SNIC Documentation - User contributions [en]

Swestore-irods

2014-06-26T10:42:45Z

Andreas Lindqvist (NSC): /* Community iRODS version 3.3 */

= National Storage using iRODS =
[[Category:Storage]]
[[Category:SweStore]]

== Getting access ==
; Apply for storage
: Please follow the instructions on the [[Apply for storage on SweStore]] page.

;iRODS user authentication
: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.
:Yubikey has a status as pilot now. It can be changed in the future.

; iRODS usage Pilot. - How to acquire a SweStore yubikey
: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. 
:Yubikey has a status as pilot now. It can be changed in the future.

== Support ==

If you have any issues using SweStore please do not hesitate to contact [mailto:support@swestore.se support@swestore.se].

 Be careful with filenames. Don't use filename with '. 
 We have memory issues with many files or bigfiles transferring now. Be careful when moving files bigger than 50GB and 20000 files at one time. 

== Usage monitoring ==
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]

== Supported clients ==

: iDrop web - Point your Web browser to [https://iweb.swestore.se iweb.swestore.se]
: E-iRODS iCommands 3.0 - Command line client [ftp://ftp.renci.org/pub/eirods/releases/3.0 Download E-iRODS icommands]

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.

=== Web GUI (iDrop web) ===
Please see the specific documentation for [[iDrop web]].

=== Community iRODS version 3.3 ===
The community iRODS client version 3.3 also should work, with PAM authentication. 
Please install the OpenSSL include files and libraries:
<pre>
$ sudo apt-get install libssl-dev (debian based system)
# yum install openssl-devel (redhat-based systems)
</pre>
Download irods 3.3 from http://irods.sdsc.edu/download.html and unpack the tar.gz archive.

Please enable the following defines in the Makefile iRODS/config/config.mk.in
<pre>
PAM_AUTH = 1
PAM_AUTH_NO_EXTEND = 1
USE_SSL = 1
</pre>
Please run irodssetup to compile the irods community client with PAM authentication.

== SweStore iRODS usage documentation ==

To use the system you need to have the E-iRODS command line client installed or using iDROP web.

=== Command line client ===

For Linux systems the iRODS command line client is available as an installable package for various
Linux platforms from the e-iRODS website downloads section.

The command line client is natural to use for Unix users.
There are versions of the usual ls, rm, mv, mkdir, pwd, rsync
commands prefixed with an i for iRODS, i.e. irm, imv, imkdir etc.

As expected iput and iget move files to and from the irods system.
All these commands print short help when using the -h option.

==== iCommands environment file ====

There is an environment file .irodsEnv in the .irods subdirectory
of the home directory ($HOME/.irods/.irodsEnv) which contains information where and how
to access the iRODS metadata (iCAT) server.

It looks like (placeholders are in <>):
<pre>
irodsHost 'irods.swestore.se'
irodsPort 1247
irodsDefResource 'snicdefResc'
irodsHome '/snicZone/proj/<PROJECT_NAME>'
irodsCwd '/snicZone/proj/<PROJECT_NAME>'
irodsUserName '<USERNAME>'
irodsZone 'snicZone'
irodsAuthScheme 'PAM'
</pre>

The iCAT server is irods.swestore.se.
The default irods zone name is snicZone.
The default resource is snicdefResc.
It is best to set the home directory to the same as the
project directory, which would be a subdirectory under
the /snicZone/proj directory tree.

==== Yubikey instructions ====

Prerequisite: A correct iCommands environment file, see above for instructions.

# Insert the yubikey in an available USB-slot in your computer.
# Type iinit
# Touch the conductive surface on the yubikey to send an one-time password to the system.

<pre>

$ iinit
Enter your current PAM (system) password:
$ ils
/snicZone/proj/<projectname>:
$
</pre>

After that we can use the usual iCommands for 8 hours.

More details on the iCommands are available at
https://www.irods.org/index.php/icommands

==== iCommands ====

Having initialized the session as described above we can use tie iRODS versions
of the basic Unix commands. The project directory is under /snicZone/proj, all
members of the project should have write access to this directory. We can use
the command
<pre>
icd /snicZone/proj/projectname
</pre>
to move to the project directory, or to change to an another project directory
when we are members of more than one project.

