) which contains information where and how
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| − | to access the iRODS metadata (iCAT) server.
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| − | | |
| − | It looks like (placeholders are in <>):
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| − | <pre>
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| − | irodsHost 'irods.swestore.se'
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| − | irodsPort 1247
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| − | irodsDefResource 'snicdefResc'
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| − | irodsHome '/snicZone/proj/<PROJECT_NAME>'
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| − | irodsCwd '/snicZone/proj/<PROJECT_NAME>'
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| − | irodsUserName '<USERNAME>'
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| − | irodsZone 'snicZone'
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| − | irodsAuthScheme 'PAM'
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| − | </pre>
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| − | | |
| − | The iCAT server is irods.swestore.se.
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| − | The default irods zone name is snicZone.
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| − | The default resource is snicdefResc.
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| − | It is best to set the home directory to the same as the
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| − | project directory, which would be a subdirectory under
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| − | the /snicZone/proj directory tree.
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| − | | |
| − | ==== Yubikey instructions ====
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| − | | |
| − | Prerequisite: A correct iCommands environment file, see above for instructions.
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| − | | |
| − | # Insert the yubikey in an available USB-slot in your computer.
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| − | # Type iinit
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| − | # Touch the conductive surface on the yubikey to send an one-time password to the system.
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| − | | |
| − | <pre>
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| − | | |
| − | $ iinit
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| − | Enter your current PAM (system) password:
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| − | $ ils
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| − | /snicZone/proj/<projectname>:
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| − | $
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| − | </pre>
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| − | | |
| − | After that we can use the usual iCommands for 8 hours.
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| − | | |
| − | More details on the iCommands are available at
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| − | https://www.irods.org/index.php/icommands
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| − | | |
| − | ==== iCommands ====
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| − | | |
| − | Having initialized the session as described above we can use tie iRODS versions
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| − | of the basic Unix commands. The project directory is under /snicZone/proj, all
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| − | members of the project should have write access to this directory. We can use
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| − | the command
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| − | <pre>
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| − | icd /snicZone/proj/projectname
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| − | </pre>
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| − | to move to the project directory, or to change to an another project directory
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| − | when we are members of more than one project.
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| − | | |
| − | All commands give short help when invoked with the -h flag.
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| − | | |
| − | To put files files into the iRODS system we can use:
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| − | <pre>
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| − | iput localfile irodsfile
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| − | </pre>
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| − | or, to put a whole directory tree:
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| − | <pre>
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| − | iput -r localdirectory irodscollection
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| − | </pre>
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| − | | |
| − | To load large amout of data it might be more advantageous to use
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| − | <pre>
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| − | irsync -r localdirectory irodscollection
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| − | </pre>
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| − | It might be a good idea to use -K so then checksums will be computed,
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| − | stored and checked.
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| − | | |
| − | To create directories (collections in iRODSspeak) we use:
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| − | <pre>
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| − | imkdir collection
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| − | </pre>
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| − | as it would be expected.
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| − | | |
| − | To get those files back we can use
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| − | <pre>
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| − | iget irodsfile localfile
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| − | </pre>
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| − | or
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| − | <pre>
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| − | irsync -r irodscollection localdirectory
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| − | </pre>
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| − | | |
| − | To remove files we use:
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| − | <pre>
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| − | irm
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| − | </pre>
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| − | or
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| − | <pre>
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| − | irm -r
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| − | </pre>
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| − | | |
| − | Removing files like that would put the files into the trashcan (path: /snicZone/trash/).
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| − | Time to time we would need to empty the trashcan, using
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| − | <pre>
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| − | irmtrash
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| − | </pre>
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| − | | |
| − | ==== Using iCommands on SNIC HPC clusters ====
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| − | | |
| − | On SNIC-clusters the icommands command line tools are either available in the PATH or by adding the irods module, e.g.
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| − | : module load irods
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| − | :If the irods commands are not available at the SNIC HPC cluster, please contact support@swestore.se
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| − | We also need to setup the iCommands environment file $HOME/.irods/.irodsEnv
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| − | | |
| − | === Storage Project directory structure ===
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| − | | |
| − | Your storage project is available at /snicZone/proj/<PROJECT NAME>
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| − | | |
| − | /snicZone/home/<USERNAME> is just a small home directory.
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| − | | |
| − | === iDROP web client ===
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| − | | |
| − | See the [[iDrop web]] specific page.
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| − | | |
| − | === Upstream documentation ===
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| − | Detailed documentation, papers and resources are available from
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| − | the [http://www.eirods.org E-iRODS web site]
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| − | | |
| − | [http://www.irods.org Community iRODS]
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| − | | |
| − | [https://groups.google.com/d/forum/irod-chat User forum]
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