removed old consortium-wiki

-# 3D on Linux

-

-## Stereo (3D) for Structural Biology Workstations

-

-_Last update: October 11, 2013_

-

-Stereo technology has fully transitioned from using CRT monitors with emitters

-and shutter glasses to LCDs with either shutter glasses or passive image

-polarization. Whereas CRT stereo technology sprouted from the demands in

-engineering and research, LCD stereo is being targeted largely towards the

-gaming community. This, combined with the fact that LCD support is relatively

-new to the consumer market, means we can't be certain to what extent the

-stereo LCD technology will develop for Linux research workstation purposes.

-Regardless, we'll continue to test the latest options available and advise

-structural biologists that recognize a benefit in stereo 3D imaging.

-

-### What are our LCD Stereo Options?

-

-There are two recommended stereo LCD configurations. The technology you choose

-is largely dependent on your budget, workstation type (Mac/Linux) and desired

-application support.

-

-

-

-## Active LCD Stereo

-

-Active stereo is provided through LCDs that offer a high refresh rate (120Hz).

-This allows LCDs to provide a similar stereo experience as the old CRTs. And

-like the CRT stereo solution, it requires the purchase of an NVIDIA quadro

-card and an emitter/glasses (the NVIDIA 3D Vision kit). This solution is

-Linux-only.

-

-Nvidia maintains a list of monitors compatible with their 3D Vision

-technology. [Click here to access their list](http://www.nvidia.com/object/3d-

-vision-displays.html "http://www.nvidia.com/object/3d-vision-displays.html" ).

-

-

-### Notes on select 120Hz monitors:

-

- * The [Asus VG278H](http://www.asus.com/Display/LCD_Monitors/VG278H/ "http://www.asus.com/Display/LCD_Monitors/VG278H/" ) and VG236H have been working great for us and are our current recommended monitors.

-

-

-

-### Required graphics cards:

-

- * [NVidia Quadro FX 3700 or higher graphics card](http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html "http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html" ). Linux support requires the card to have a 3-pin DIN output. According to the NVIDIA driver documentation, you can**not** use USB emitters without the 3-pin cable for Linux stereo. The latest NVIDIA drivers are required for the best Linux support. Newest drivers support dual monitors, where one is in 3D and one in 2D.

-

-

-

-### Required emitter/glasses:

-

- * [NVIDIA 3D Vision Kit](http://www.nvidia.com/object/product_GeForce_3D_VisionKit_us.html "http://www.nvidia.com/object/product_GeForce_3D_VisionKit_us.html" )

-

-

-

-## Passive LCD Stereo

-

-Passive LCD monitors superimposes two images onto the same screen through

-different polarizing filters. As each filter passes only that light which is

-similarly polarized and blocks the light polarized in the opposite direction,

-each eye sees a different image. Despite its overall lower cost, passive

-stereo is qualitatively lower quality than the NVIDIA solution and in stereo

-mode, you have half the monitor's vertical resolution available to you due to

-the underlying polarization technology. Because it doesn't require specific

-graphics cards / drivers, this solution is the only viable stereo for Mac

-users.

-

-We don't have much recent experience with passive monitors as most of our

-stereo users on using Linux workstations.

-

-### Available Passive LCD Monitors:

-

- * LG DM2352D-PZ

- * ASUSVG27AH

-

-### Previous Passive LCD Monitor Recommendation:

-

- * [Zalman ZM-M240W](http://www.zalman.com/eng/product/Product_Read.php?Idx=391) \- The Zalman requires software to be explicitly configured to support the monitor. PyMOL and a few other applications do have support (email us for the latest list of SBGrid software with support).

-

-### Required graphics card:

-

- * No special graphics card is required, so you can use this monitor with Macs as well as Linux workstations.

-

-### Required emitter/glasses:

-

- * No emitter is required for passive LCD stereo. Polarized glasses are included with the monitor.

-

-## Can We Stick With CRT?

