Wikidata Snapshot (Virtuoso PAGO) EBS-backed EC2 AMI

hwilliams · July 7, 2022, 10:49pm

Introduction

The Wikidata Snapshot (Virtuoso PAGO) starts as a static instance, preloaded with the Wikidata 2022-12 dataset dump, mirroring the public Wikidata instance found at our live Wikidata SPARQL Query Service Endpoint.

This type of AMI provides several fundamental benefits including —

Virtuoso DBMS Server is preinstalled with basic tuning for the host operating system. (That said, since we support many AMI machine types/sizes, you should still tune the configuration to suit the available RAM in your instance.)
Wikidata Dataset is preloaded and preconfigured (and may be configurable to auto-update).
You can start and stop the Wikidata instance without having to terminate its host AMI.
With the hourly model, you pay only for the time the AMI is used.

Who is this for?

Anyone seeking a preloaded and pre-configured Wikidata instance for personal or service-specific use
Anyone seeking SQL and GraphQL access to Wikidata
Anyone seeking ODBC or JDBC access to Wikidata via client productivity tools and development environments that support those data access protocols

Usage

Prerequisites

An Amazon Web Services (AWS) account.
Recently created AWS accounts will have been automatically signed up for the Amazon S3 and EC2 Web Service. If you created your AWS account a long time ago, you may now need to manually sign up for these services.
Ensure an AWS security group allowing access to ports 22 (standard SSH), 80 (standard HTTP), and 8890 (Virtuoso HTTP-based Admin) is used. (This is the setup of the AMI offerings.)

Instantiating Wikidata Snapshot (Virtuoso PAGO) via Web Interface

Locate the Wikidata Snapshot (Virtuoso PAGO) image in AWS Marketplace and click the Continue to Subscribe button.

Click on the Accept Terms button.

Click on the Continue to Configuration button.

Select the Region to where the AMI should be deployed and click on the Continue to Launchbutton.

Select the EC2 Instance Type, Security Group Settings, Key Pair Settings the AMI should be started with and click on the Launch button.

The deployment is now complete. Click on the EC2 Console link to view the launched instance in the AWS EC2 console

From the EC2 Console note the Public IP address of the instance for accessing it via ssh, http etc

First-time Setup & Usage Notes

These steps in this section are only necessary the first time you start the Virtuoso instances on the AMI. This section may be ignored thereafter, as it is not necessary after AMI reboots.

There are two Virtuoso instances in this AMI. One which comes up quickly, with no significant content, so you know the AMI is basically functional; and one which comes up more slowly, with the full Wikidata dataset, which takes significant time to start due to some Amazon requirements for such AWS instances.

Wikidata Instance

ssh into your instantiated AMI using a command of the form —

ssh -i {secure-pem-file} ubuntu@{amazon-ec2-dns-name-or-ip-address}

The Virtuoso DBMS Server for the Basic Instance will have started with the AMI. You can verify this with –

ps -ef | grep "virt*" | grep -v grep

If you do not see a running instance, execute the following command, and then repeat the command above.

sudo service virtuoso status
sudo service virtuoso start
sudo service virtuoso status

We strongly recommend you now use the Conductor to change the password for the dba user from the the AMI instance-id .

Retrieve the AMI instance-id by either –
- checking the AMI properties presented by the Amazon AWS console UI –

* executing the following command in the Linux shell –

curl http://169.254.169.254/latest/meta-data/instance-id

Load the Conductor interface.

http://{amazon-ec2-ami-dns-name-or-ip-address}/conductor

If you get any error at this point, execute the following commands, and then re-try loading the Conductor in your web browser.

sudo service virtuoso start
sudo service virtuoso status

At the authentication challenge, log in as the dba user, with the AMI instance-id as the password. Note: If unable to connect to the Virtuoso server using the instance-id as password, please register with our Support Site, and create a Support Case for fastest assistance.
Drill down to System Admin → User Accounts .
Locate the dba user, and click the associated Edit link.
The form allows many things to be changed. For now, just input your desired password into both Password and Confirm Password boxes, and click the Save button.
You can now perform other administrative tasks through the Conductor interface, or return to basic use.

