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Centos is an open-source version of a Redhat linux enterprise server operating system. The page describes creating a new virtual machine with Centos 7. The advantage of Centos 7 over earlier versions is some level of support for parallel processing, which FSL or FreeSurfer may take advantage of. The GUI has changed quite a bit from Centos 6.

Note: VM = virtual machine.

First Steps

  • Install VMware Workstation (not player); this usually requires a restart.
  • (probably not needed from 2019) Enable Intel Virtualization in the BIOS; this is required to run a 64-bit VM.
  • Download the standard Centos 7 DVD image (*.iso file); do not use the minimal *.iso image. Save this so it's visible to the computer where you will be running the installation.
  • Decided on a name for the VM (e.g., Linux7VM), a user long name, a user name for use in Linux ("user" as of 2013), and a password. These should be pretty generic as many people will use the VM.
  • Start Workstation and create a new VM. Follow the instructions, usually choosing the default options. The virtual disk size should be increased to a few 100 GB (e.g., 300; this will not take up physical space until required).
  • Edit the VM settings in Workstation to set the max memory so something like 8GB minimum, add some processors, and enable shared folders, with a "LinuxShare." (All of these can easily be changed later.)

Network

  • Edit the virtual machine settings and set the network to "Bridged" - theoretically "NAT" should work, but it does not (2019-08-06)
  • In Linux, go to the Network in Settings, and turn on the "Wired" network:

 

Updates

  • Got to Software updates

  • Update everything

Customizing

  • Click yellow "updates" icon on right top bar, and install all updates; turn update check to off (since it will later not be connected to the network).
  • In VMware settings, set time to sync with host and update VMware tools

  • Remove Email and Notes icons from top bar.
  • Add a terminal icon to to Desktop and top bar; drag from Applications => System Tools menu

  • Remove any software not needed (System => Administration => Add/Remove Software).
  • Note this menu includes an "Update Software" entry, to manually update software when the VM is temporarily connected to the network.
  • Add gedit and File Browser icons to Desktop (Under System submenus).
  • Open the File Browser, navigate to /mnt/hgfs/LinuxShare, and add as a bookmark (Bookmark => Add Bookmark); you will now be able to nativage there direction from the File Browser, and from under the "Places" top bar menu.
    • If LinuxShare does not appear, reinstall VMtools by selecting this option from the Workstation menu, and running through the steps within Linux (copy DVD files to temp folder, unpack (tar xvzf ...), and run script within folder created).
  • Turn off the screensaver and screensaver lock: System => Preferences => Background.
  • Change the default login to tsch: System => Administration => Users and Groups; enter the password, select user, and change the login shell to "/bin/tcsh".
  • To allow "sudo" commands, edit the /etc/sudoers file with EDITOR=nano visudo; add the user by entering another line in the "MACHINE=COMMANDS" section:

  • To allow normal users to install software (FSL, FreeSurfer), change the permissions on the /usr/local folder to allow writing: su, cd /usr, chmod 777 local

After Installing FSL and FreeSurfer

Reset the network connection to Host-only, under the VM Settings in Workstation (VM => Settings => Harware, Network adapter). If you want to run updates, change temporarily to NAT. You will likely need to edit the connection settings when you change back to Host-only


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