All commands give short help when invoked with the -h flag.

To put files files into the iRODS system we can use:
<pre>
iput localfile irodsfile
</pre>
or, to put a whole directory tree:
<pre>
iput -r localdirectory irodscollection
</pre>

To load large amout of data it might be more advantageous to use
<pre>
irsync -r localdirectory irodscollection
</pre>
It might be a good idea to use -K so then checksums will be computed,
stored and checked.

To create directories (collections in iRODSspeak) we use:
<pre>
imkdir collection
</pre>
as it would be expected.

To get those files back we can use
<pre>
iget irodsfile localfile
</pre>
or
<pre>
irsync -r irodscollection localdirectory
</pre>

To remove files we use:
<pre>
irm
</pre>
or
<pre>
irm -r
</pre>

Removing files like that would put the files into the trashcan (path: /snicZone/trash/).
Time to time we would need to empty the trashcan, using
<pre>
irmtrash
</pre>

==== Using iCommands on SNIC HPC clusters ====

On SNIC-clusters the icommands command line tools are either available in the PATH or by adding the irods module, e.g.
: module load irods
:If the irods commands are not available at the SNIC HPC cluster, please contact support@swestore.se
We also need to setup the iCommands environment file $HOME/.irods/.irodsEnv

=== Storage Project directory structure ===

Your storage project is available at /snicZone/proj/<PROJECT NAME>

/snicZone/home/<USERNAME> is just a small home directory.

=== iDROP web client ===

See the [[iDrop web]] specific page.

=== Upstream documentation ===
Detailed documentation, papers and resources are available from
the [http://www.eirods.org E-iRODS web site]

[http://www.irods.org Community iRODS]

[https://groups.google.com/d/forum/irod-chat‎ User forum]

IDrop web

2014-02-24T10:04:46Z

Andreas Lindqvist (NSC): moved Swestore-irods/IDrop web to IDrop web over redirect

= iDrop web =

For web access, simply log in at [https://iweb.swestore.se https://iweb.swestore.se] with your assigned username and yubikey.

[[File:idropLogin.png]]

After logging in, you will be on your home view (probably Starred Files). To browse your accessible directory tree, select Browse in the black menu line on top.

[[File:idropHomeView.png]]

== Browsing ==

In browsing mode, you can move around in your accessible collection tree. To enter browsing mode, select Browse from the menu bar on top.

The interface should be similar to other file browsers although object information is somewhat more focused on object information than normally (one can switch between object information and collection browsing with the “Browse” and “Info” buttons).

== Uploading ==

You can upload files by selecting Quick upload in your home view or selecting Upload in the browse view to put your file in a particular collection. The upload dialog should mention where files are stored (“parent collection”)

[[File:idropQuickUpload.png]]

== Interface walk through ==

This intends to be an explanation of most parts of the iDrop web interface, feel free to skip this part.

=== Top menu ===

[[Image:irods-web-top.png|frame|none|alt=]]

The top menu line (in black) gives access to generic short cuts and default options. The actual functions are currently

* Home
takes you to your home view, featuring starred and shared files and collections.
* Browse
takes you to the browsing interface, letting you walk around your file tree.
* Profile
let's you see and modify your profile page. This is currently not used.
* Search
gives access to search functionality, unfortunately, in the current version of the web interface this is limited to tags previously assigned.
* Tools
let’s you access various tools. Currently, the only such tool is a quick start of iDrop Desktop which doesn’t work correctly for the moment.
* Account
various more account and session related features can be found here, particularly, the logout function is located under this menu option. The menu has also
options to ‘Change password’ (which is not possible for the moment) and changing the default resource files are stored in (don’t change this).

=== Home view ===

The home view gives quick access to selected files (either starred or shared) and an upload button.

