iRODS System

System Summary

Hardware configuration

The iRODS system consists of the following systems.

  • Four iRODS servers
  • Two iRODS DB servers (Active-Standby)

Hardware specifications

The hardware specification of the iRODS system is shown below.

SYSTEMiRODSiRODS DB
MODELIBM System X3650 M5IBM System X3550 M5
CPUXeon E5-2620v3 2.4GHz 6coreXeon E5-2620v3 2.4GHz 10core
MEMORY32GB32GB
HDD300GB x2(RAID1)300GB x2(RAID1)

Available resources

The iRODS system can use the following file systems as data area.

  • GPFS (General Parallel File System)
  • GHI File System

About iRODS

See here for an overview of iRODS.

Registration to iRODS system

See here for Application Registration Form list.

If you do not have any account of KEK Central Computing System, please submit two forms to the Administration Office of the KEK Computing Research Center.
- KEK Computing Research Center System Application Form
- iRODS system application form
If you already have an account on the system, you need only one form to the Administration Office.
- iRODS system application form

How to use iRODS commands

This section introduces typical iRODS commands.
iRODS commands are called icommands, which usually has an "i" added to the head of UXIX commands.
For details of each command, please refer to the help menu by specifying the option -h.

iRODS provides a similar space definition to UNIX file systems.
Here are some words used for irods:

Glossary of Terms

Data-Object:Corresponds to a file in UNIX.
Collection:Collection of Data-Object

init command

Initializes the user environment. Please run this command first after your account is issued. Please enter the password you gave at registration.

Usage: iinit [option]

[Example]

 $> iinit ↓
Enter your current iRODS password:  ←Input your password and click enter.
[-]     libnative.cpp:336:native_auth_client_response :  status [CAT_INVALID_AUTHENTICATION]
  errno [] -- message [Call to rcAuthResponseFailed.]

failed with error -826000 CAT_INVALID_AUTHENTICATION

Initialization is complete if password authentication succeeds. After this, you will not be asked to input a password for icommands.

If the password is incorrect, the following message will appear.

 $> iinit ↓
Enter your current iRODS password: ←Input your password and click enter.

When you log in for the first time, please be sure to change password with ipasswd commamd.

[Example]

$> ipasswd ↓
Enter your current iRODS password:    ←Input current password and click enter.
Enter your new iRODS password:        ←Input new password and click enter.
Reenter your new iRODS password:      ←Input new password and click enter.

ils command

Displays data objects and collections stored in iRODS.

Usage:ils [option] dataObj|collection ...

[Example]

 $> ils -l testdata1 ↓
 $> ils -L colle1 ↓

If you set -l option, the details of dataObj and collection are shown. If you set -L option, the output includes more details than option -l.
The line 1 of above example shows the information of the object"testdata1".
The line 2 shows the information of the collection "colle1" with physical file path.

icp command

Copies an irods data-object or collection to another data-object or collection.

Usage : icp [option] srcDataObj|srcColl ... destDataObj|destColl

[Example]

 $> icp testfile1 testfile2
 $> icp -r colle1 colle2

If you set -R option, it will copy the whole collection.
For the line 1 of the above example, the object "testfile1" is copied to another object "testfile2" which is in the same directory as "testfile1".
For line 2, the collection "colle1" are copied to another collection "colle2" which is in the same directory as "colle1".

iput command

Saves a local file or directory into iRODS. Without a specified target destination, it will save into the current irods directory and a default input file name.

Usage: iput [option] localSrcDir ... destDataObj|destColl

[Example]

 $> iput /tmp/test1.dat test2.dat
 $> iput -r  /tmp/colle1 colle2

If you set -R option, it will store the whole directory.
For line 1 of the above example, the file /tmp/test1.dat is uploaded to iRODS as an object named "test2.dat".
For line 2, the directory /tmp/colle2 is uploaded to iRODS as a collection "colle2".

iget command

Gets data-objects or collections from irods, either to the specified local area or to the current working directory.

Usage:iget [option] srcDataObj|srcCollection ... destLocalFile|destLocalDir
[Example]

 $> iget test2.dat /tmp/test3.dat
 $> iget -r colle2 /tmp/colle3

If you set -R option, it will get the whole collection.
For line 1 of the above example, the object "test2.dat" is transferred to /tmp/test3.dat.
For line 2, the collection "colle2" is transferred to /tmp/colle3.

irm command

removes one or more data-object or collection from iRODS space.

Usage: irm [option] dataObj|collection ...

[Example]

 $> irm -f testfile2

By defaut, the data-objects are moved to the trash.
The -f option deletes data-object immediately. The -R option removes the whole sub-tree.

Remove one or more data-object or collection from a RODS trash with irmtrash command.
The path of RODS trash is /<Zone name>/trash/home/<myUserName>.

[Example]

 $> irmtrash ↓          ←empty the trash bin.
 $> irmtrash /KEKZone/trash/home/user1/testdata1

If you want to check <Zone name>, please refer to the irodszone variable in ienv command.

[Example]

 $> ienv ↓

Last-modified: 2016-08-31 (水) 18:29:22 (930d)