Skip to content

Latest commit

 

History

History
304 lines (221 loc) · 6.83 KB

01-Install-iRODS.md

File metadata and controls

304 lines (221 loc) · 6.83 KB

Installation of iRODS 4.2

This document describes how to install iRODS4.2 on a Ubuntu machine with a postgresql database as iCAT.

Environment

The documentation is tested with an Ubuntu 16.04 and Ubuntu 18.04 server.

Prerequisites

1. Add repo key, Update and upgrade if necessary

Ubuntu16 and 18

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 -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
sudo apt-get update

2. Set firewall

sudo apt-get install iptables-persistent
sudo service netfilter-persistent start
sudo invoke-rc.d netfilter-persistent save
sudo service netfilter-persistent stop

mkdir iptables-rules
  • create ~/iptables-rules/ruleset-v4
*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [4538:480396]
-A INPUT -m state --state INVALID -j DROP
-A INPUT -p tcp -m tcp ! --tcp-flags FIN,SYN,RST,ACK SYN -m state --state NEW -j DROP
-A INPUT -f -j DROP
-A INPUT -p tcp -m tcp --tcp-flags FIN,SYN,RST,PSH,ACK,URG NONE -j DROP
-A INPUT -p tcp -m tcp --tcp-flags FIN,SYN,RST,PSH,ACK,URG FIN,SYN,RST,PSH,ACK,URG -j DROP
-A INPUT -p icmp -m limit --limit 5/sec -j ACCEPT
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp --dport 22 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 1248 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 1247 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 20000:20199 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 4443 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 443 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 5432 -j ACCEPT
-A INPUT -j LOG
-A INPUT -j DROP
COMMIT
sudo iptables-restore < ~/iptables-rules/ruleset-v4 
sudo iptables -S
sudo dpkg-reconfigure iptables-persistent

3. Set host name

Example hosts-file:

127.0.0.1   localhost
127.0.1.1	alice-server
IPa.ddr.ess  alice.eudat-sara.vm.surfsara.nl alice-server

4. Install postgresql

sudo apt-get install postgresql
sudo pg_createcluster 10 main --start

Installing iRODS

5. Configure and create postgresql database

sudo su - postgres
/usr/lib/postgresql/10/bin/pg_ctl -D /var/lib/postgresql/10/main -l logfile start

If necessary fix locale settings before proceeding.

psql
CREATE DATABASE "ICAT";
CREATE USER irods WITH PASSWORD 'irods';
GRANT ALL PRIVILEGES ON DATABASE "ICAT" to irods;
\q
exit

Known issues

If you encounter the error:

postgres@scomp1447:~$ psql
psql: could not connect to server: No such file or directory
	Is the server running locally and accepting
	connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?

Then do:

sudo mkdir -p /var/lib/pgsql/data/
sudo chown -R postgres:postgres /var/lib/pgsql
sudo su - postgres
/usr/lib/postgresql/10/bin/initdb /var/lib/pgsql/data/pg_hba.conf
/usr/lib/postgresql/10/bin/pg_ctl -D /var/lib/pgsql/data/pg_hba.conf -l logfile start
psql
CREATE DATABASE "ICAT";
CREATE USER irods WITH PASSWORD 'irods';
GRANT ALL PRIVILEGES ON DATABASE "ICAT" to irods;
\q
exit

6. Install iRODS packages

sudo apt-get install irods-server irods-database-plugin-postgres

7. Configuring iRODS

sudo python /var/lib/irods/scripts/setup_irods.py

Set the following variables

iRODS user [irods]: 
iRODS group [irods]: 

+--------------------------------+
| Setting up the service account |
+--------------------------------+

Existing Group Detected: irods
Existing Account Detected: irods
Setting owner of /var/lib/irods to irods:irods
Setting owner of /etc/irods to irods:irods
iRODS server's role:

1. provider

+-----------------------------------------+
| Configuring the database communications |
+-----------------------------------------+

You are configuring an iRODS database plugin. The iRODS server cannot be started until its database has been properly configured.

ODBC driver for postgres:

PostgreSQL ANSI

Database server's hostname or IP address []: localhost
Database server's port [5432]: 
Database name [ICAT]: 
Database username [irods]: 

-------------------------------------------

Database Type: postgres
ODBC Driver:   PostgreSQL ANSI
Database Host: localhost
Database Port: 5432
Database Name: ICAT

+--------------------------------+
| Configuring the server options |
+--------------------------------+

iRODS server's zone name [tempZone]: aliceZone
iRODS server's port [1247]: 
iRODS port range (begin) [20000]: 
iRODS port range (end) [20199]: 
Control Plane port [1248]: 
Schema Validation Base URI (or off) [file:///var/lib/irods/configuration_schemas]: 
iRODS server's administrator username [rods]: alice

-------------------------------------------

Zone name:                  aliceZone
iRODS server port:          1247
iRODS port range (begin):   20000
iRODS port range (end):     20199
Control plane port:         1248
Schema validation base URI: file:///var/lib/irods/configuration_schemas

iRODS server administrator: alice

Please confirm [yes]: 
iRODS server's zone key: ALICE_ZONE_KEY
iRODS server's negotiation key (32 characters):

8. Login to iRODS

iinit
Enter the host name (DNS) of the server to connect to: localhost
Enter the port number: 1247
Enter your irods user name: alice
Enter your irods zone: aliceZone
  • Test whether you can list your iRODS directory
ils

iRODS resource configuration

We now configure another resource on the same server. We need to grant the user who runs iRODS (usually irods) read and write access:

sudo mkdir /irodsVault
sudo chown -R irods:irods /irodsVault
iadmin mkresc aliceResc unixfilesystem alice-server:/irodsVault

System control

As user irods you can use the command irodsctlto retrieve status, start and stop the service.

irods@scomp1447:/var/lib/irods/irodsctl status 
irodsServer :
  Process 21356
  Process 21357
irodsReServer :
  Process 21359

Additional Server configuration

Logging

iRODS creates a lot of log files, which are not cleaned up automatically. To do so start a cron-job:

sudo vim /etc/cron.d/irods

Add

# cleanup old logfiles older than 14 days
11      1       *       *       *       root    find /var/lib/irods/iRODS/server/log/{re,rods}Log.* -mtime +14  -exec rm {} \;

to the file. Now root will delete all reLog and rodsLog files that are older than 14 days. The command will be executed everyday at 11.01am.

Pinning packages

To prevent automatic package updates of the iRODS server create the file /etc/apt/preferences.d/irods with:

Package: irods-dev
Pin: version 4.2.8
Pin-Priority: 999



Package: irods-server
Pin: version 4.2.8
Pin-Priority: 999



Package: irods-runtime
Pin: version 4.2.8
Pin-Priority: 999



Package: irods-icommands
Pin: version 4.2.8
Pin-Priority: 999

as content.