[[File:idropHomeView.png]]

* Quick upload
opens a dialog to store files in a collection called uploads in your home collection.
* Starred Files
list your starred files. The list view will have buttons for quick download, browse to file and show the description given to the file when it was starred as well as the file name.
* Starred Folders
list your starred collections. The list view will have buttons for a uploads to that collection, browse to collection and show the description given to the file when it was starred as well as the collection name.* * Folders shared by me
this should list collections you’ve shared with others. It is currently not always available.
* Folders shared with me
this should list collections shared with you by others. It is currently not always available.

=== Browse view ===

This is the main view which let’s you walk around your file tree, upload and download files as well as work with metadata and sharing.

[[File:irodsBrowseView.png]]

Just below the menu bar is information about where you’re currently browsing as well as quick links to collections earlier in the path.

Next comes a row of buttons:

[[File:irodsButtonRow1.png]]

* Refresh
updates the current view.
* New folder
creates a new collection in the currently selected path
* Browse
chooses browsing mode - collections will show contents instead of information for the collection
* Info
chooses information mode - collections will show information instead of contents.

Next comes the actual browsing area divided in two panes; to the left is the actual browsing pane which shows the directory tree from the current anchor point. To the right is information for the currently selected object or a collection list if a collections is selected and “Browse” has been selected.

==== Browsing pane ====

The browsing pane has three buttons

[[File:irodsButtonRow2.png]]

* Refresh
refreshes the view. Can be needed to show changes done from other places after the page was loaded
* Home
resets the browsing to the home directory of the logged in user
* Up
resets root to the actual top of the tree, this can be needed if the user has previously restricted the tree using “Set this as the root of the tree”

below these buttons is an expandable view of the tree where you can click the arrows to expand/collapse collections. You can select a data object or collection to view information or for collections see a content listing in the information pane.

===== Information pane =====

The information pane has two modes, Browse (for collections only) or Info. You can select which mode you want to use with the corresponding button in the row above the pane.

====== Browse mode ======

For data objects, Browse mode is identical to Info mode. For collections, the contents of the collection is listed. Each row has the following columns

[[File:irodsBrowseViewZoom.png]]

* Expansion
this row allows expansion/collapse of a particular object within the Browse view
* Action
by selecting this box, particular actions can be done for multiple actions at the same time
* Name
the name of the object
* Type
this column lists the type of the selected object. The most common ones are COLLECTION and DATA_OBJECT
* Modified
timestamp for the last recorded modification
* Size
size of the object (0 bytes for collections)

All of the actual data rows (Name, Type, Modified and Size) can be used for sorting ascending/descending.

Through the button at the top of the Action column, selected objects in that column can be added to the “cart” for later download or deleted.

====== Info mode ======

The info mode lets the user display and (possibly) modify information about the selected object.

[[File:irodsInfoView.png]]

Object information is displayed under 5 different tabs

* Info
displays general file metadata
* Metadata
allows the display and editing of custom (AVU) metadata
* Sharing
here you can find various information and operations related to sharing
* Tickets
tab for handling of tickets (a system for giving access to certain resources, currently not used by BILS).
* Audit
shows audit data, currently not used byt BILS.

There are some things worth to note:

Under Info, various tags can be added to objects. These are currently the only thing that are searchable with iDrop web.

For data objects, it’s possible to see information about where the object is stored under Info (Data path, Resource).

Swestore-irods/IDrop web

2014-02-24T10:04:46Z

Andreas Lindqvist (NSC): moved Swestore-irods/IDrop web to IDrop web over redirect

#REDIRECT [[IDrop web]]

2013-12-13T17:14:09Z

Andreas Lindqvist (NSC):

[[Category:Storage]]
[[Category:SweStore]]

'''This is not official yet'''

SNIC is building a storage infrastructure to complement the computational resources.

Many forms of automated measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.

Swestore is in collaboration with [http://www.ecds.se/ ECDS], [http://snd.gu.se/ SND], Bioimage Sweden, [http://www.bils.se/ BILS], [http://www.uppnex.uu.se/ UPPNEX],[http://wlcg.web.cern.ch/ WLCG], [http://www.nrm.se/ NaturHistoriska RiksMuseet].

