The easiest way to get started with SciDB is using Amazon Web Services (AWS). There are multiple SciDB Amazon Machine Images (AMI) provided by Paradigm4 (the company behind SciDB). For each AMI, the type of Amazon Elastic Cloud Compute (EC2) instance recommended by Paradigm4 is pretty beefy. We recommend following the Paradigm44 instructions. The EC2 instances can be easily stopped or terminated from the EC2 Instances page.
Available SciDB AMIs
The official Paradigm4 SciDB AMIs for different SciDB versions are listed below. For each, we provide a link to the EC2 Images search page on AWS. These links require a valid AWS account.
|Version||Release Month||Docs||Name||AMI ID||AMI||Quick Start|
|15.12||Apr ‘16||Docs||SciDB 15.12 Bioinformatics and Finance||
||AMI||Available on request1|
|15.7||Aug ‘15||Docs||No AMI available|
|14.12||Jan ‘15||Docs||SciDB 14.12 + shim + SciDBR + SciDBPy + IPython Notebook||
|Quick Start (Sec.2)|
||AMI||Quick Start2 (Sec.2.2)|
|13.12||Jan ‘14||Docs||Scidb 13.12 Quick Start image||
||AMI||Quick Start (Sec.2.2)|
Additionally, you can see a list of all AMI with SciDB in their name by using AMI Name
SciDB as search criteria (AMIs ). Use with caution. Below is a screenshot of the EC2 Images result list.
SciDB 15.12 AMI
Let’s take a look at the AMI provided for SciDB 15.12. The Quick Start guide is not directly available. Interested parties have to contact Paradigm4 in order to obtain it.
When the AMI is started, SciDB, Shim, RStudio, and Jupyter are also started. Shim is a simple HTTP client which allows you to run queries against SciDB from the web browser. It also has a Dashboard page listing the SciDB instances. Shim starts on port
8080. Below is a screenshot of Shim running on the AMI.
RStudio starts on port
8787. There are quite a few examples of using SciDB from R provided with the AMI. Below is a screenshot of RStudio running on the AMI.
Finally, Jupyter (IPython) starts on port
8888. Provided with the AMI is an example of financial data analysis. In order to access this example you have to first remote-login on the instance and run:
sudo cp -r ~scidb_finance/TAQ ~scidb_bio/ sudo chown -R scidb_bio:scidb_bio ~scidb_bio/TAQ
These two commands copy the example files from the
scidb_finance account into the
scidb_bio account and set their ownership to
scidb_bio. This is required because the Jupyter service starts under the
scidb_bio account. Below is a screenshot of Jupyter running on the AMI.