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. The 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:

First, we need to verify your identity, this is done through the following steps:

1. Sign in with your organisation B2ACCESS; the page requests a valid personal certificate (e.g. GEANT). Accounts with "Low" level of assurance are not granted access to IT4I zone.

2. Confirm your certificate in the browser:

   

3. Confirm your certificate in the OS (Windows):

   

4. Sign to EUDAT/B2ACCESS:

   

5. After successfull login to B2Access:

6. For Non IT4I Users

Sign in to our AAI through your B2Access account. You have to set a new password for iRods access.

1. For IT4I Users

Sign in to our AAI through your B2Access account and link your B2ACCESS identity with your existing account. The IRODS password will be the same as your IT4I LDAP password (i.e. code.it4i.cz password).

1. Contact support@it4i.cz, so we can create your account at our iRODS server.

2. Fill this request on EOSC-MARKETPLACE (recommended) or at EUDAT, please specify the requested capacity.

   

Access to iRods Collection From Karolina

Access to iRods Collection requires access to the Karolina cluster (i.e. IT4I account), since iRODS clients are provided as a module on Karolina (Barbora is in progress). The irodsfs module loads config file for irodsfs and icommands, too.

Note that you can change password to irods aai.it4i.cz.

Mounting Your Collection

ssh some_user@karolina.it4i.cz
ml irodsfs

Now you can choose between the 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_user@login4.karolina ~]$ iinit
Enter your current PAM password:

[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

Access to iRods Collection From Other Resource

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

You Need a Client to Connect to iRods Server

• There are many iRods clients, but we recommend theese:
• Cyberduck - for windows / mac, GUI .
• Fuse (irodsfs lite) - for linux, cli
• iCommands - for linux, cli .
• for access set PAM passwords at AAI

Cyberduck

• download Cyberduck
• download connection profile for IT4I irods server
• left doubleclick at this file opens connection

Fuse

• work with your irods collection like ordinary directory
• this is linux client only, basic knowledge of commandline is neccessary

cd ~
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 ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/config.yml
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods/
sed -i 's,~,'"$HOME"',g' ~/irods/irods_environment.json

• edit ~/.irods/config.yml with username from AAI

How to 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
• we recommend Centos7, ubuntu 20 is optional

steps for Ubuntu20:

LSB_RELEASE="bionic"
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE}  main" \
>   | sudo tee /etc/apt/sources.list.d/renci-irods.list
deb [arch=amd64] https://packages.irods.org/apt/ bionic  main

sudo apt-get update
apt-cache search irods
wget -c \
  http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \
  http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.10_amd64.deb
sudo apt install \
  ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  ./python-requests_2.18.4-2ubuntu0.1_all.deb \
  ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
sudo rm -rf \
  ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
  ./python-requests_2.18.4-2ubuntu0.1_all.deb \
  ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
sudo apt install -y irods-icommands
mkdir ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/irods_environment.json
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods
sed -i 's,~,'"$HOME"',g' ~/.irods/irods_environment.json

Steps for centos

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
mkdir ~/.irods/ && cd "$_" && wget https://docs.it4i.cz/irods_environment.json
wget https://pki.cesnet.cz/_media/certs/chain_geant_ov_rsa_ca_4_full.pem -P ~/.irods
sed -i 's,~,'"$HOME"',g' ~/.irods/irods_environment.json

• edit irods_user_name in ~/.irods/irods_environment.json with username from AAI

[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.