= National storage =
The Swestore Nationally Accessible Storage, commonly called just Swestore, is a robust, flexible and expandable long term storage system aimed at storing large amounts of data produced by various Swedish research projects. It is based on the [http://www.dcache.org dCache] and [http://www.irods.org iRODS]
storage systems.

Swestore is distributed across the SNIC centres [http://www.c3se.chalmers.se/ C3SE], [http://www.hpc2n.umu.se/ HPC2N], [http://www.lunarc.lu.se/ Lunarc], [http://www.nsc.liu.se/ NSC], [http://www.pdc.kth.se PDC] and [http://www.uppmax.uu.se Uppmax]. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.

One of the major advantages to the distributed nature of dCache and iRODS is the excellent aggregated transfer rates possible. This is achieved by bypassing a central node and having transfers going directly to/from the storage elements if the protocol allows it. The Swestore Nationally Accessible Storage system can achieve aggregated transfer rates in excess of 100 Gigabit per second, but in practice this is limited by connectivity to each University (usually 10 Gbit/s) or a limited number of files (typically
max 1 Gbit/s per file/connection).

To protect against silent data corruption the dCache storage system checksums all stored data and periodically verifies the data using this checksum.

The dCache system does NOT yet provide protection against user errors like inadvertent file deletions and so on. The iRODS system provides this protection. Deleted files are moved to a trashcan.

== Getting access ==
; Apply for storage
: Please follow the instructions on the [[Apply for storage on SweStore]] page.

;Difference between dCache and iRODS user authentication
:SweStore's dCache system uses eScience client certificates.
: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.
:Yubikey has a status as pilot now. It can be changed in the future.

; dCache usage - How to acquire an eScience client certificate
: Follow the instructions on [[Grid_certificates#Requesting_a_certificate|Requesting a certificate]] to get your client certificate. This step can be performed while waiting for the storage application to be approved and processed. Of course, if you already have a valid eScience certificate you don't need to acquire another one.
:; For Terena certificates
:: If intending to access SweStore from a SNIC resource, please make sure you also [[Exporting_a_client_certificate|export the certificate]], transfer it to the intended SNIC resource and [[Preparing_a_client_certificate|prepare it for use with grid tools]] (not necessarily needed with ARC 3.x, see [[Grid_certificates#Creating_a_proxy_certificate_using_the_Firefox.2FThunderbird_credential_store|proxy certificates using Firefox credential store]]).
:; For Nordugrid certificates
:: Please make sure to also [[Requesting_a_grid_certificate_from_the_Nordugrid_CA#Installing_the_certificate_in_your_browser|install your client certificate in your browser]].
:; Request membership in the SweGrid VO
:: Follow the instructions on [[Grid_certificates#Requesting_membership_in_the_SweGrid_VO|Requesting membership in the SweGrid VO]] to get added to the SweGrid Virtual Organisation (VO) and request membership to your allocated storage project.

; iRODS usage - How to acquire a SweStore yubikey
: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. 
:Yubikey has a status as pilot now. It can be changed in the future.

== Support ==

If you have any issues using SweStore please do not hesitate to contact [mailto:support@swestore.se support@swestore.se].

== dCache ==

=== Access protocols ===
; Currently supported protocols
: GridFTP - gsiftp://gsiftp.swestore.se/
: Storage Resource Manager - srm://srm.swegrid.se/
: Hypertext Transfer Protocol (read-only), Web Distributed Authoring and Versioning - http://webdav.swestore.se/ (unauthenticated), https://webdav.swestore.se/
: NFS4.1

For authentication eScience certificates are used, which provides a higher level of security than legacy username/password schemes.

