initial sharp info, remove dokuwiki

-====== New Account Information ======

-

-Welcome to SBGrid. If your lab subscribes to our System Admin services, this information will help you get started using the workstations and associated SBGrid services.

-

-If you have already received an account for accessing your lab network, please continue reading. If you need an account, you should ask your PI or lab contact to email us at help@sbgrid with your full name and email address.

-

-====== Using Delphi to calculate electropotential data ======

-AKA: How to replace Grasp's functionality on Linux

-

-create a parameters file called delphi.prm with the contents:<code>

-in(pdb, file="/path/to/your/filename.pdb")

-in(crg, file="/programs/i386-linux/delphi/1.1/full.crg")

-AC = true

-CS = false

-SP = true

-PF = 60

-SC = 1.2

-PR = 1.4

-FC = false

-LG = false

-LP = false

-MD = false

-PX = false

-PY = false

-PZ = false

-BC = 4

-ID = 2

-ED = 80

-GC = 0.0

-IS = 0.0

-IR = 0.0

-NI = 0

-energy(G, S, C)

-out(phi, file="/path/to/your/filename.phi")

-</code>(remember to set the path and filename for the input pdb and output phi file)

-

-then run delphi ./delphi.prm

-====== How to Use Dock6 by UCSF ======

-

- - Overview of Dock6

- * [[http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm]]

- - Preparing the Ligand and Protein Structures for Docking

- *[[http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm]]

- - Characterizing the Active Site Using Sphere Generation and Selection

- * [[http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm]]

- - Preparing the Scoring Grids

- * [[http://dock.compbio.ucsf.edu/DOCK_6/tutorials/grid_generation/generating_grid.html]]

- - Docking (Rigid and Flexible)

- * [[http://dock.compbio.ucsf.edu/DOCK_6/tutorials/ligand_sampling_dock/ligand_sampling_dock.html]]

- - Docking a Library Using MPI

- * Open the dock.in input file and put the path and name for the library under "ligand_atom_file" \\ Type the Following Commands in a Terminal to Start the Process (Do not type anything after the ##. They are just comments):

-

- ssh mn ## Log in to the Master Node (may have to type password)

- ssh n1 ## Access Node 1

- mpd_init.sh ## Initialize the MPI, a list of nodes should appear after this is typed in

- mpirun -np #_of_proc dock6.mpi -i dock.in -o dock.out [-v2] ## Starts the docking program

- ## #_of_proc is the number of processors to use

- ## dock.in is the parameter input file

- ## Note: Do not use relative paths in the parameter input file

-

-Other information about Dock6 can be found in the user's manual:

- *[[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm]]

-

-

-

-====== Development Network ======

-The basic account is a UNIX shell account accessible via SSH. This network account will let you access designated machines in the developer network. Along with the shell account you also get up to 10 GB of data storage, access to high performance compilers, basic development tools like version control systems (svn, git, etc) and shell text editors.

-

-Once you have an account, you can access the developer network by connecting via SSH to:

- * developer.sbgrid.org - Scientific Linux 6 x86_64

-

-This machine (internally named sbgrid-dev-architect) is the only external facing host on the network, and it hosts your home directory and acts as the SSH bastion host for the network. From this machine you can SSH to any of the build and test hosts via their hostname in the table below in order to compile software, run tests, etc.

-

-The following are the always-on operating system/hardware combinations. They are generally kept at the latest point release:

-

-^ Hostname ^ Operating System ^ Architecture ^ Notes ^

-| sbgrid-c5b | CentOS 5 | x86 | Red Hat 5 compatible, base SBGrid 32-bit Linux build VM |

-| sbgrid-c5b-64 | CentOS 5 | x86_64 | Red Hat 5 compatible, base SBGrid 64-bit Linux build VM |

-| sbgrid-c5t-64 | CentOS 5 | x86_64 | Red Hat 5 compatible, minimal install for portability testing |

-| sbgrid-c6b | CentOS 6 | x86 | Red Hat 6 compatible |

-| sbgrid-c6b-64 | CentOS 6 | x86_64 | Red Hat 6 compatible, full build environment |

-| sbgrid-c6t-64 | CentOS 6 | x86_64 | Red Hat 6 compatible, minimal install for portability testing |

-| sbgrid-dev-vm-07 | Debian 5 | x86 | |

-| sbgrid-dev-vm-08 | Debian 5 | x86_64 | |

-| sbgrid-dev-vm-16 | Debian 6 | x86 | |

-| sbgrid-dev-vm-17 | Debian 6 | x86_64 | |

-| sbgrid-dev-vm-03 | Ubuntu 10.10 | x86 | |

-| sbgrid-dev-vm-04 | Ubuntu 10.10 | x86_64 |

-| sbgrid-dev-vm-14 | OpenSuSE 11.3 | x86 | |

-| sbgrid-dev-vm-15 | OpenSuSE 11.3 | x86_64 | |

-| sbgrid-m106 | OS X 10.6 | x86/x86_64 | Base SBGrid OS X Intel build machine |

-| sbgrid-m107 | OS X 10.7 | x86/x86_64 | |

-| sbgrid-m108 | OS X 10.8 | x86/x86_64 | |

-| sbgrid-m109 | OS X 10.9 | x86/x86_64 | |

-| sbgrid-m1010 | OS X 10.10 | x86/x86_64 | |

-| sbgrid-dev-flange | OS X 10.5 | PowerPC | |

-

-

-We have the latest versions of the Intel, Portland and Absoft (PPC) compilers:

