Swestore-irods

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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.
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

To apply for a SweStore yubikey, please send an email to 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 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:

Slides and more

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

Usage monitoring

iRODS

Build and install the SNIC iCAT server

Build postgres

We use postgres version 9.4 with unixodbc and build it from source.

The binaries will be built under /usr/postgres since the e-irods install script expects the postgres directory tree to be under /usr. The userid postgres will own the directory tree.

Data will be owned by the postgres userid and under /postgres since that is necessary for the peaceful co-existence with unixodbc. We will use xfs for the database file system. The file system is created as a RAID6 slice on an array with 10 x 3TB spindles. We plan to obtain a mirrored pair of disks for the online logs to have them separate.

An account and a group called postgres is created. In it's home directory there is an install subdirectory with the command line history and the two scripts, postgres-build.sh and unixodbc-build.sh which are used to build the software. There is a tarball of the result of make install and to be used on the iCAT hosts. Use: 

 cd
 cd src
 tar -xf ../tar/postgresql-9.2.4.tar.gz
 cd postgresql-9.2.4
 cp ~/install/scripts/postgres-build.sh .
 ./postgres-build.sh 2>&1 | tee -a postgres-build.log
 cd
 cd src
 tar -xf ../tar/unixODBC-2.3.1.tar.gz
 cd unixODBC-2.3.1
 ./unixodbc-build.sh  2>&1 | tee -a unixodbc-build.log

This should create everything under /usr/postgres. A tarball is manually created under ~postgres/install/tar as postgres-9.4-snic-build.tar.gz.

The database will run on snic-irods, so the /usr/postgres tree is taken and transplanted from snic-irods-mgmt using the tarball.


Running postgres on the iCAT server

The userid postgres is added to the puppet manfiests.

Puppet manifests will also need to be amended with mount options for the /postgres file system.

Create the data file system manually as: 

 mkfs.xfs -b size=4096 -d su=64k,sw=8 -l size=64m,su=64k \
       -i maxpct=1 -L /pgsql /dev/xvdc

Logged as: 

meta-data=/dev/xvdc              isize=256    agcount=32, agsize=8388592 blks
         =                       sectsz=512   attr=2, projid32bit=0
data     =                       bsize=4096   blocks=268434944, imaxpct=1
         =                       sunit=16     swidth=128 blks
naming   =version 2              bsize=4096   ascii-ci=0
log      =internal log           bsize=4096   blocks=16384, version=2
         =                       sectsz=512   sunit=16 blks, lazy-count=1
realtime =none                   extsz=4096   blocks=0, rtextents=0

Mount the file system with the options: 

 logbufs=8,logbsize=256k,largeio,inode64

so update /etc/fstab accordingly.

Mount it: 

 mkdir /postgres
 mount -a
 chown postgres.postgres /postgres
 chmod g+w /postgres
 chmod g+s /postgres

The default umask for unkown reason is 002. Might be changed to 022. Create profile for postgres user as: 

# Add postgres stuff.
export PATH=$PATH:/usr/postgres/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/postgres/lib
export MANPATH=/usr/share/man:/usr/postgres/share/man

# Fix umask.
umask 022

# Simple prompt.
PS1="$ "
export PS1

# Colourless and odorless.
alias ls='ls --color=never'

Change limits in /etc/security/limits.conf as: 

postgres         -       core            unlimited
postgres         -       data            unlimited
postgres         -       fsize           unlimited
postgres         -       memlock         unlimited
postgres         -       nofile          8192
postgres         -       rss             unlimited
postgres         -       stack           unlimited
postgres         -       cpu             unlimited
postgres         -       nproc           2048
postgres         -       as              unlimited
postgres         -       msgqueue        unlimited

eirods           -       core            unlimited
eirods           -       data            unlimited
eirods           -       fsize           unlimited
eirods           -       memlock         unlimited
eirods           -       nofile          8192
eirods           -       rss             unlimited
eirods           -       stack           unlimited
eirods           -       cpu             unlimited
eirods           -       nproc           2048
eirods           -       as              unlimited
eirods           -       msgqueue        unlimited