== Download and upload data ==
; Interactive browsing and manipulation of single files
: SweStore is accessible in your web browser in two ways, as a simple and reliable directory index interface at https://webdav.swestore.se/ and with a richer interactive file manager at https://webdav.swestore.se/browser/. '''Note''' that the interactive file manager has a lot of features and functions not supported in SweStore, only the basic file transfer features are supported.
: To browse private data you need to have your certificate installed in your browser (default with Terena certificates, see above). Projects are organized under the <code>/snic</code> directory as <code><nowiki>https://webdav.swestore.se/snic/YOUR_PROJECT_NAME/</nowiki></code>.
; Upload and delete data interactively or with automation
There are several tools that are capable of using the protocols provided by SweStore national storage.
For interactive usage on SNIC clusters we recommend using the ARC tools which should be installed on all SNIC resources.
As an integration point for building scripts and automated systems we suggest using the curl program and library.
: Use the ARC client. Please see the instructions for [[Accessing SweStore national storage with the ARC client]]. '''Recommended''' method when logged in on SNIC resources.
: Use lftp. Please see the instructions for [[Accessing SweStore national storage with lftp]].
: Use cURL. Please see the instructions for [[Accessing SweStore national storage with cURL]].
: Use globus-url-copy. Please see the instructions for [[Accessing SweStore national storage with globus-url-copy]].

=== Tools and scripts ===

There exists a number of tools and utilities developed externally that can be useful. Here are some links:

* [https://github.com/samuell/arc_tools ARC_Tools] - Convenience scripts for the arc client (Only a recursive rmdir so far).
* [http://sourceforge.net/projects/arc-gui-clients ARC Graphical Clients] - Contains the ARC Storage Explorer (SweStore supported development).
* Transfer script, [[SweStore/swetrans_arc|swetrans_arc]], provided by Adam Peplinski / Philipp Schlatter
* [http://www.nordugrid.org/documents/SWIG-wrapped-ARC-Python-API.pdf Documentation of the ARC Python API (PDF)]

=== Slides and more ===

[http://docs.snic.se/wiki/Swestore/Lund_Seminar_Apr18 Slides and material from seminar for Lund users on April 18th]

=== Usage monitoring ===
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]

== iRODS ==

There is a SNIC iRODS system available under Swestore.

=== Supported clients ===

: iDrop web - Point your Web browser to [https://iweb.swestore.se iweb.swestore.se]
: E-iRODS iCommands 3.0 - Command line client [ftp://ftp.renci.org/pub/eirods/releases/3.0 Download E-iRODS icommands]

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.

==== Community iRODS version 3.3 ====
The community iRODS client version 3.3 also should work, with PAM authentication. 
Please install the OpenSSL include files and libraries:
<pre>
$ sudo apt-get install libssl-dev (debian based system)
# yum install openssl-devel (redhat-based systems)
</pre>
Download irods 3.3 from https://www.irods.org/index.php/Downloads and unpack the tar.gz archive.

Please enable the following defines in the Makefile iRODS/config/config.mk.in
<pre>
PAM_AUTH = 1
PAM_AUTH_NO_EXTEND = 1
USE_SSL = 1
</pre>
Please run irodssetup to compile the irods community client with PAM authentication.

=== SweStore iRODS usage documentation ===

To use the system you need to have the E-iRODS command line client installed or using iDROP web.

==== Command line client ====

For Linux systems the iRODS command line client is available as an installable package for various
Linux platforms from the e-iRODS website downloads section.

The command line client is natural to use for Unix users.
There are versions of the usual ls, rm, mv, mkdir, pwd, rsync
commands prefixed with an i for iRODS, i.e. irm, imv, imkdir etc.

As expected iput and iget move files to and from the irods system.
All these commands print short help when using the -h option.

===== iCommands environment file =====

There is an environment file .irodsEnv in the .irods subdirectory
of the home directory ($HOME/.irods/.irodsEnv) which contains information where and how
to access the iRODS metadata (iCAT) server.

It looks like (placeholders are in <>):
<pre>
irodsHost 'irods.swestore.se'
irodsPort 1247
irodsDefResource 'snicdefResc'
irodsHome '/snicZone/proj/<PROJECT_NAME>'
irodsCwd '/snicZone/proj/<PROJECT_NAME>'
irodsUserName '<USERNAME>'
irodsZone 'snicZone'
irodsAuthScheme 'PAM'
</pre>

The iCAT server is irods.swestore.se.
The default irods zone name is snicZone.
The default resource is snicdefResc.

===== Yubikey instructions =====

Prerequisite: A correct iCommands environment file, see above for instructions.

