dice.md

What Is DICE Project?

DICE (Developing Innovation and Creativity in Education) is an international project co-funded by the Erasmus+ Programme of the European Union.

Its main goals are related to fostering innovation and creativity in education.

This project attempts to be a leading initiative that supports educational community to make progress in the field of innovation and creativity through effective, authentic, practical, sustainable actions. This project has been funded with support from the European Commission. For more information, see [http://www.diceproject.eu/][b].

IT4Innovations participates in DICE. DICE uses the iRods software

The integrated Rule-Oriented Data System (iRODS) is an open source data management software used by research organizations and government agencies worldwide. iRODS is released as a production-level distribution aimed at deployment in mission critical environments. It virtualizes data storage resources, so users can take control of their data, regardless of where and on what device the data is stored. As data volumes grow and data services become more complex, iRODS is serving an increasingly important role in data management, see [https://irods.org/][c].

How to Put Your Data to Our Server

Prerequisities:

We have to be sure about your identity, this will be done throught this steps:

• at the first, fill this request for EUDAT

• sign to MyAccessID , after that, please create account at B2ACCESS , pages requests valid personal certificate (e.g from GEANT)

• confirm your certificate in browser

• confirm your certificate in OS ( windows )

• sign to EUDAT/B2ACCESS

• after successfull login to B2Access, please sign in to our AAI throught your B2Access account. You can set new password. this new password will work for cyberduck and icommands.

• finally, contact our support@it4i.cz by mail, we will create your account at our iRODS server.

IT4I User (You Have IT4I Account With Access to Cluster Already)

• iRODS clients are provided as a module on our Karolina cluster ( Barbora is in progress )
• module irodsfs contains config file for irodsfs nad for icommands too
• PAM passwords is password, you set in aai.it4i.cz

How to mount your collection

ssh some_user@karolina.it4i.cz
ml irodsfs

• config files for irodsfs and icommands will be loaded
• now you can choose between Fuse client or iCommands

Fuse

ssh some_user@karolina.it4i.cz
[some_use@login4.karolina ~]$ ml irodsfs

irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml
iRODS environment file has been created at /home/dvo0012/.irods/irods_environment.json

to start irodsfs, run:          irodsfs -config ~/.irods/config.yml ~/IRODS
to start iCommands, run:        iinit

For more information, see https://docs.it4i.cz/dice/

To mount your iRODS collection to ~/IRODS, run

[some_user@login4.karolina ~]$ irodsfs -config ~/.irods/config.yml ~/IRODS
time="2022-08-04 08:54:13.222836" level=info msg="Logging to /tmp/irodsfs_cblmq5ab1lsaj31vrv20.log" function=processArguments package=main
Password:
time="2022-08-04 08:54:18.698811" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main
time="2022-08-04 08:54:18.699080" level=info msg="Running the process in the background mode" function=parentRun package=main
time="2022-08-04 08:54:18.699544" level=info msg="Process id = 27145" function=parentRun package=main
time="2022-08-04 08:54:18.699572" level=info msg="Sending configuration data" function=parentRun package=main
time="2022-08-04 08:54:18.699730" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main
time="2022-08-04 08:54:18.922490" level=info msg="Successfully started background process" function=parentRun package=main

To unmount it, run

fusermount -u ~/IRODS

you can work with fuse as an ordinary directory ( ls, cd, cp, mv etc )

iCommands

ssh some_user@karolina.it4i.cz
[some_use@login4.karolina ~]$ ml irodsfs
irodsfs configuration file has been created at /home/dvo0012/.irods/config.yml.
      to start irods fs run: irodsfs -config ~/.irods/config.yml ~/IRODS

iCommands environment file has been created at /home/$USER/.irods/irods_environment.json.
      to start iCommands run: iinit

[some_use@login4.karolina ~]$ iinit
Enter your current PAM password:

• put you password you set in keycloak

[some_use@login4.karolina ~]$ ils
/IT4I/home/some_user:
  test.1
  test.2
  test.3
  test.4

• upload iput , download iget
• for more help, type ihelp

Users Without IT4I Account (No Access to Cluster)

• we suppose, you will upload your data from your local pc/vm

You Need a Client to Connect to iRods Server

• There are many iRods clients, but we recommend theese:
• Cyberduck - for windows / mac, GUI . Password from aai.it4i.cz (keycloak) works
• Fuse (irodsfs lite) - for linux, cli
• iCommands - for linux, cli . Password from aai.it4i.cz (keycloak) works

Cyberduck

• download at [https://cyberduck.io/download/][i]
• download connection profile for IT4I irods server irods.cyberduckprofile
• left doubleclick at this profile file opens connection