Wikidata Snapshot (Virtuoso PAGO) Database Interaction via Web Interface

Once online, your Wikidata Snapshot instance will be ready for use from —

Faceted Browsing Endpoint

http://{amazon-ec2-ami-dns-name-or-ip-address}/fct

Advanced Faceted Browsing Page

http://{amazon-ec2-ami-dns-name-or-ip-address}/describe/?uri=http://dbpedia.org/resource/DBpedia

SPARQL Query Service Endpoint

http://{amazon-ec2-ami-dns-name-or-ip-address}/sparql

Virtuoso Instance Administration Page (Virtuoso Conductor)

http://{amazon-ec2-ami-dns-name-or-ip-address}/conductor

Administering the Virtuoso Instance via SSH

Make a ssh connection to the VM using the public key ( pem-file ) and username ( ubuntu by default) chosen when creating the deployment, and the Public IP address from the previous section as follows:

ssh -i {pem-file} ubuntu@{Public IP address}

Once connected it is strongly recommended to update the VM to get the latest operating system and Virtuoso updates with the command:

sudo apt-get upgrade

Check the Virtuoso server is automatically started post deployment with the command:

sudo service virtuoso status

The following commands can be used to Administer the Virtuoso server:

Start the Virtuoso Server:

sudo service virtuoso start

Stop the Virtuoso Server:

sudo service virtuoso stop

Restart the Virtuoso Server:

sudo service virtuoso restart

Check status of Virtuoso Server:

sudo service virtuoso status

Determine the random password set for the dba user with the command:

sudo cat /opt/virtuoso/database/.initial-password

A SQL connection can then be made Virtuoso with the isql command line tool with the command on port 1111:

isql 1111

Typical output for running these steps are:

$ ssh -i certificates/virtuoso.pem ubuntu@54.221.25.206
The authenticity of host '54.221.25.206 (54.221.25.206)' can't be established.
ECDSA key fingerprint is SHA256:QGsOFcQoa4x5DBavtdHWDQUUQtBdHJ/OkizKep8UOcM.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added '54.221.25.206' (ECDSA) to the list of known hosts.
Welcome to Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-1025-aws x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage

  System information as of Fri Jan 29 12:41:03 UTC 2021

  System load:  0.0                Processes:           104
  Usage of /:   2.0% of 116.27GB   Users logged in:     0
  Memory usage: 4%                 IP address for eth0: 10.0.0.214
  Swap usage:   0%


 * Canonical Livepatch is available for installation.
   - Reduce system reboots and improve kernel security. Activate at:
     https://ubuntu.com/livepatch

9 packages can be updated.
0 updates are security updates.


Last login: Tue Sep 22 19:26:19 2020 from 108.26.205.225
ubuntu@ip-10-0-0-214:~$ cd /opt/virtuoso/database
ubuntu@ip-10-0-0-214:/opt/virtuoso/database$ sudo bash
root@ip-10-0-0-214:/opt/virtuoso/database# cat .initial-password 
i-0343ad51fe5e4f196
root@ip-10-0-0-214:/opt/virtuoso/database# service virtuoso status
● virtuoso.service - OpenLink Virtuoso Database
   Loaded: loaded (/lib/systemd/system/virtuoso.service; enabled; vendor preset: enabled)
   Active: active (running) since Fri 2021-01-29 12:04:31 UTC; 38min ago
  Process: 878 ExecStart=/opt/virtuoso/bin/virtuoso-start.sh $VIRTUOSO_DB_NAMES (code=exited, status=0/SUC
 Main PID: 1170 (virtuoso)
    Tasks: 15 (limit: 4915)
   CGroup: /system.slice/virtuoso.service
           └─1170 ./virtuoso

Jan 29 12:04:25 ip-10-0-0-214 systemd[1]: Starting OpenLink Virtuoso Database...
Jan 29 12:04:26 ip-10-0-0-214 virtuoso-start.sh[878]: Starting Virtuoso instance in [database]
Jan 29 12:04:26 ip-10-0-0-214 virtuoso-start.sh[878]:   - Starting the database
Jan 29 12:04:31 ip-10-0-0-214 systemd[1]: Started OpenLink Virtuoso Database.
root@ip-10-0-0-214:/opt/virtuoso/database# /opt/virtuoso/bin/isql 1111
OpenLink Virtuoso Interactive SQL (Virtuoso)
Version 08.03.3323 as of Apr 19 2022
Type HELP; for help and EXIT; to exit.