# Insert the yubikey in an available USB-slot in your computer.
# Type iinit
# Touch the conductive surface on the yubikey to send an one-time password to the system.

<pre>

$ iinit
Enter your current PAM (system) password:
$ ils
/snicZone/home/<USERNAME>:
$
</pre>

After that we can use the usual iCommands for 8 hours.

More details on the iCommands are available at
https://www.irods.org/index.php/icommands

===== Using iCommands on SNIC HPC clusters =====

On SNIC-clusters the icommands command line tools are either available in the PATH or by adding the irods module, e.g.
: module load irods
We also need to setup the iCommands environment file $HOME/.irods/.irodsEnv

==== Storage Project directory structure ====

Your storage project is available at /snicZone/proj/<PROJECT NAME>

/snicZone/home/<USERNAME> is just a small home directory.

==== iDROP web client ====

The web client is accessible via the URL https://iweb.swestore.se/.
The login screen consists of two prompts:

: Username:
: Password:

#Please type in your SweStore username.
#Insert the yubikey in an available USB-slot in your computer.
#Touch the conductive golden surface on the yubikey (for at least a second) to send an one-time password to the system.

==== Upstream documentation ====
Detailed documentation, papers and resources are available from
the [http://www.eirods.org E-iRODS web site]

[http://www.irods.org Community iRODS]

[https://groups.google.com/d/forum/irod-chat‎ User forum]

= Center storage =
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre, and a unified structure and nomenclature for all centra. Unlike cluster storage which is tightly associated with a single cluster, and thus has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.

== Unified environment ==
To make the usage more transparent for SNIC users, a set of environment variables are available on all SNIC resources:

* <code>SNIC_BACKUP</code> – the user's primary directory at the centre (the part of the centre storage that is backed up)
* <code>SNIC_NOBACKUP</code> – recommended directory for project storage without backup (also on the centre storage)
* <code>SNIC_TMP</code> – recommended directory for best performance during a job (local disk on nodes if applicable)

2013-10-31T14:15:04Z

Andreas Lindqvist (NSC): /* SNIC HPC clusters */

[[Category:Storage]]
[[Category:SweStore]]

'''This is not official yet'''

SNIC is building a storage infrastructure to complement the computational resources.

Many forms of automated measurements can produce large amounts of data. In scientific areas such as high energy physics (the Large Hadron Collider at CERN), climate modeling, bioinformatics, bioimaging etc., the demands for storage are increasing dramatically. To serve these and other user communities, SNIC has appointed a working group to design a storage strategy, taking into account the needs on many levels and creating a unified storage infrastructure, which is now being implemented.

Swestore is in collaboration with [http://www.ecds.se/ ECDS], [http://snd.gu.se/ SND], Bioimage Sweden, [http://www.bils.se/ BILS], [http://www.uppnex.uu.se/ UPPNEX],[http://wlcg.web.cern.ch/ WLCG], [http://www.nrm.se/ NaturHistoriska RiksMuseet].

= National storage =
The Swestore Nationally Accessible Storage, commonly called just Swestore, is a robust, flexible and expandable long term storage system aimed at storing large amounts of data produced by various Swedish research projects. It is based on the [http://www.dcache.org dCache] and [http://www.irods.org iRODS]
storage systems.

Swestore is distributed across the SNIC centres [http://www.c3se.chalmers.se/ C3SE], [http://www.hpc2n.umu.se/ HPC2N], [http://www.lunarc.lu.se/ Lunarc], [http://www.nsc.liu.se/ NSC], [http://www.pdc.kth.se PDC] and [http://www.uppmax.uu.se Uppmax]. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.

One of the major advantages to the distributed nature of dCache and iRODS is the excellent aggregated transfer rates possible. This is achieved by bypassing a central node and having transfers going directly to/from the storage elements if the protocol allows it. The Swestore Nationally Accessible Storage system can achieve aggregated transfer rates in excess of 100 Gigabit per second, but in practice this is limited by connectivity to each University (usually 10 Gbit/s) or a limited number of files (typically
max 1 Gbit/s per file/connection).

To protect against silent data corruption the dCache storage system checksums all stored data and periodically verifies the data using this checksum.