Change file for authd

Change /etc/xinetd.d/auth as: 

service auth
{
	disable	= no
        socket_type     = stream
        wait            = no
        user            = ident
        cps             = 4096 10
        instances       = UNLIMITED
        server          = /usr/sbin/in.authd
        server_args     = -t60 --xerror --os
}


Create the database

Make sure the locale is set to UTF8. Use: 

 /bin/su - postgres
 mkdir /postgres/icats01 /postgres/icats01/data /postgres/icats01/log
 chmod g+w /postgres/icats01 /postgres/icats01/data /postgres/icats01/log
 initdb -D /postgres/icats01/data -X /postgres/icats01/log \
   -E UTF8 --locale=UTF8 -U postgres

Get the startup script as: 

 cp ~postgres/install/postgresql /etc/init.d/postresql

As root: 

 /etc/init.d/postgresql start


Changes relative to e-iRODS 3.0

A git repository of the original tree for e-iRODS 3.0 had been created by Andreas. It is accessible as ssh://datil.nsc.liu.se/srv/git/e-irods.git. It is accessed via ssh so first on the computer which has the ssh keys: 

 ssh-add
 ssh -A snic-irods-mgmt

Then 

 git clone ssh://datil.nsc.liu.se/srv/git/e-irods.git

In ./iRODS/config/config.mk various options changed. Actually this is generated, it is config.mk.in to be changed. 

 vi ./iRODS/config/config.mk.in

Define POSTGRES_HOME here as it seems to be an option here as well:

Enable syslog logging (will also switch of file logging). 

IRODS_SYSLOG = 1

PAM authentication. This is now default, no need to change. 

PAM_AUTH = 1

Location of the executable, should be read only for iRODS. 

PAM_AUTH_CHECK_PROG=/usr/sbin/PamAuthCheck

To get unique .irodsA credential tokens per session with a TTL defaulting to 8 hrs instead of two weeks, making it more difficult for an attacker to use a stolen .irodsA file. Change in platform.mk to add CFLAG for previous define 

PAM_AUTH_NO_EXTEND = 1

For the encryption of communication channel between client/server when sending PAM password). Now on as default. 

USE_SSL = 1

Suggestion from Pontus. 

UNI_CODE = 1

Update the version number. In file ./packaging/VERSION. Like: 

EIRODSVERSION=3.0.1b1-snic2

 vi ./packaging/VERSION
 git commit -m "Customized local version" ./packaging/VERSION

 git commit -m "Our config changes" config.mk.in


We leave this since reviewing the source we believe this is fixed. But it's not. Replace in the function definition startIrods. In the script eirods_setup.pl the call to the function "run" to run a script to start irods gets stuck. The call is to be replaced with the "system" call (does not return diagnostics output but works). 

 vi ./iRODS/scripts/perl/eirods_setup.pl
 git commit -m "Startup changed in function startIrods" ./iRODS/scripts/perl/eirods_setup.pl

In ./iRODS/server/core/include/rodsServer.h raise the number of connections MAX_SVR_SVR_CONNECT_CNT to some number above a hundred at least. Also, raise NUM_READ_WORKER_THR. 

 vi ./iRODS/server/core/include/rodsServer.h
 git commit -m "Raising resource limits" ./iRODS/server/core/include/rodsServer.h

In 

./iRODS/scripts/perl/irodsctl.pl.orig

iRODS server is changed

to start up always in the background. 

 vi ./iRODS/scripts/perl/irodsctl.pl
 git commit -m "Start always in the background and wait" ./iRODS/scripts/perl/irodsctl.pl

More extensive changes in 

./packaging/postinstall.sh

. 

 vi ./packaging/postinstall.sh

Running a command with su requires - to pick up the environment of that user. Put cd inside the -c command string. 

