NIDB is easy to install. Most of the installation steps are automated, if you install on CentOS 6.3. You are welcome to try to install NIDB on something other than CentOS 6.3, but it may not work the way you anticipate.

There are two installation routes: virtual machine and physical server. A working virtual machine is available for download, but the steps used to create that VM are available if you want to try it on your own. A physical server is recommended so you can manage the storage space.

Virtual Machine (optional)

Using Oracle VM VirtualBox, create a virtual machine for Linux->Redhat 64-bit, with the following settings:

Memory → 1024MB
Disk Space → at least 10GB
Video memory → 128MB
Extended Features → Enable 3D Acceleration
Network → Bridged Adapter

Server Hardware (Requirements)

NIDB should be run on a dedicated server. It can work fine on any environment, but to handle heavy loads, its ideal to give NIDB its own server. This doesn’t mean you need to go out and buy a $10,000 server to store 100 subjects! You can install CentOS 6.3 on any Intel compatible hardware, including an old desktop PC. NIDB will run just fine on a desktop PC, or even a laptop.

Performance of the system will be better if you use better hardware, but it will still work just fine if you have a small workload. ONRC currently use mirrored Silicon Mechanics servers. Each has 12GB RAM, dual 8-core Xeon processors, and 40TB of continuous disk space formatted with XFS filesystem. This serves 6TB of raw data to 50+ users. More RAM, more and faster cores will give you better performance. You should also use local storage for the data, or at least an NFS or other network mount.

Operating System

Download CentOS 6.3 and start a graphical installation.

  1. At the CentOS 6 welcome screen, click Next
  2. Choose your language, click Next
  3. Choose your keyboard layout, click Next
  4. Configure storage devices. NIDB expects a contiguous storage volume to store the data archive. It is not possible to break up this archive over multiple volumes. Click Next and follow the instructions to setup your storage.
  5. Choose the hostname. Then click Configure Network. Select your Wired (or Wireless) connection (probably System eth0), click Edit…. Edit your network connection to configure a static IP if you have one, and make sure to check off Connect automatically. Click Apply… then Close, and then click Next
  6. Choose your timezone, click Next
  7. Enter your root password, click Next
  8. You probably want to choose Use All Space as the installation type, unless you have some specific configuration you want to use for your system. Click Next
  9. The installer will then create the partitions and storage and may prompt you to confirm
  10. Select the Desktop installation. Select Customize Now, click Next
    1. Under the Databases tab, check off MySQL client and MySQL server. And for each of those, click the Optional packages button and then check off all of the available packages.
    2. Under the Development tab, check off the following (No need to click the Optional packages button for these)
      1. Additional Development
      2. Desktop Platform Development
      3. Development tools
      4. Server Platform Development
    3. Under the Web Services tab, check off PHP Support and Webserver, click the Optional packages button and check off all available packages for both PHP Support and Webserver
  11. Then click Next, and the installer will install all the packages and ask you to reboot the system. Click Reboot

Upon reboot, it will ask for some configuration options. At the Create User screen, create an an account called ‘nidb’, with password ‘password’. NIDB can authenticate using NIS. If you want to authenticate using Linux logins, setup the authentication methods by clicking the Use Network Login… button. Continue the configuration, and it will eventually display the login screen.

OS Installation Notes

  1. You’re welcome to choose any of the  install types: Desktop, Minimal, Database servers, etc. However you must make sure the necessary packages are installed. Since the above install path is the only one tested, and an exact package list is not provided other than the groups specified, you may end up installing packages by trial and error.
  2. The development options are included to allow the recompilation of certain image processing packages to include non-standard options, such as including fft support in ImageMagick.

NIDB Installation

Your server must be able to access the internet to install NIDB!

As root, run the following (replace the NIDBx.y.z with the latest version number such 4.1.4)

> su
> wget
> tar -xvzf nidb.tar.gz
> cd installer
> ./

Follow the prompts on the screen. It will ask for your input a few times. A program called CPAN will ask you for confirmation to continue. Just hit <enter> to continue. It will later ask you for a password for the ‘nidb’ account. It will also ask you to do some system administration tasks by visiting the Webmin page on the server. Follow all the directions until the end.

The following modules are disabled by default because they depend on FSL and they’ll fail every time cron starts them until you install FSL on the system.

  • mriqa
  • mristudyqa

To enable those modules, you’ll need to install FSL. This is not included with this installer because the FSL download is more than 1GB in size… and I’m sure the FSL folks would like to know who is downloading their software. Install FSL to the default path /usr/local .

Once FSL is installed, enable the modules in cron by opening Webmin (https://hostname:10000), go to the System tab on the left, click Scheduled Cron Jobs. A list of cron jobs will be displayed. Select the two jobs starting with “FSLDIR=…” and “DISPLAY=…” and click Enable Selected Jobs.

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