-

-The problem with CRTs is that they are only available as used/remanufactured

-from 3rd party vendors and the Quadro cards required to drive them are

-becoming increasingly expensive. That said, if you have a CRT monitor (or can

-find one) that's capable of sufficient refresh rates and a Quadro NVIDIA card

-with a 3-pin stereo DIN, you can continue to use them for your stereo needs.

-

-### What you need for CRT stereo:

-

- 1. NVidia Quadro FX 3700 graphics card or one of the cards in their “Ultra-High-End” product line. Or, if you search for older models, any Quadro FX with the 3-pin Mini DIN stereo output.

- 2. CRT display capable of at least 100Hz refresh rate @ 1280×1024+. These are becoming very hard to find. The latest model we saw produced with these specs was the ViewSonic G225fB, but it is no longer available. Try searching eBay for ”[SGI 061-0061-001](http://shop.ebay.com/?_nkw=sgi+061-0061-001)”. Visit <http://pymol.sourceforge.net/stereo3d.html> for some more recommendations. Note that at this point, if a CRT has problems or fails, it may be very difficult to replace or repair.

- 3. CRT Stereo emitter and glasses ([http://www.reald.com](http://www.reald.com/ "http://www.reald.com" ): E2 emitter and CrystalEyes 3 glasses)

-

-

-

-## Software configuration required

-

- 1. Install the latest [NVidia "Linux AMD64"](http://www.nvidia.com/object/unix.html "http://www.nvidia.com/object/unix.html" ) binary drivers

- 2. **For CRT stereo displays only:**

- * Edit the “Screen” section of /etc/X11/xorg.conf to include:

-

- Option "Stereo" "3" Option "AllowDFPStereo" "1" Option "UBB" "1"

-

- 3. **For LCD stereo displays only:**

- * Edit the “Screen” section of /etc/X11/xorg.conf to include:

-

- Option "Stereo" "10" Option "AllowDFPStereo" "1" Option "UBB" "1"

-

- 4. Add the following to the end of your xorg.conf:

-

- Section "Extensions" Option "Composite" "Disable" EndSection

-

-

-

-## For more information

-

- * <http://pymolwiki.org/index.php/Stereo_3D_Display_Options>

- * <http://en.wikipedia.org/wiki/LCD_shutter_glasses>

- * <http://en.wikipedia.org/wiki/Polarized_3D_glasses>

-

-# Global Overrides for SBGrid sites

-

-## Administrator Software Blacklist

-

-Site administrators can prevent the shell initialization files from

-configuring software on a host by creating an empty file at

-**/programs/local/conf/disabled-hosts/&lt;hostname&gt;**, where

-**&lt;hostname&gt;** is the output of the _hostname -s_ command. This is

-useful for encouraging users not to run jobs on bastion hosts, file servers,

-etc.

-

-## Administrator Software Version Overrides

-

-Most of the software titles installed in the SBGrid Suite have several

-versions available. Typically, we try to provide at least three versions of

-each software package, although very old or very new applications may have

-fewer versions.

-

-There are two methods for site admins to configure version overrides using

-files placed in a **/programs/local/conf/** directory.

-

-### Site-wide Version Overrides

-

-A file named **site.conf** will be read when any SBGrid shell is initialized

-from the installation.

-

-### Per-host Version Overrides

-

-A file named **&lt;hostname.conf&gt;**, where **&lt;hostname&gt;** is the

-output of the _hostname -s_ command, will be read after the site.conf on the

-host matching that hostname.

-

-### Precedence

-

-There are three files that will be examined for version overrides during shell

-initialization. In order from lowest to highest precedence:

-

- * /programs/local/conf/site.conf

-

- * /programs/local/conf/&lt;hostname.conf&gt;

-

- * $HOME/.sbgrid.conf

-

-The overrides are reported during shell initialization:

-

-

- Configuration options in effect for this shell: Variable Setting Configuration SPIDER_L 18.10 site CNS_L 1.21 machine CCP4_L 6.1.2 personal

-

-See [this

-page](https://sbgrid.org/wiki/usage/versions#overriding-software-versions_overriding-default-versions ) for details on the override syntax.