   :%s/su --shell/\/bin\/su - --shell/
 git commit -m "Run su with -" ./packaging/postinstall.s

In 

./packaging/build.sh

find Postgresql installed under 

/usr/postgres

. 

 vi ./packaging/build.sh
 git commit -m "Find Postgresql under /usr" ./packaging/build.sh

In the template listing of package files add profile with postgres access. Can also take the copy of the Postgres profile. The profile content is: 

export PATH=$PATH:/usr/postgres/bin
export LD_LIBRARY_PATH=$PATH:/usr/postgres/lib
export MANPATH=/usr/share/man:/usr/postgres/share/man
umask 022

Add the file itself like: 

 cat >packaging/eirods-dot-profile
 git add ./packaging/eirods-dot-profile
 git commit -m "New file profile" ./packaging/eirods-dot-profile
 vi ./packaging/eirods.list.template
 git commit -m "Profile addedd" ./packaging/eirods.list.template

Startup script is broken, fix it. 

 vi ./packaging/eirods
 git commit -m "Startup script fixed" ./packaging/eirods

Finish. 

 git commit
 git push


Bulding the packages

An additional dependency is: 

 yum install fuse-devel

Run the build shell script to build the iCAT server package. 

 cd
 rm -rf rpmbuild
 cd src/e-irods
 cd packaging
 ./build.sh icat postgres 2>&1 | tee -a eirods-build.log

For the resource server package: 

 cd
 cd src/e-irods
 cd packaging
 ./build.sh resource 2>&1 | tee -a eirods-build.log

Packages are created in: 

 cd build


To uninstall

Run: 

 rpm -e eirods-3.0.1b1-0.x86_64
 /bin/su - postgres -c 'dropdb EICAT; dropuser eirods;'
 /usr/sbin/userdel eirods


Install the eirods packages

As root run rpm -i --nodeps to install the package which was built on the management node.

Get the environment for postgres since the install script does not do /bin/su - to run .profile. 

 . ~postgres/.profile
 export PS1='# '

Install the package. 

 cd /root/kits/eirods-3.0.1b1/rpm
 rpm -vv -i --nodeps eirods-3.0.1b1-snic2-64bit-icat-postgres-centos6.rpm
 rom -vv -i eirods-dev-3.0.1b1-snic2-64bit-centos6.rpm

Check the output because finishes even when inside the postinstall script fails.

Check the log: 

 view /var/lib/eirods/iRODS/installLogs/eirods_setup.log

If the postinstall script fails to re-run it like: 

 /var/lib/eirods/packaging/postinstall.sh /var/lib/eirods eirods icat post

gres postgres EICAT localhost 5432 eirods lly2YOjjPEHkM0p


Modify the default zone and set password

Run: 

 /bin/su - eirods
 iadmin modzone tempZone name snicZone

Confirm local zone change.

Change the iRODS environment file accordingly. 

 vi .irods/.irodsEnv

Replace tempZone with snicZone everywhere.

Modify password: 

 iadmin moduser rods password password
 iexit full
 iinit


Client install

The client will have prerequisits as: 

 yum -y install openssl098e
 yum -y install postgresql-odbc
 yum -y install fuse fuse-libs

Install the package: 

 rpm -vv -i kits/eirods-3.0.1b1/eirods-3.0.1b1-snic2-64bit-resource-centos6.rpm

Run setup: 

 /bin/su - eirods
 ./packaging/setup_resource.sh
 snic-irods.nsc.liu.se
 1247
 snicZone
 rods
 password

