Running
PHENIX under Windows via a Virtual Machine running Linux
Mike Blaber 08/22/10
I wanted to try to run PHENIX
(Linux-based) under Windows. There were
three different Virtual Machine (VM) programs I tried: 1) Oracle VM Virtual
Box, 2) Micosoft Virtual PC 2007 and 3) VMware
Player. I initially worked with Oracle
VM Virtual Box. It installed and I was
able to run and load CCP4, COOT and PHENIX.
These programs worked on the VM; however, the COOT window was
infrequently updated and had issues with incorrectly displaying menu items,
etc., due to this issue. I was working
around the problem by using a working directory that was a shared folder
between the Linux and Windows OS’s, then running COOT under Windows. This was O.K., but I decided to try other VM
programs to see if the problem was universal.
Next I tried Microsoft’s Virtual PC 2007 (this is for non Windows 7
computers). I had problems in installing
a VM with this program; also, the control of the mouse pointer was awkward (the
mouse pointer was not released from the Linux window unless you used a
particular key-stroke combination). Then I tried VMware Player and this seemed
to have the fewest problems, and also displayed and updated the COOT window
correctly under Linux. Here is the installation
process I followed (using Ubuntu 10.04 version of Linux):
Procedure (Note: all software is free)
1. Download Ubuntu (www.ubuntu.com) (free Linux operating system)
a. This will be an "ISO" file
that you need to burn to disk (CD)
b. Ubuntu 10.04 was the version I used
(8/22/10)
c. Download InfraRecorder (free) to enable
burning of ISO files (http://infrarecorder.org/)
d. Burn Ubuntu onto CDROM using the
installed InfraRecorder software
2. Download free VMware Player software at
http://www.vmware.com/products/player/overview.html
3. Install
a. Put the Ubuntu diskette into the CDROM
b. Create a new virtual machine
c. Select the CDROM that will load the
Ubuntu OS (should be automatically detected)
d. Should say Ubuntu detected and "this
operating system will use Easy Install"
e. Enter full name, user name, and
password
f. Select virtual machine name and
location (note: location should be on the local machine and not a network drive
– too slow otherwise)
g. Select max disk size of 100 GB
h. Store virtual disk as single file
i. Customize hardware:
i. Memory size (1.5 GB)
ii. Processor cores (2)
iii. Display – accelerate 3D graphics
j. Power on virtual machine after creation
k. Finish
4. First time power up
a. Ubuntu installs. VM reboots
b. VMware Tools should install
automatically (provides capability for shared folders, and installs a SVGA
driver for improved video performance).
The installation screen pauses and states the VMware Tools are being
installed. This package can be installed
later if it is not installed now (it is installed as part of the "Easy
Install" process)
c. Ubuntu login window appears. Login with the password you set up earlier.
d. Check the time (upper right). Click "Locations" then edit if the
time is incorrect
e. Lower left may indicate update manager
has updated files to install. Click
& update files as necessary.
i. Note: had some issue about installing "Grub",
but chose option to continue without installation of this package
f. Shut down the Linux VM
5. Setting up shared folders
a. Create a folder in Windows (e.g.
C:\windbuntu)
i. Permit sharing permission on this
folder
b. Start VMware Player
c. Select Ubuntu VM (don’t start it
though)
d. Select "Options" tab
i. Click on "Shared folders"
ii. Click on "Always enable" on
the folder sharing window on the right
iii. Add the path to the shared folder on
Windows (e.g. C:\winbuntu)
iv. Click next, click "enable this
share". Click finish
e. Start the Linux VM
f. Note: the shared folder should be in
/mnt/hgfs
g. If the shared folder is not visible,
maybe the VMware Tools was not installed (or it was an old version). Click Virtual Machine at very top of window.
Select "Reinstall VMware Tools…"
i. A file browser will open up with a
compressed file (VMwareTools-8.4.3-282343.tar.gz). Right click, select "open with archive
manager"
ii. Click extract (to folder where you have
permission; e.g. create folder:
/user-name/temp)
iii. Open terminal window; go to the folder
you extracted the files to. Type $ sudo ./vmware-install.pl
iv. Restart system after installation
h. Now go to /mnt/hgfs and confirm that
the shared folder is visible
i. Note: if you open a file browser and
drag this folder icon to the left menu, it will be accessible when you click on
"Places" tab on the top of the window
6. CCP4 (NOTE: install CCP4, then COOT,
then PHENIX in this order)
a. Download the CCP4 suite of programs
(enables modeling within PHENIX and modeling with COOT) free from http://www.ccp4.ac.uk/download.php
b. Note: you can either do this from
Windows and save into the winbuntu folder (visible to Ubuntu) or download from
within Ubuntu (either way, download the Linux version)
c. Right click the file and select "open
with archive manager"
d. Extract all files
e. Suggest making a folder /home/user-name/data/ccp4 and either copying
or extracting the files to this folder (where user-name is your user name)
f. Open a terminal window and go to /home/user-name/data/ccp4
g. Then type:
$ ./install.sh
h. Select location to install (accept
default since you have write privileges in this folder)
i. The installation offers to modify the
environment variables to enable running without having to (re)source the
environment variables. Do this.
j. Open a new terminal window and type "ccp4i";
the CCP4 program should run
7. COOT
a. Although the CCP4 package is supposed
to include COOT it doesn’t seem to install a functioning version, so download
appropriate OS version free from http://www.biop.ox.ac.uk/coot/devel/build-info.html
b. For Ubuntu I tried binary-Linux-i686-ubuntu-8.04.4-python-gtk2 (this
worked)
c. Make a directory /home/user-name/data/coot and extract to this
folder
d. Edit /home/user-name/data/ccp4/setup-scripts/sh/ccp4-others.setup to change
the directory that the coot executable is now in (after installing the i686
Ubuntu version). This appears to be
sourced upon opening a terminal window
i. Open a terminal window and type
$ which coot
ii. This should show the correct executable
directory
iii. Type $ coot to try it out (should
execute coot)
8. PHENIX
a. Request a free download password from http://www.phenix-online.org/download/
b. Make directory "phenix" from
the "data" directory.
c. Extract then install to this directory
d. Open terminal window, go to the
/data/phenix/phenix-installer-1.6.4-486 directory
e. Type $ sudo ./install (this will
install in /usr/local/ which requires sudo
permission)
f. Set up sourcing of phenix location by
editing the previously edited ccp4 script:
g. $ gedit
/home/user-name/data/ccp4/setup-scripts/sh/ccp4-others.setup
h. Add ". /usr/local/phenix-1.6.4-486/phenix_env.sh"
at the end
i. Open a new terminal window and start
PHENIX by typing $ phenix
9. Everything should work now. Opening a
terminal window and typing $ phenix will start PHENIX and COOT should load
during refinement
10. NOTE: Phenix uses csh/tcsh commands when running the OMIT MAP wizard (and
possibly other routines). To install csh/tcsh type:
$ sudo apt-get update
$ sudo apt-get install csh