-

-# Install SBGrid software on your Mac from the SBGrid Central Server

-

-Download instructions as a [PDF](https://dl.dropboxusercontent.com/u/5977164/Laptop_Installation_Script.pdf) presentation

-and see the [YouTube tutorial](https://www.youtube.com/watch?v=B1orLccn1GA#t=4m17s), starting at 4'17" for additional information.

-# launching remote schrodinger jobs from maestro

-

-The maestro GUI supports running jobs on remote systems (usually ones with

-more computational resources). Setting this up requires 3 things: [set up SSH with keys](faq-setting-up-key-based-ssh)

-to the remote system; configuring `schrodinger.hosts` for the system; and

-launching the jobs on the appropriate system.

-

-## Configuring `schrodinger.hosts`

-

-The `schrodinger.hosts` file should be located (or created) in your home

-directory; in `$HOME/.schrodinger`.

-

-An example `schrodinger.hosts` file:

-

- name: localhost

- tmpdir: /tmp/

-

- # remote system

- name: sbgrid-zorin

- user: my_remote_username

- host: zorin.sbgrid.org

- tmpdir: /tmp

- processors: 32

-

-## launching jobs on the remote system

-

-To launch a job on a remote system, the name under "Host" should match the

-`name` line for the remote system in your `schrodinger.hosts`.

-

-

-# Overriding Software Versions

-

-## Overview

-Most of the software titles installed in the SBGrid software collection have

-several versions available. We try to provide at least three versions of each

-software package, although very old or very new applications may have fewer

-versions.

-

-## Display Available Software Versions

-

-You can display a list of available software versions for your particular

-platform using the  sbgrid utility:  _s_bgrid -l. From a Linux machine, a

-search for CCP4 versions looks like this:

-

- $ sbgrid -l ccp4 Version information for: /programs/x86_64-linux/ccp4

- Default version: 6.4.0

- In-use version: 6.4.0

- Other available versions: 6.3.0 6.2.0

- Overrides use this shell variable: CCP4_X

-

-Running sbgrid -L will display the available versions for the three current

-platforms (OS X PowerPC and Intel, Linux). The output below uses the gnuplot

-application as an example:

-

- $ sbgrid -L gnuplot Version information for: /programs/x86_64-linux/gnuplot

- Default version: 4.6.4

- In-use version: 4.6.4

- Other available versions: 4.6.0 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_X

-

- Version information for: /programs/i386-linux/gnuplot

- Default version: 4.6.0

- Other available versions: 4.4.3 4.2.6

- Overrides use this shell variable: GNUPLOT_L

-

- Version information for: /programs/i386-mac/gnuplot

- Default version: 4.6.4

- Other available versions: 4.4.3 4.2.6 4.6.0

- Overrides use this shell variable: GNUPLOT_M

-

-## Overriding Default Versions

-

-To override the default version of a software title, you will need to create

-an override file. The shell configuration scripts will read this file and

-override the default version.

-

-The override file is named .sbgrid.conf and should be found in your `$HOME`

-directory. The syntax for overrides is a simple key=value pair. E.G. it should

-look like this:

-

- APPLICATION_X=1.2

-

-APPLICATION_X is the name of the application followed by an underscore and the

-shorthand initial for the architecture. The last field on the line is the

-software version number you want to use. The initials for each software branch

-are:

-

-Software Directory| Shorthand Initial

----|---

-powermac | `_P`

-x86_64-linux | `_X`

-i386-mac | `_M`

-

-

-

-To open the overrides file in your default $EDITOR, run this command:_

-_sbgrid-overrides -e.

-

-When you open a new shell, you will see a message about the overridden

-version. Note that a site administrator can create site-wide or machine-

-specific overrides as well.

-

-The example output below shows a default version change for CCP4 on Linux:

-

- Configuration options in effect for this shell: Variable Setting Configuration CCP4_M 6.3.0 personal

-

-## Disabling a Software Package

-

-To disable a specific software package, set its version to “disable” in your

-~/.sbgrid.conf file.