Create resources

Create directories from admin workstation: 

 ssh root@snic-sr-001 mkdir /snic-sr-001/Vault
 ssh root@snic-sr-002 mkdir /snic-sr-002/Vault
 ssh root@snic-sr-003 mkdir /snic-sr-003/Vault
 ssh root@snic-sr-004 mkdir /snic-sr-004/Vault

 ssh root@snic-sr-001 chown eirods.eirods /snic-sr-001/Vault
 ssh root@snic-sr-002 chown eirods.eirods /snic-sr-002/Vault
 ssh root@snic-sr-003 chown eirods.eirods /snic-sr-003/Vault
 ssh root@snic-sr-004 chown eirods.eirods /snic-sr-004/Vault

Create resources on the iCAT server: 

 iadmin mkresc snic-sr-001-lfs01 "unix file system" snic-sr-001.nsc.liu.se:/snic-sr-001/Vault
 iadmin mkresc snic-sr-002-lfs01 "unix file system" snic-sr-002.nsc.liu.se:/snic-sr-002/Vault
 iadmin mkresc snic-sr-003-lfs01 "unix file system" snic-sr-003.nsc.liu.se:/snic-sr-003/Vault
 iadmin mkresc snic-sr-004-lfs01 "unix file system" snic-sr-004.nsc.liu.se:/snic-sr-004/Vault

Create directories from the admin workstation: 

 irods-do ssh "/bin/su - eirods -c \"mkdir /swestore/eirods\""
 irods-do ssh "/bin/su - eirods -c \"mkdir /swestore/eirods/Vault\""

Create nfs resources: 

 iadmin mkresc snic-sr-001-nfs01 "unix file system" snic-sr-001.nsc.liu.se:/swestore/eirods/Vault
 iadmin mkresc snic-sr-002-nfs01 "unix file system" snic-sr-002.nsc.liu.se:/swestore/eirods/Vault
 iadmin mkresc snic-sr-003-nfs01 "unix file system" snic-sr-003.nsc.liu.se:/swestore/eirods/Vault
 iadmin mkresc snic-sr-004-nfs01 "unix file system" snic-sr-004.nsc.liu.se:/swestore/eirods/Vault


Test composable resource replication

Create composable test resource: 

 iadmin mkresc tmp1 replication
 iadmin mkresc tmp11 "unix file system" snic-sr-001.nsc.liu.se:/tmp/Vault1
 iadmin mkresc tmp12 "unix file system" snic-sr-002.nsc.liu.se:/tmp/Vault2
 iadmin addchildtoresc tmp1 tmp11
 iadmin addchildtoresc tmp1 tmp12


Create default resource

/bin/su - eirods 

 iadmin mkresc snicdefResc "unix file system" snic-sr-001.nsc.liu.se:/swes

tore/eirods/snicdefResc/Vault


Accessing files as another user

Set environment variable: 

 export clientUserName=user

Then you can run icommands as user.


Setting up project hierarchy

As eirods user run: 

 imkdir /snicZone/proj/p1
 iadmin mkgroup p1
 iadmin atg p1 u1
 ichmod -r read p1 /snicZone/proj/p1
 ichmod -r write p1 /snicZone/proj/p1
 ichmod -r inherit /snicZone/proj/p1

Any member of p1 should able to read/write everything under the project group directory tree.


= Security efix

Do: 

 /bin/su - eirods
 cd
 cd iRODS/server/bin/cmd
 mkdir -p /var/lib/eirods/save/cmd-removed
 mv hello test_execstream.py univMSSInterface.sh /var/lib/eirods/save/cmd-removed/

Supported clients

iDrop web - Point your Web browser to iweb.swestore.se
E-iRODS iCommands - 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.

The community iRODS client also should work, with PAM authentication e.g. the following changes to the Makefile iRODS/config/config.mk and a recompile: 

PAM_AUTH = 1
PAM_AUTH_NO_EXTEND = 1
USE_SSL = 1

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 ($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/home/<email address>'
irodsCwd '/snicZone/home/<email address>'
irodsUserName '<email address>'
irodsZone 'snicZone'
irodsAuthScheme 'PAM'

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 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

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)
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