Enter password for dba :
Connected to OpenLink Virtuoso
Driver: 08.03.3323 OpenLink Virtuoso ODBC Driver
SQL> status('');
REPORT
VARCHAR
_______________________________________________________________________________

OpenLink Virtuoso VDB Server
Version 08.03.3323-pthreads for Linux as of Apr 19 2022 
Started on: 2021-01-29 12:45 GMT+0
CPU: 0.05% RSS: 148MB PF: 0

Database Status:
  File size 67108864, 8192 pages, 5733 free.
  20000 buffers, 1115 used, 85 dirty 0 wired down, repl age 0 0 w. io 0 w/crsr.
  Disk Usage: 1074 reads avg 0 msec, 0% r 0% w last  23 s, 138 writes flush          0 MB/s,
    34 read ahead, batch = 17.  Autocompact 0 in 0 out, 0% saved.
Gate:  166 2nd in reads, 0 gate write waits, 0 in while read 0 busy scrap. 
Log = virtuoso.trx, 8325 bytes
VDB: 0 exec 0 fetch 0 transact 0 error
2309 pages have been changed since last backup (in checkpoint state)
Current backup timestamp: 0x0000-0x00-0x00
Last backup date: unknown
Clients: 1 connects, max 1 concurrent
RPC: 6 calls, 1 pending, 1 max until now, 0 queued, 0 burst reads (0%), 0 second 0M large, 10M max
Checkpoint Remap 38 pages, 0 mapped back. 0 s atomic time.
    DB master 8192 total 5733 free 38 remap 1 mapped back
   temp  256 total 251 free

Lock Status: 0 deadlocks of which 0 2r1w, 0 waits,
   Currently 1 threads running 0 threads waiting 0 threads in vdb.

24 Rows. -- 2 msec.
SQL>

Performance Notes

There are a range of AWS VM instance types with different system memory and CPU combinations. Collectively, the factors above affect the performance of your Virtuoso instance. Thus, use AWS VM Instance Type s with more memory and CPU cores for best performance.

Note: This VM is configured to use minimal system memory. For the instance type chosen, the NumberOfBuffer and MaxDirtyBuffers parameters in the /opt/virtuoso/database/virtuoso.ini configuration file should be increased to match the available memory, as detailed in the Virtuoso Performance Tuning Guide , for example —

VM Instance Type	System RAM	`NumberOfBuffers`	`MaxDirtyBuffers`
`m5.large`	8 GB	`680000`	`500000`
`m5.xlarge`	16 GB	`1360000`	`1000000`
`m5.2xlarge`	32 GB	`2720000`	`2000000`
`m5.4xlarge`	64 GB	`5450000`	`4000000`
`r6i.4xlarge`	128 GB	`10900000`	`8000000`

– and restart the Virtuoso server as detailed above.

Extrapolate the NumberOfBuffers and MaxDirtyBuffers parameters accordingly for different sized VMs.

Troubleshooting

If the Virtuoso server fails to start:

Run the command sudo service virtuoso status to see if the Virtuoso server is running
Check the /opt/virtuoso/database/virtuoso.log file to see why the server might have failed to start
Ensure the file /opt/virtuoso/database/virtuoso.lck does not exist before starting the server
Attempt to start the Virtuoso server with the command sudo service virtuoso start
Run the command sudo service virtuoso status again to see if the Virtuoso server is running
If it is now running, attempt a connect via the SQL or HTTP interfaces as detailed above