-

-# Preparing Linux Workstations to run SBGrid Software

-

-All Linux machines need installations of a recent version (6.17+) of csh/tcsh. Red Hat Enterprise Linux 6 and other recent distributions usually have an up to date version.

-

-There are RPMs for Red Hat/CentOS/Scientific Linux 5.x in the software tree in the architecture specific directories:

-

-* /programs/i386-linux/system/RPMs

-* /programs/x86_64-linux/system/RPMs

-

-## SELinux

-SELinux must be disabled.

-

-## 64-Bit Machines

-64-bit machines need a number of 32-bit compatibility packages installed **even when using the 64-bit software branch**.

-

-This is due to a number of binary-only and legacy packages that are only available as 32-bit applications. Additional fonts for Tcl/Tk, Motif and Xview applications are also encouraged.

-

-### RHEL/CENTOS/Scientific Linux 5

-Packages for RHEL 5 and compatible machines:

-

-```

-yum install glibc.i686 libgcc.i386 libX11.i386 libXaw.i386 libXext.i386 ncurses.i386 redhat-lsb.i386 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc

-```

-

-### RHEL/CENTOS/Scientific Linux 6

-Packages for RHEL 6 and compatible machines:

-```

-yum install glibc.i686 libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 ncurses-libs.i686 redhat-lsb.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc

-```

-

-### Debian/Ubuntu

-

-The same 32-bit requirement applies for 64-bit Debian and Ubuntu machines. This is supported via the [Multiarch](https://wiki.debian.org/Multiarch/HOWTO "https://wiki.debian.org/Multiarch/HOWTO" ) system.

-

-You'll need at least the following packages to run most of the software. Please email us if you discover we have left some out.

-

-```

-apt-get install libc6-i386 lsb tcsh gawk libjpeg62 curl libx11-6:i386 libxext6:i386

-```

-

-For more information, please check our wiki page

-[here](https://sbgrid.org/wiki/workstation_setup "SBGrid Wiki" ):

-# Preparing Macs for SBGrid Installation

-

-Prior to OS X 10.8, the stock X11 has better compatibility than the Xquartz development version available from MacOSForge.

-

-With the OS X 10.8 release, X11 is no longer included by Apple, and you'll need to install the latest Xquartz version offered on the MacOSForge site to run X11-based applications.

-

-# Recommended Hardware

-

-## Linux Workstations

-

-SBGrid's preferred hardware vendor is [ThinkMate](http://thinkmate.com/

-"http://thinkmate.com" ) and we have some [recommended

-configurations](http://www.thinkmate.com/sbgrid

-"http://www.thinkmate.com/sbgrid" ) for structural biology computing.

-

-## Apple Workstations

-

-Any Apple machine can be a capable computer for structural biology. The basic

-Apple educational discount is available through their online web store, and

-your institution may have negotiated an even better deal with their Apple

-representative. SBGrid has several labs that run exclusively on Macs and OS X.

-

-# SBGrid Computing Resources

-

-SBGrid currently has a 64 core 512G RAM compute system `heron.sbgrid.org` available to consortium members for use in running computationally intensive

-jobs.

-

-`heron.sbgrid.org` is accessable over `ssh`; please contact use at

-[help@sbgrid.org](mailto:help@sbgrid.org) to arrange access.

-

-# Supported Operating Systems

-

-The SBGrid Software Suite can run on Linux, OS X and IRIX machines.

-

-## Linux

-

-We build and test software under 64-bit Red Hat 6. The majority of our Linux

-users are using the Red Hat/CentOS/Scientific Linux or Fedora distributions,

-but we also have labs using the software with Ubuntu, Debian and OpenSuSE. We

-don't explicitly test the software on these distributions, but it is known to

-work, and we will work to resolve problems reported by users of these Linux

-distributions.

-

-We officially support the two most recent releases of Red

-Hat/CentOS/Scientific Linux (currently 6 and 7) and the two most recent

-releases of Fedora Linux. At this time, only 64-bit versions of linux are

-fully supported. As of January 2015, we are no longer updating the 32-bit

-software branch, though we will work to resolve reported problems.