The dCache system does NOT yet provide protection against user errors like inadvertent file deletions and so on. The iRODS system provides this protection. Deleted files are moved to a trashcan.

== Getting access ==
; Apply for storage
: Please follow the instructions on the [[Apply for storage on SweStore]] page.

;Difference between dCache and iRODS user authentication
:SweStore's dCache system uses eScience client certificates.
: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.

; dCache usage - How to acquire an eScience client certificate
: Follow the instructions on [[Grid_certificates#Requesting_a_certificate|Requesting a certificate]] to get your client certificate. This step can be performed while waiting for the storage application to be approved and processed. Of course, if you already have a valid eScience certificate you don't need to acquire another one.
:; For Terena certificates
:: If intending to access SweStore from a SNIC resource, please make sure you also [[Exporting_a_client_certificate|export the certificate]], transfer it to the intended SNIC resource and [[Preparing_a_client_certificate|prepare it for use with grid tools]] (not necessarily needed with ARC 3.x, see [[Grid_certificates#Creating_a_proxy_certificate_using_the_Firefox.2FThunderbird_credential_store|proxy certificates using Firefox credential store]]).
:; For Nordugrid certificates
:: Please make sure to also [[Requesting_a_grid_certificate_from_the_Nordugrid_CA#Installing_the_certificate_in_your_browser|install your client certificate in your browser]].
:; Request membership in the SweGrid VO
:: Follow the instructions on [[Grid_certificates#Requesting_membership_in_the_SweGrid_VO|Requesting membership in the SweGrid VO]] to get added to the SweGrid Virtual Organisation (VO) and request membership to your allocated storage project.

; iRODS usage - How to acquire a SweStore YubiKey

To apply for a SweStore yubikey, please send an email to [mailto:support@swestore.se?subject=Yubikey support@swestore.se] and provide a shipping address to where the yubikey should be sent.

== Support ==

If you have any issues using SweStore please do not hesitate to contact [mailto:support@swestore.se support@swestore.se].

== dCache ==

=== Access protocols ===
; Currently supported protocols
: GridFTP - gsiftp://gsiftp.swestore.se/
: Storage Resource Manager - srm://srm.swegrid.se/
: Hypertext Transfer Protocol (read-only), Web Distributed Authoring and Versioning - http://webdav.swestore.se/ (unauthenticated), https://webdav.swestore.se/
: NFS4.1

For authentication eScience certificates are used, which provides a higher level of security than legacy username/password schemes.

=== Download and upload data ===
; Interactive browsing and manipulation of single files
: SweStore is accessible in your web browser in two ways, as a directory index interface at https://webdav.swestore.se/ and with an interactive file manager at https://webdav.swestore.se/browser/. '''Note''' that the interactive file manager has a lot of features and functions not supported in SweStore, only the basic file transfer features are supported.
: To browse private data you need to have your certificate installed in your browser (default with Terena certificates, see above). Projects are organized under the <code>/snic</code> directory as <code><nowiki>https://webdav.swestore.se/snic/YOUR_PROJECT_NAME/</nowiki></code>.
; Upload and delete data interactively or with automation
There are several tools that are capable of using the protocols provided by SweStore national storage.
For interactive usage on SNIC clusters we recommend using the ARC tools which should be installed on all SNIC resources.
As an integration point for building scripts and automated systems we suggest using the curl program and library.
: Use the ARC client. Please see the instructions for [[Accessing SweStore national storage with the ARC client]]. '''Recommended''' method when logged in on SNIC resources.
: Use lftp. Please see the instructions for [[Accessing SweStore national storage with lftp]].
: Use cURL. Please see the instructions for [[Accessing SweStore national storage with cURL]].
: Use globus-url-copy. Please see the instructions for [[Accessing SweStore national storage with globus-url-copy]].

