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Indiana University

The Research Database Complex (RDC) at Indiana University

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System overview


The Indiana University Research Database Complex (rdc.uits.iu.edu) supports research-related databases and data-intensive applications that require databases. The RDC supports Oracle and MySQL databases, and provides an environment (rdcweb.uits.iu.edu) for database-driven web applications focusing on research.

The system runs Red Hat Enterprise Linux 5 (RHEL 5). User home directories reside on a network-attached storage (NAS) device. You have a 100 GB (default) disk quota, which is shared with Big Red II, Karst, Quarry, and Mason, if you have accounts on those systems.

Note: The RDC is strictly devoted to supporting research; it is not an instructional or classroom environment. If you need to use Oracle or Microsoft SQL Server in an instructional environment, see Database and web server access for instruction.

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Databases

The RDC offers Oracle 11g Release 2 (version 11.2.0.2) and MySQL Enterprise Server (version 5.5.8 Advanced) database accounts, with a full suite of Oracle components that support:

Content management

  • Advanced Security Option (ASO): Provides data encryption and strong authentication services to the Oracle database

  • Application Express: Offers development and deployment of secure applications through a rapid, web-application development tool for use with Oracle databases

  • Large objects (LOBs): Lets you store and manipulate large blocks of unstructured data, such as text, graphic images, video clips, and sound waveforms, in binary or character format

  • Oracle Multimedia (formerly Oracle interMedia): Provides a platform for a wide range of multimedia-intensive applications

  • Oracle Text: Indexes any document or textual content to add fast, accurate retrieval of information to Internet content management applications, e-business catalogs, news services, and job postings; indexes content stored in file systems, databases, or on the web

  • Oracle XML Database: Treats XML as a native datatype in the database

  • Oracle XDK: Contains the basic building blocks for reading, manipulating, transforming, and viewing XML documents, whether on a file system or stored in a database

  • Partitioning: Lets you split large tables and indexes into smaller, manageable components, without requiring changes to underlying applications

Advanced analytics

  • Oracle Data Mining (ODM): Provides a way to access information buried in the data by creating models to find hidden patterns in large, complex collections of data; embeds data mining within the Oracle database; algorithms operate natively on relational tables or views, eliminating the need to extract and transfer data into other tools, applications, or servers

  • Online Analytical Processing (OLAP): Offers in-database, advanced multidimensional analytic capabilities

Java

  • JServer Java Virtual Machine: A Java virtual machine (VM) that runs within the Oracle database server's address space

  • Oracle Database Java Packages: Classes for relational database management system (RDBMS) features

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System information

Note: The RDC maintenance window is the first Tuesday of each month, 8am-5pm. Notice of any emergency downtime will be posted at IT Notices.

System configuration Aggregate information Per-node information
Machine type Research database system  
Operating system Red Hat Enterprise Linux 5 (RHEL 5)  
Memory model Distributed and shared  
Processor cores 36  
CPUs Intel Xeon E5620 2.40 GHz (HP)
Intel Xeon Quad Core 1.6 GHz (Dell)
 
Nodes 3 Hewlett Packard DL 180 G6 Oracle servers
1 Hewlett Packard DL 180 G6 MySQL server
1 Dell 2950 Database Driven Web Services
 
RAM 288 GB 72 GB (HP)
8 GB (Dell)
RPeak 307.2 gigaFLOPS 76.8 gigaFLOPS
Storage information
Database storage and file systems

Note: Before storing data on this system, make sure you understand the information in the Working with ePHI research data section (below).

Oracle and MySQL storage is provided via RAID 6 volumes (block-level striping with double distributed parity) on a fiber channel array, currently 48 TB in size.

Home directories with 100 GB default quotas are provided via NAS over NFS.

Shared scratch space is hosted on the Data Capacitor II (DC2) file system. The DC2 scratch directory is a temporary workspace. Scratch space is not allocated, and its total capacity fluctuates based on project space requirements. The DC2 file system is mounted on IU research systems as /N/dc2/scratch and behaves like any other disk device. If you have an account on an IU research system, you can access /N/dc2/scratch/username (replace username with your IU Network ID username). Access to /N/dc2/projects requires an allocation. For details, see The Data Capacitor II and DC-WAN high-speed file systems at Indiana University. Files in shared scratch space more than 60 days old are periodically purged, following user notification.