-

-

-### Linux Currently Supported

-

- * Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.

- * Fedora releases actively supported by the Fedora community. Check  <https://fedoraproject.org/wiki/Releases>  for the current list.

- * We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible. RHEL5 users may not receive the latest versions of software, but RHEL5 systems will continue to be functional and supported with existing titles

-

-

-

-## OS X Intel

-

-We build and test the programs under the most four most recent OS X releases.

-

-Currently Supported:

-

- * OS X Intel 10.9 - 10.11

-

-## OS X PowerPC

-

-The OS X PowerPC branch is currently frozen. The applications are stable and

-work well on our PowerPC hardware, but they are not being updated.

-

-Currently Supported:

-

- * OS X PowerPC 10.4 - 10.5

-

-## IRIX

-

-The IRIX programs branch is currently frozen. The applications are stable and

-work well on our SGI hardware, but they are not being updated.

-

-Currently Supported:

-

- * IRIX 6.5.26 + bugfix releases

-

-

-Please check [here](https://sbgrid.org/wiki/ "SBGrid Wiki" ) for the

-latest information :

-

-

-* <https://sbgrid.org/wiki/>

-

-

-

-### Download instructions as a

-[PDF](https://dl.dropboxusercontent.com/u/5977164/Laptop_Installation_Script.pdf)

-presentation

-

-### and

-

-### see the  [ YouTube

-tutorial](https://www.youtube.com/watch?v=B1orLccn1GA&list=PLVetO1F9gm_pYNk5VcwUMfpNWI3xGOM90

-"SBGrid TV" ), starting at 4'17" for additional information.

-

-

-

-# Updating SBGrid software on your mac from your local server

-

-If you run a machine that is frequently disconnected from the network, like a

-laptop, or don't want to set up an NFS-shared software installation, it is

-possible to install the software to the hard disk on your local machine.

-

-There are two scripts in the programs tree that can be used to create a copy

-of the software on your local hard disk. The `sbgrid-laptop` script allows you

-to select individual applications from the software distribution for

-installation on your laptop. By default only the latest version of the

-selected applications will be installed. The `localsync` script allows you to

-copy an entire operating system software branch to your local machine. This

-script can be used on laptops, but each branch is quite large in terms of disk

-space usage.

-

-## Laptop Script

-

-You can create a customized local installation of the software using the

-`sbgrid-laptop` script located at `/programs/share/bin/sbgrid-laptop`. This

-script requires you to have an SSH login to a computer that has access to an

-SBGrid software installation and will let you specify which packages you want

-to install.

-

- sbgrid-laptop: a tool for creating a local installation of the

- SBGrid software on a laptop.

-

- Usage: sbgrid-laptop [-ituv] [-e list|config]

-

- -d Debug mode creates a log file for troubleshooting purposes.

- -e [list|config]

- Edit the software download list.

- -i Initial set up and installation of the SBGrid software.

- -s Re-run SSH key set up process.

- -t Test your current configuration.

- -u Update an existing installation using the current

- configuration.

- -v Verbose option for the file transfer.

-

- You need an SSH login to a machine with the SBGrid software installed

- to use this script. The script will create an SSH key and run an SSH

- agent process to handle authentication for the file transfers.

-

-Copy the script the machine you want to install the software on, and then run

-it in install mode: `./sbgrid-laptop -i`. Follow the prompts on the screen to

-create your configuration file, your software installation list and to enable

-logins using an SSH key for authentication.

-

-## Sync Script

-

-There is a script in the programs tree that can be used to copy the

-appropriate branch from a shared installation to your laptop or workstation.

-

-Copy /programs/share/bin/localsync from the machine that has the software to

-your home directory on the standalone machine:

-

- scp your.server.name:/programs/share/bin/localsync ~/

-

-Then run the script like this:

-

- chmod 755 ~/localsync

- ~/localsync [yourusername@your.server.name](mailto:yourusername@your.server.name)

-

-The script will prompt you for your sudo (admin) password in order to create

-the programs directory, and then it will prompt you for your login password to

-the server that hosts your programs installation.

