|
|
| Line 90: |
Line 90: |
| | == iRODS == | | == iRODS == |
| | | | |
| − | | + | There is a SNIC iRODS system available under Swestore. |
| − | | |
| − | == 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 <code>/usr/postgres</code>
| |
| − | since the e-irods install script expects the postgres directory
| |
| − | tree to be under <code>/usr</code>. The userid <code>postgres</code>
| |
| − | will own the directory tree.
| |
| − | | |
| − | Data will be owned by the <code>postgres</code> userid and under
| |
| − | <code>/postgres</code> 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, <code>postgres-build.sh</code>
| |
| − | and <code>unixodbc-build.sh</code> 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 <code>/usr/postgres</code>.
| |
| − | A tarball is manually created under <code>~postgres/install/tar</code>
| |
| − | as <code>postgres-9.4-snic-build.tar.gz</code>.
| |
| − | | |
| − | The database will run on snic-irods, so the
| |
| − | <code>/usr/postgres</code> tree is taken and transplanted
| |
| − | from snic-irods-mgmt using the tarball.
| |
| − | | |
| − | | |
| − | === Running postgres on the iCAT server ===
| |
| − | | |
| − | The userid <code>postgres</code> is added to the puppet manfiests.
| |
| − | | |
| − | Puppet manifests will also need to be amended with mount options
| |
| − | for the <code>/postgres</code> 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:
| |
| − | <pre>
| |
| − | 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
| |
| − | </pre>
| |
| − | | |
| − | Mount the file system with the options:
| |
| − | logbufs=8,logbsize=256k,largeio,inode64
| |
| − | so update <code>/etc/fstab</code> 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:
| |
| − | | |
| − | <pre>
| |
| − | # 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'
| |
| − | </pre>
| |
| − | | |
| − | Change limits in /etc/security/limits.conf as:
| |
| − | <pre>
| |
| − | 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
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | === Change file for authd ===
| |
| − | | |
| − | Change <code>/etc/xinetd.d/auth</code> as:
| |
| − | <pre>
| |
| − | 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
| |
| − | }
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | === 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
| |
| − | <code>ssh://datil.nsc.liu.se/srv/git/e-irods.git</code>.
| |
| − | It is accessed via <code>ssh</code> 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 <code>./iRODS/config/config.mk</code> various options changed.
| |
| − | Actually this is generated, it is config.mk.in to be
| |
| − | changed.
| |
| − | vi ./iRODS/config/config.mk.in
| |
| − | | |
| − | Define <code>POSTGRES_HOME</code> here as it seems to be an option here
| |
| − | as well:
| |
| − | | |
| − | Enable syslog logging (will also switch of file logging).
| |
| − | <pre>
| |
| − | IRODS_SYSLOG = 1
| |
| − | </pre>
| |
| − | | |
| − | PAM authentication. This is now default, no need to change.
| |
| − | <pre>
| |
| − | PAM_AUTH = 1
| |
| − | </pre>
| |
| − | | |
| − | Location of the executable, should be read only for iRODS.
| |
| − | <pre>
| |
| − | PAM_AUTH_CHECK_PROG=/usr/sbin/PamAuthCheck
| |
| − | </pre>
| |
| − | | |
| − | 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
| |
| − | <pre>
| |
| − | PAM_AUTH_NO_EXTEND = 1
| |
| − | </pre>
| |
| − | | |
| − | For the encryption of communication channel between
| |
| − | client/server when sending PAM password). Now on as default.
| |
| − | <pre>
| |
| − | USE_SSL = 1
| |
| − | </pre>
| |
| − | | |
| − | Suggestion from Pontus.
| |
| − | <pre>
| |
| − | UNI_CODE = 1
| |
| − | </pre>
| |
| − | | |
| − | Update the version number. In file ./packaging/VERSION.
| |
| − | Like:
| |
| − | <pre>
| |
| − | EIRODSVERSION=3.0.1b1-snic2
| |
| − | </pre>
| |
| − | 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 <code>eirods_setup.pl</code> 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 <code>./iRODS/server/core/include/rodsServer.h</code>
| |
| − | raise the number of connections MAX_SVR_SVR_CONNECT_CNT to some
| |
| − | number above a hundred at least.
| |
| − | Also, raise <code>NUM_READ_WORKER_THR</code>.
| |
| − | vi ./iRODS/server/core/include/rodsServer.h
| |
| − | git commit -m "Raising resource limits" ./iRODS/server/core/include/rodsServer.h
| |
| − | | |
| − | In <pre>./iRODS/scripts/perl/irodsctl.pl.orig</pre> 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 <pre>./packaging/postinstall.sh</pre>.
| |
| − | 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 <pre>./packaging/build.sh</pre> find Postgresql installed under
| |
| − | <pre>/usr/postgres</pre>.
| |
| − | 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:
| |
| − | <pre>
| |
| − | 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
| |
| − | </pre>
| |
| − | | |
| − | 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 == | | == Supported clients == |
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
There is a SNIC iRODS system available under Swestore.
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)