Irodsfs Lite

• work with your irods collection like ordinary directory
• this is linux client only, basic knowledge of commandline is neccessary
• PAM passwords is password, you set in aai.it4i.cz

cd ~
wget https://docs.it4i.cz/irods1.it4i.cz.crt [k]
wget https://github.com/cyverse/irodsfs/releases/download/v0.7.6/irodsfs_amd64_linux_v0.7.6.tar
tar -xvf ~/irodsfs_amd64_linux_v0.7.6.tar
mkdir ~/IRODS

settings:

[some_user@local_pc ~]$ vim ~/.rods/config.yml

host: irods1.it4i.cz
port: 1247
proxy_user: some_user
client_user: some_user
zone: IT4I

authscheme: "pam"
ssl_ca_cert_file: "~/irods1.it4i.cz.crt"
ssl_encryption_key_size: 32
ssl_encryption_algorithm: "AES-256-CBC"
ssl_encryption_salt_size: 8
ssl_encryption_hash_rounds: 16

path_mappings:
  - irods_path: /IT4I/home/some_user
    mapping_path: /
    resource_type: dir

How to start - mount your collection:

[some_user@local_pc ~]$ ./irodsfs -config ~/.irods/config.yml ~/IRODS
time="2022-07-29 09:51:11.720831" level=info msg="Logging to /tmp/irodsfs_cbhp2rucso0ef0s7dtl0.log" function=processArguments package=main
Password:

time="2022-07-29 09:51:17.691988" level=info msg="Found FUSE Device. Starting iRODS FUSE Lite." function=parentMain package=main
time="2022-07-29 09:51:17.692683" level=info msg="Running the process in the background mode" function=parentRun package=main
time="2022-07-29 09:51:17.693381" level=info msg="Process id = 74772" function=parentRun package=main
time="2022-07-29 09:51:17.693421" level=info msg="Sending configuration data" function=parentRun package=main
time="2022-07-29 09:51:17.693772" level=info msg="Successfully sent configuration data to background process" function=parentRun package=main
time="2022-07-29 09:51:18.008166" level=info msg="Successfully started background process" function=parentRun package=main

How to put your data to iRODS

[some_use@local_pc ~]$ cp test1G.txt ~/IRODS

It works as ordinary filesystem

[some_user@local_pc ~]$ ls -la ~/IRODS
total 0
-rwx------ 1 some_user some_user 1073741824 Nov  4  2021 test1G.txt

How to stop - unmout your collection:

[some_user@local_pc ~]$ fusermount -u ~/IRODS

iCommands

• this is linux client only, basic knowledge of commandline is neccessary
• manual is for centos7
• for ubuntu20 - there is [http://docs.snic.se/wiki/IRODS_iCommands_installation_on_Ubuntu_20.04#Authenticate_and_test_iRODS_iCommands_client][j]
• please do NOT install icommands 4.3.0, it is NOT working with PAM

sudo rpm --import https://packages.irods.org/irods-signing-key.asc
sudo wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo
sudo yum install epel-release -y
sudo yum install python-psutil python-jsonschema
sudo yum install irods-icommands-4.2.7-1.x86_64
mkdir ~/.irods/
cd ~ && wget https://docs.it4i.cz/irods1.it4i.cz.crt [k]

Copy&paste + edit irods_user_name

[some_user@local_pc ~]$ vim ~/.irods/irods_environment.json
{
    "irods_host": "irods1.it4i.cz",
    "irods_port": 1247,
    "irods_user_name": "some_user",
    "irods_zone_name": "IT4I",
    "irods_authentication_scheme": "PAM",
    "irods_ssl_verify_server": "cert",
    "irods_ssl_ca_certificate_file": "~/irods1.it4i.cz.crt",
    "irods_encryption_algorithm": "AES-256-CBC",
    "irods_encryption_key_size": 32,
    "irods_encryption_num_hash_rounds": 16,
    "irods_encryption_salt_size": 8
}

[some_user@local_pc ~]$ pwd
/some_user/.irods

[some_user@local_pc ~]$  ls -la
total 16
drwx------. 2 some_user some_user 136 Sep 29 08:53 .
dr-xr-x---. 6 some_user some_user 206 Sep 29 08:53 ..
-rw-r--r--. 1 some_user some_user 253 Sep 29 08:14 irods_environment.json

How to Start:

step 1:

[some_user@local_pc ~]$ iinit
Enter your current PAM password:

[some_user@local_pc ~]$ ils
/IT4I/home/some_user:
  file.jpg

how to put your data to IRODS

[some_user@local_pc ~]$ iput cesnet.crt

[some_user@local_pc ~]$ ils
/IT4I/home/some_user:
  cesnet.crt

How to download data

[some_user@local_pc ~]$ iget cesnet.crt
ls -la ~
-rw-r--r--. 1 some_user some_user 1464 Jul 20 13:44 cesnet.crt

For more commands, use the ihelp command.