DBpedia Live (Virtuoso PAGO) EBS-backed EC2 AMI

Introduction
Prerequisites
Instantiating DBpedia Live (Virtuoso PAGO) via Web Interface
First-time Setup & Usage Notes
DBpedia Snapshot (Virtuoso PAGO) Database Interaction via Web Interface
Administering the Virtuoso Instance via SSH
Performance Notes
Troubleshooting
Related Items

Introduction

In addition to the Instance-backed EC2 AMI that has been available since 2008, a standard unpopulated Virtuoso instance is available as an EBS-backed EC2 AMI based on either a BYOL (Bring Your Own License) or a PAGO (Pay As You Go) basis. In each case, the AMI delivers a preconfigured Virtuoso instance.

We also now offer two PAGO variants, each pre-loaded with a DBpedia dataset.

The DBpedia Snapshot (Virtuoso PAGO) (documented on this page) starts as a static instance, preloaded with the DBpedia 2021-09 dataset, mirroring the public DBpedia instance found at OpenLink Virtuoso SPARQL Query Editor. You can make changes to this data, but it will not track changes made to Wikipedia nor DBpedia-Live.

The DBpedia Live (Virtuoso PAGO) (documented on this page) starts as a static instance, preloaded with the DBpedia 2016-04 dataset, and includes an optional switch that enables data updates based on the Wikipedia firehose, effectively giving you a mirror of the public DBpedia-Live instance found at http://live.dbpedia.org/sparql.

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.)
DBpedia Dataset is preloaded and preconfigured (and may be configurable to auto-update).
You can start and stop the DBpedia instance without having to terminate its host AMI.
With the hourly model, you pay only for the time the AMI is used.

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 DBpedia Live (Virtuoso PAGO) via Web Interface

Locate the DBpedia 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 Launch button.
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 not 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 DBpedia dataset, which takes significant time to start due to some Amazon requirements for such AWS instances.

ssh into your instantiated AMI using:


ssh -i {secure-pem-file} ubuntu@{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.
1. 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
```
2. Load the Conductor interface
```
http://{amazon-ec2-ami-dns-name-or-ip-address}/conductor
```
3. 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 create a Support Case for fastest assistance.
4. Drill down to System Admin → User Accounts.
5. Locate the dba user, and click the associated Edit link.
6. 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.
7. You can now perform other administrative tasks through the Conductor interface, or return to basic DBpedia use.

DBpedia Snapshot (Virtuoso PAGO) Database Interaction via Web Interface

Once online, your DBpedia Live instance will be ready for use from —

Basic Linked Data Exploration Page — an obvious starting point


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

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:
1. Start the Virtuoso Server:
```
    sudo service virtuoso start
```
2. Stop the Virtuoso Server:
```
   sudo service virtuoso stop
```
3. Restart the Virtuoso Server:
```
    sudo service virtuoso restart
```
4. 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 08.03.3319 as of Sep  1 2020
Type HELP; for help and EXIT; to exit.

Enter password for dba :
Connected to OpenLink Virtuoso
Driver: 08.03.3319 OpenLink Virtuoso ODBC Driver
SQL> status('');
REPORT
VARCHAR
_______________________________________________________________________________

OpenLink Virtuoso VDB Server
Version 08.03.3319-pthreads for Linux as of Sep  1 2020 
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

Please be aware of the following, which impact the performance and utility of your AMI:

This AMI includes a bundled Virtuoso license which enables 10 Database Sessions and the use of 4 logical processors. Licenses that upgrade these attributes are available as paid upgrade options.

Virtuoso always takes full advantage of the memory it's configured to use. This may be much less than is found in its host environment/AMI. This AMI is pre-configured for an m5.xlarge EC2 Instance Type, so will use 16GB or RAM. If you choose a larger EC2 Instance Type, then the NumberOfBuffer and MaxDirtyBuffers parameters in the /opt/virtuoso/database/virtuoso.ini configuration file should be increased to correspond to the chosen Instance Type's available memory, as detailed in the Virtuoso Performance Tuning Guide. A few examples are shown below. After changing these or any other settings in the INI file, restart the Virtuoso server as described above.

EC2 Instance Type	System RAM	NumberOfBuffers?	MaxDirtyBuffers?
m5.xlarge	16 GB	1360000	1000000
m5.2xlarge	32 GB	2720000	2000000
m5.4xlarge	64 GB	5440000	4000000
m5.8xlarge	128 GB	10880000	8000000

There are a wide range of AMI choices, offering various combinations of system memory and logical processors. To improve performance, use an EC2 Instance Type with more memory and more logical processors. To make use of additional processors, you will need to also acquire an upgraded Virtuoso license.

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