Swestore-irods

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 ECDS, SND, Bioimage Sweden, BILS, UPPNEX,WLCG, 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 dCache and iRODS storage systems.

Swestore is distributed across the SNIC centres C3SE, HPC2N, Lunarc, NSC, PDC and 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 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 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 export the certificate, transfer it to the intended SNIC resource and prepare it for use with grid tools (not necessarily needed with ARC 3.x, see proxy certificates using Firefox credential store).

For Nordugrid certificates

Please make sure to also install your client certificate in your browser.

Request membership in the SweGrid VO

Follow the instructions on 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 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 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 /snic directory as https://webdav.swestore.se/snic/YOUR_PROJECT_NAME/.

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:

• ARC_Tools - Convenience scripts for the arc client (Only a recursive rmdir so far).
• ARC Graphical Clients - Contains the ARC Storage Explorer (SweStore supported development).
• Transfer script, swetrans_arc, provided by Adam Peplinski / Philipp Schlatter
• Documentation of the ARC Python API (PDF)

Slides and more

Slides and material from seminar for Lund users on April 18th

Usage monitoring

• 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 iweb.swestore.se

E-iRODS iCommands 3.0 - Command line client 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:

$ sudo apt-get install libssl-dev (debian based system)
# yum install openssl-devel (redhat-based systems)

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

PAM_AUTH = 1
PAM_AUTH_NO_EXTEND = 1
USE_SSL = 1 

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 <>):

irodsHost 'irods.swestore.se'
irodsPort 1247
irodsDefResource 'snicdefResc'
irodsHome '/snicZone/proj/<PROJECT_NAME>'
irodsCwd '/snicZone/proj/<PROJECT_NAME>'
irodsUserName '<USERNAME>'
irodsZone 'snicZone'
irodsAuthScheme 'PAM'

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

Yubikey instructions

With the corrent environment file all we need is a Yubikey and we can run the iinit command to authenticate to the iCAT server. Insert the yubikey into USB-slot of computer. Type iinit. Touch the conductive surface on the yubikey to send an one-time password to the system.

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

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/. 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 E-iRODS web site

Community iRODS

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:

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