Backup and purge policies Incremental backups of the RDC Oracle databases occur at various times between 1am and 6am, Sunday through Friday.

Full backups occur 1am-5am every Saturday. Backups are retained for 30 days.

Backups for MySQL database servers on the RDC are the responsibility of the user.

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Working with ePHI research data

The Health Insurance Portability and Accountability Act of 1996 (HIPAA) established rules protecting the privacy and security of personal health data. The HIPAA Security Rule set national standards specifically for the security of protected health information (PHI) that is created, stored, transmitted, or received electronically (i.e., electronic protected health information, or ePHI). To ensure the confidentiality, integrity, and availability of ePHI data, the HIPAA Security Rule requires organizations and individuals to implement a series of administrative, physical, and technical safeguards when working with ePHI data.

Although you can use this system for processing or storing electronic protected health information (ePHI) related to official IU research:

  • You and/or the project's principal investigator (PI) are responsible for ensuring the privacy and security of that data, and complying with applicable federal and state laws/regulations and institutional policies. IU's policies regarding HIPAA compliance require the appropriate Institutional Review Board (IRB) approvals and a data management plan.

  • You and/or the project's PI are responsible for implementing HIPAA-required administrative, physical, and technical safeguards to any person, process, application, or service used to collect, process, manage, analyze, or store ePHI data.

The UITS Advanced Biomedical IT Core provides consulting and online help for Indiana University researchers who need help securely processing, storing, and sharing ePHI research data. If you need help or have questions about managing HIPAA-regulated data at IU, contact the ABITC. For additional details about HIPAA compliance at IU, see HIPAA & ABITC and the Office of Vice President and General Counsel (OVPGC) HIPAA Privacy & Security page.

Important: Although UITS HIPAA-aligned resources are managed using standards surpassing official standards for managing institutional data at IU and are appropriate for storing HIPAA-regulated ePHI research data, they are not recognized by the IU Committee of Data Stewards as appropriate for storing institutional data elements classified as Critical that are not ePHI data. For help determining which institutional data elements classified as Critical are considered ePHI, see Which data elements in the classifications of institutional data are considered protected health information (PHI)?

The IU Committee of Data Stewards and the University Information Policy Office (UIPO) set official classification levels and data management standards for institutional data in accordance with the university's Management of Institutional Data policy. If you have questions about the classifications of institutional data, contact the appropriate Data Steward. To determine the most sensitive classification of institutional data you can store on any given UITS service, see the "Choosing an appropriate storage solution" section of At IU, which dedicated file storage services and IT services with storage components are appropriate for sensitive institutional data, including ePHI research data?

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System access

Requesting an RDC account

To request an account on an Indiana University research system, use the Account Management Service (AMS); see At IU, if I already have some computing accounts, how do I get others? Account availability depends on your eligibility. For eligibility information, see the "Research system accounts (all campuses)" section in What computing accounts are available at IU, and for whom?

You will receive confirmation in email when your RDC account is created.

Requesting an RDC database account

Your RDC account confirmation message will direct you to the RDC Database and Web Services Account Application for requesting an RDC database account.

Note: You can request a group RDC database account if your group has an established IU group account username, but you must provide the IU Network ID usernames of everyone who will be permitted to use the group database account. The person requesting the group database account will be considered the owner and responsible party for the account, and is expected to communicate system downtimes and other system information to the group.

You will receive confirmation in email when your database schema, instance, or server has been created. The confirmation notice ("Oracle/MySQL Welcome Letter") will include your database login credentials and information about connecting to your database. UITS recommends saving your "Oracle/MySQL Welcome Letter" so you can refer to it if you forget the database password. Otherwise, you will need to contact the UITS High Performance Systems (HPS) team to have your database password reset.

Connecting to your RDC database

For instructions on connecting to your RDC database, see On the Research Database Complex at IU, how do I access my Oracle or MySQL database?