-

-Here is an example run on my workstation:

-

- $ ./localsync [bene@developer.sbgrid.org](mailto:bene@developer.sbgrid.org)

- Running 'sudo mkdir /programs && sudo chown bene /programs'

- [sudo] password for bene:

- Copying the software from the i386-mac branch on your server to your local

- hard disk. Enter your ssh login password below for [bene@developer.sbgrid.org](mailto:bene@developer.sbgrid.org):

-

- receiving file list ...

-

-This will copy the entire branch for your architecture to your local hard

-drive. For the OS X branch, this will use approximately 100 GB of disk space.

-

-You should use a network cable for the initial download, since the download is

-fairly large. Subsequent runs of the 'localsync' script are differential; they

-will only copy new or changed files, so they can be run over a wireless

-connection. The script can be run at any time to make your local installation

-match the installation on your local server.

-

-## Sharing a Software Installation without NFS

-

-While we recommend that sites export their software installation via NFS to

-their workstations, it is possible to use rsync to copy the master

-installation to each workstation. This method has the drawback that it

-requires manual intervention on the part of the local sysadmin, and updates

-will not be instantaneous or simultaneous for all machines.

-

-On each client machine, you'll need an 'sbgrid' user. That user will have a

-passphraseless ssh key that lets it log into the machine that hosts your

-primary installation. Each client machine will have a cron job for that sbgrid

-user that runs at 2 AM that will sync the programs from the master

-installation to the client machine.

-

-Here is a basic command run down. 'server1' holds the programs installation

-and 'client1' is what will be connecting to it.

-

-* Login as root/administrator on client1

-* Create the 'sbgrid' user on client1

-* Check the free space on /.

-* If there's enough free space, set up the programs directory:

-

- ```

- mkdir /programs

- chown -R sbgrid:sbgrid /programs

- ```

-

-* If there is not enough free space on the root volume, you'll need to find space on a local volume.

-* Login as 'sbgrid' on client1.

-* Create the passphraseless ssh key:

-

- ``` ssh-keygen -d ```

-

-(hit enter to confirm default file location, no passphrase, etc)

-

-* Copy the ssh key to server1:

-

- ``` cat ~/.ssh/id_dsa.pub | ssh server1 'cat - >> ~/.ssh/authorized_keys' ```

-

-* Copy the localsync script from server1 to client1. From client1:

-

- ``` scp sbgrid@server1:/programs/share/bin/localsync . ```

-

-(May prompt to accept the host key. If you can't login without a password, the

-ssh key stuff above has failed, and you'll need to troubleshoot that.)

-&lt;/code&gt; chmod 755 localsync ./localsync sbgrid@server1 &lt;/code&gt;

-(This will take a while depending on the speed of the machines/network.)

-

-* Test the installation

- * tcsh

-

- ``` source /programs/sbgrid.cshrc ```

-

- * bash

-

- ``` source /programs/sbgrid.shrc ```

-

-(You should get a message like this: )

-

-

-

- Welcome to SBGrid!

- ********************************************************************************

- Your use of the applications contained in the /programs directory constitutes

- acceptance of the terms of the SBGrid License Agreement included in the file

- /programs/share/LICENSE. The applications distributed by SBGrid are licensed

- exclusively to member laboratories of the SBGrid Consortium.

-

- To hush this license message, run 'touch ~/.agree2sbgrid'.

- ********************************************************************************

- Please submit bug reports and help requests to: <[bugs@sbgrid.org](mailto:bugs@sbgrid.org)> or

- <[http://sbgrid.org/bugs>](http://sbgrid.org/bugs>)

- This installation last updated: 20110411

- ********************************************************************************

- Total time to initialize: 1 second(s)

-

-

-* Add a cronjob for the updates. As the 'sbgrid' user on client1:

-

- ``` echo "0 2 * * * ~/localsync sbgrid@server1" | crontab ```

-

-* Check the cronjob:

-

- ``` crontab -l ```

-

-You're done!

-