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UITS Research Technologies

Cyberinfrastructure enabling research and creative activities

The Research Database Complex (RDC) at Indiana University

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System overview

The Indiana University Research Database Complex supports research-related databases and data-intensive applications that require databases. The RDC supports MySQL and Oracle databases, and provides an environment 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 your accounts on IU's research computing systems.

The RDC is strictly devoted to supporting research; it is not an instructional or classroom environment.


The RDC offers the following database accounts:

  • MySQL: The RDC supports MySQL Enterprise Server (version 5.5.8 Advanced). Access to phpMyAdmin is created for you by default.
  • Oracle: MySQL can meet the majority of database needs. However, if your research has an immediate requirement for specific functionality in Oracle, you may request to be considered for an Oracle database account (Oracle Database 11g Enterprise Edition Release - 64bit Production). To do so, follow the instructions in the RDC Database and Web Services Account Application.

System information

Note: The RDC maintenance window is the first Tuesday of each month, 7am-7pm. Notice of any emergency downtime will be posted at Status.IU.

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

Before storing data on this system, make sure you understand the information in the Working with data containing PHI section (below).

Database storage and file systems

MySQL and Oracle 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-WAN2 high-speed file systems at Indiana University. Files in shared scratch space may be purged if they have not been accessed for more than 60 days.

Backup and purge policies

RDC MySQL database account owners are responsible for creating backups of their databases.

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.

Working with data containing PHI

The Health Insurance Portability and Accountability Act of 1996 (HIPAA) established rules protecting the privacy and security of individually identifiable health information. The HIPAA Privacy Rule and Security Rule set national standards requiring organizations and individuals to implement certain administrative, physical, and technical safeguards to maintain the confidentiality, integrity, and availability of protected health information (PHI).

This system meets certain requirements established in the HIPAA Security Rule that enable its use for research involving data that contain protected health information (PHI). You may use this resource for research involving data that contain PHI only if you institute additional administrative, physical, and technical safeguards that complement those UITS already has in place.

Although PHI is one type of institutional data classified as Critical at IU, other types of institutional data classified as Critical are not permitted on Research Technologies systems. For help determining which institutional data elements classified as Critical are considered PHI, see Which data elements in the classifications of institutional data are considered protected health information (PHI)?

For more, see When using UITS Research Technologies systems and services, what are my legal responsibilities for protecting the privacy and security of data containing protected health information (PHI)?

If you need help or have questions, contact UITS HIPAA Consulting.

System access

Requesting an RDC account

To request an account on an Indiana University research system, see At IU, if I already have some computing accounts, how do I get others? Account availability depends on your eligibility.

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 Applicationfor requesting an RDC database account.

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 a message in email confirming the creation of your database schema, instance, or server. This "RDC Welcome Letter" will include your database login credentials and information about connecting to your database. UITS recommends saving this email message for future reference (e.g., in case you forget the database password; otherwise, you would need to contact the UITS High Performance Systems 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 MySQL database?

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):


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

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

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

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

    For enhanced security, SSH connections that have been idle for 60 minutes will be disconnected. To protect your data from misuse, remember to log off or lock your computer whenever you leave it.
  • 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's password:
      Connected to
      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 it to transfer files?

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.


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.


The RDC is strictly devoted to supporting research. The RDC is not an instructional, classroom environment.

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 for IU research computing systems, software, and services is provided by various UITS Research Technologies units. For help, see Research computing support at IU.