=== Tools and scripts ===

There exists a number of tools and utilities developed externally that can be useful. Here are some links:

* [https://github.com/samuell/arc_tools ARC_Tools] - Convenience scripts for the arc client (Only a recursive rmdir so far).
* [http://sourceforge.net/projects/arc-gui-clients ARC Graphical Clients] - Contains the ARC Storage Explorer (SweStore supported development).
* Transfer script, [[SweStore/swetrans_arc|swetrans_arc]], provided by Adam Peplinski / Philipp Schlatter
* [http://www.nordugrid.org/documents/SWIG-wrapped-ARC-Python-API.pdf Documentation of the ARC Python API (PDF)]

=== Slides and more ===

[http://docs.snic.se/wiki/Swestore/Lund_Seminar_Apr18 Slides and material from seminar for Lund users on April 18th]

=== Usage monitoring ===
* [http://status.swestore.se/munin/monitor/monitor/ Per Project Monitoring of Swestore usage]

== iRODS ==

=== Supported clients ===

: iDrop web - Point your Web browser to [https://iweb.swestore.se iweb.swestore.se]
: E-iRODS iCommands - Command line client [http://eirods.org/download/ Download E-iRODS icommands]

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.

The community iRODS client also should work, but you need to modify the makefile (iRODS/config/config.mk) and recompile it:
<pre>
PAM_AUTH = 1
PAM_AUTH_NO_EXTEND = 1
USE_SSL = 1
</pre>

=== SweStore iRODS usage documentation ===

To use the system you need to have the E-iRODS command line client installed or using iDROP web.

==== Command line client ====

For Linux systems the iRODS commandline client is available as an installable package for various
Linux platforms from the e-iRODS website downloads section.

The command line client is natural to use for Unix users.
There are versions of the usual ls, rm, mv, mkdir, pwd, rsync
commands prefixed with an i for iRODS, i.e. irm, imv, imkdir etc.

As expected iput and iget move files to and from the irods system.
All these commands print short help when using the -h option.

===== iCommands environment file =====

There is an environment file .irodsEnv in the .irods subdirectory
of the home directory which contains information where and how
to access the iRODS metadata (iCAT) server.

It looks like (placeholders are in <>):
<pre>
irodsHost 'irods.swestore.se'
irodsPort 1247
irodsDefResource 'snicdefResc'
irodsHome '/snicZone/home/<email address>'
irodsCwd '/snicZone/home/<email address>'
irodsUserName '<email address>'
irodsZone 'snicZone'
irodsAuthScheme 'PAM'
</pre>

The iCAT server is irods.swestore.se.
The default irods zone name is snicZone.
The default resource is snicdefResc.

With the corrent environment file all we need is a Yubikey and we can run the iinit command to authenticate to the iCAT server. After that we can use the usual iCommands for 8 hours.

More details on the iCommands are available at
https://www.irods.org/index.php/icommands

===== Using iCommands on SNIC:s HPC clusters =====

On SNIC-clusters the icommands command line tools are either available in the PATH or by adding the irods module, e.g.
: module load irods
$HOME/.irods/.irodsEnv need to be setup.

==== iDROP web client ====

The web client is accessible via the URL https://iweb.swestore.se/.
A login screen will be presented first and your Yubikey should
be used to log in.

==== Upstream documentation ====
Detailed documentation, papers and resources are available from
the [http://www.eirods.org E-iRODS web site]

[http://www.irods.org Community iRODS]

[https://groups.google.com/d/forum/irod-chat‎ User forum]

= Center storage =
Centre storage, as defined by the SNIC storage group, is a storage solution that lives independently of the computational resources and can be accessed from all such resources at a centre. Key features include the ability to access the same filesystem the same way on all computational resources at a centre, and a unified structure and nomenclature for all centra. Unlike cluster storage which is tightly associated with a single cluster, and thus has a limited life-time, centre storage does not require the users to migrate their own data when clusters are decommissioned, not even when the storage hardware itself is being replaced.

== Unified environment ==
To make the usage more transparent for SNIC users, a set of environment variables are available on all SNIC resources:

* <code>SNIC_BACKUP</code> – the user's primary directory at the centre (the part of the centre storage that is backed up)
* <code>SNIC_NOBACKUP</code> – recommended directory for project storage without backup (also on the centre storage)
* <code>SNIC_TMP</code> – recommended directory for best performance during a job (local disk on nodes if applicable)