The Research Database Complex (RDC) at Indiana University
On this page:
- System overview
- System information
- Storage information
- Working with data containing PHI
- System access
- Computing environment
- Transferring your files to the RDC
- Application development
The Indiana University Research Database Complex
rdc.uits.iu.edu) supports research-related databases and
data-intensive applications that require databases. The RDC supports
MySQL and Oracle 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, 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.
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. See the RDC Home Page for an overview of the RDC and information to help you get started.
- 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 126.96.36.199 - 64bit Production). To do so, follow the instructions in the RDC Database and Web Services Account Application.
The RDC offers a full suite of Oracle components that support:
- 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
- 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
- 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
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|
|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|
Note: 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
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 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 physical, administrative, and technical safeguards that complement those UITS already has in place. 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? If you need help or have questions, contact UITS HIPAA Consulting.
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 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 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?
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
~ (tilde) represents your home
~/.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,
VARNAMEwith the name of an environment variable (e.g.,
- 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,
VARNAMEwith the name of an environment variable (e.g.,
EDITOR) and replace
VALUEwith 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=VALUEline to your
For example, to make
viyour default text editor, add this line to your
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:
Changing your shell
In addition to the Bash shell, the RDC supports the TC (
tcsh), C (
csh), Korn (
and Bourne (
sh) shells. To change your shell on the
RDC, use the
||Changes your shell only on the node on which you run it, and leaves the other nodes of the cluster unchanged|
||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
- 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
usernamewith your IU Network ID username):
scp ~/foo.txt email@example.com:~/foo.txt
- 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
usernamewith your IU Network ID username; at the
passwordprompt, enter your Network ID passphrase):
$ sftp firstname.lastname@example.org email@example.com'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 it to transfer files?
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:
- Oracle Database New Features Guide
- Oracle Database Concepts
- Oracle Database Online Documentation Library Master Glossary
- Advanced Application Developer's Guide
- Oracle Database Reference
- SQL Language Reference
- PL/SQL Language Reference
- Application Express (ApEx) Documentation
- ApEx Developer's Guide
- ApEx Application Builder User's Guide
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. 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.
- If you have a system-specific question about Big Red II, Karst, Mason, or the Research Database Complex (RDC), contact the High Performance Systems (HPS) team.
- If you have questions about the Research File System (RFS) or Scholarly Data Archive (SDA), contact the Research Storage team.
- If you have questions about shared scratch or project space on the Data Capacitor II or Data Capacitor Wide Area Network (DC-WAN) file system, contact the High Performance File Systems (HPFS) unit.
- If you have questions about the development tools, compilers, scientific or numerical libraries, or debuggers available on the research computing system, email the Scientific Applications and Performance Tuning (SciAPT) team.
- If you have questions about the statistical and mathematical applications available on the research computing systems, email the Research Analytics group.
- If you have questions about the bioinformatics and genome analysis packages available on the research computing systems, email the National Center for Genome Analysis Support (NCGAS).
For general inquiries about UITS Research Technologies systems and services, use this form to request help or information from Research Technologies.
This is document amuw in the Knowledge Base.
Last modified on 2015-11-17.
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