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Computing environment

The Bash shell

By default, new accounts on the RDC are assigned the Bourne-again shell (i.e., the Bash shell). When you log in, the Bash shell reads and executes commands from the following startup files (in this order):

/etc/profile ~/.bash_profile ~/.bashrc

When you log out, the Bash shell reads and executes commands from ~/.bash_logout.

Note: The ~ (tilde) represents your home directory (e.g., ~/.bash_profile is the .bash_profile file in your home directory).

In the Bash shell:

  • To display the value of an environment variable, on the command line, enter: echo $VARNAME

    Replace VARNAME with the name of an environment variable (e.g., PATH).

  • To temporarily change the value of an environment variable and make programs that use the variable aware of the new value, on the command-line, enter: export VARNAME=VALUE

    Replace VARNAME with the name of an environment variable (e.g., EDITOR) and replace VALUE with the desired value (e.g., vi). The value will remain changed until you log out from the system or exit the shell.

  • To permanently change the value of an environment variable, add the export VARNAME=VALUE line to your ~/.bash_profile file.

    For example, to make vi your default text editor, add this line to your ~/.bash_profile file:

    export EDITOR=vi

    After you save and exit ~/.bash_profile, the new environment variable will take effect the next time you log into the system. To make your change take effect immediately, on the command line, enter:

    source ~/.bash_profile

For more about the Bash shell, see the Bash Reference Manual, or to view the bash manual page, on the command line, enter:

man bash

Changing your shell

In addition to the Bash shell, the RDC supports the TC (tcsh), C (csh), Korn (ksh), and Bourne (sh) shells. To change your shell on the RDC, use the chsh or changeshell command:

Command Function
chsh Changes your shell only on the node on which you run it, and leaves the other nodes of the cluster unchanged
changeshell Prompts you with the shells available on the system, and changes your login shell system-wide within 15 minutes

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Transferring your files to the RDC

The RDC supports SCP and SFTP for transferring files:

  • SCP: This command-line utility is included with OpenSSH. Basic use is: scp username@host1:~/file1 username@host2:~/file1_copy

    For example, to copy a file from your home directory on your local computer (e.g., ~/foo.txt) to your home directory on the RDC, on the command line, enter (replace username with your IU Network ID username):

    scp ~/foo.txt username@rdc.uits.iu.edu:~/foo.txt

    For more, see In Unix, how do I use SCP to securely transfer files between two computers?

  • SFTP: Use a command-line or graphical SFTP client to access, transfer, and manage your RDC files.

    For example, to transfer a file using command-line SFTP from your home directory on your local computer (e.g., ~/foo.txt) to your home directory on the RDC, on the command line, enter (replace username with your IU Network ID username; at the password prompt, enter your Network ID passphrase):

    $ sftp username@rdc.uits.iu.edu username@rdc.uits.iu.edu's password: Connected to rdc.uits.iu.edu. sftp> put ~/foo.txt Uploading foo.txt to /N/hd02/username/RDC/foo.txt foo.txt 100% 43MB 76.9KB/s 09:39 sftp> exit

    For more, see What is SFTP, and how do I use an SFTP client to transfer files?

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Application development

In addition to hosting research databases, the RDC provides an environment for developing database-driven web applications with a research focus. For details, see Web Services on the IU Research Database Complex.

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Reference

Oracle: For further documentation, see the Oracle Database Documentation Library, 11g Release 2 (11.2), and the following online guides:

MySQL: For further documentation, see the MySQL Reference Manual.

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Policies

The RDC is strictly devoted to supporting research. The RDC is not an instructional, classroom environment. If you are not doing research and wish to use a database, such as Oracle or Microsoft SQL Server, see Database and web server access for instruction.

For RDC usage policies, including information about your responsibilities for maintaining database security and acknowledging grant support, see Research Database Complex (RDC) usage policies.

Support

Support for research computing systems at Indiana University is provided by various units within the Systems area of the Research Technologies division of UITS:

To ask any other question about Research Technologies systems and services, use the Request help or information form.

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