-

- * Intel 12.0, 11.1, 10.1 (ifc, ifort) - any linux host, OS X Intel hosts

- * Portland 14.4, 12.6, 10.9, 10.2, 9.0-1 (pgcc, pgf77/90/95) - sbgrid-dev-architect, sbgrid-dev-moose

-

-There is a configuration file for sh-compatible shells that will enable the compilers and their environmental settings:

-

-<code>

- $ . /build/conf/buildenv.sh

-</code>

-

-Then you can use the 'build' function to control your compiler settings:

-

-<code>

-$ build help

-build: a shell function for controlling compilers

-

-Usage: build (help|32|64|list)

-

- help This help message

- 32 Configure 32-bit compilers

- 64 Configure 64-bit compilers

- list List available compilers

-</code>

-

-Additionally, there are other operating systems available as virtual machines that can be enabled (OpenSuSE, Ubuntu, Fedora, etc), and some additional hardware that can be made available (Sun SPARC, IRIX MIPS, etc) on request.

-

-Graphical access to the machines may be available through Apple Remote Desktop, VNC or the NoMachine desktop sharing client. Other tools could be made available if necessary as well. The whole thing's a bit of an experiment, really, so email us at <bugs@sbgrid.org>, and we'll see what we can work out.

-

-====== Request an Account ======

-Thanks for your interest in participating in the SBGrid Developer Network.

-

-In order to be eligible for an account, you must have software in the SBGrid software suite or be planning to make your software available through SBGrid. This requirement limits accounts to developers of scientific software used in structural biology and related disciplines.

-

-That's the only requirement for new accounts. In return for access to these resources, you must agree to not abuse the resources for:

- * sending spam

- * cracking our computers or other peoples' computers

- * other activity which is illegal in the USA or your country

-

-And you agree to take reasonable precautions to maintain the security of your password and account by not sharing this information with other people.

-

-On our end, we will:

- * take reasonable precautions to maintain the security of the network, accounts and data

- * make occasional backups of account data (but don't count on it!)

- * attempt to maintain a high availability of the developer resources

-

-We reserve the right to close accounts at any time for any reason.

-

-Still interested? Great! We want to work with you, so please email <bugs@sbgrid.org> with your account request, and we'll get back to you as soon as possible.

-====== SBGrid Developer Support Program ======

-In an effort to show our appreciation for their hard work and to encourage the continuing development and support of cutting edge structural biology software, SBGrid offers a Developer Support Program featuring a wide array of benefits for structural biology software developers.

-

-\\

-

-===== Developer Network =====

-We can provide access to a dedicated development and test network for software developers. As a developer of an SBGrid supported application, you can request an account on this network and use our infrastructure to build and test your application on a wide range of operating systems. Visit the [[developers::resources|developer network page]] for more details.

-

-\\

-

-===== Support Letters =====

-When applying for grants or financial support please let us know! We can provide support letters on behalf of members of SBGrid Consortium. Letters would include details about our membership, number of computers that can access your software, operating systems used by our community, etc. Please use the [[http://sbgrid.org/contact.php|contact form]] on the SBGrid website.

-

-\\

-

-===== Software Beta Testing =====

-You are welcome to use SBGrid laboratories to beta-test your software. Just let us know when the new beta is available, and we will install it for all participating laboratories or a limited subset that you choose.

-

-\\

-

-===== SBGrid Consortium Membership =====

-If your application is under active maintenance or development, your development group is entitled to free membership in the consortium. Letting us maintain your general structural biology software environment leaves you with more time to concentrate on your unique software contribution to the community.

-

-\\

-

-===== Annual Software Awards =====

-Members of SBGrid Consortium vote in an annual poll to select their favorite structural biology application. Paul Emsley was the winner of the first poll. He won a Macbook Air laptop for his application Coot.

-

-\\

-

-===== Stretch Your Resources =====

-First level software support is provided by the SBGrid non-profit center at Harvard Medical School. All members of the consortium communicate with the service center for assistance with software installation, upgrades, and basic troubleshooting. For many of the mundane problems involving installation, operating system portability and environmental set up, SBGrid members will never need to contact you for support. Your expertise with the software be best utilized answering questions and working on problems that directly involve the science behind your application.

-

-\\

-

-===== Broad Exposure for Your Software =====

-More than 140 structural biology laboratories from 50 institutions in 11 countries participate in the Consortium including the labs of 25 HHMI investigators and 2 Nobel Prize winners. Deployment of your application can be customized to include only non-profit labs or broadened to include industry labs as well. Please visit the Consortium website for the full list of participating groups that can benefit from rapid access to your software. Please note that most SBGrid Consortium laboratories standardize on hardware and operating systems, which simplifies the installation and support process.

-

-\\

-

-===== Connect With Users =====

-Announcing a new version of your software? We can use webex to broadcast your presentation to all laboratories participating in our consortium. We can also disseminate information about your application to our community in our monthly newsletter. Visiting Boston? Please let us know because we'd love to schedule a seminar for members of our local structural biology community.

-

-====== Recommended Hardware ======

-===== Linux Workstations =====

-SBGrid's preferred hardware vendor is [[http://thinkmate.com|ThinkMate]] and we have some [[http://www.thinkmate.com/sbgrid|recommended configurations]] 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.

-======HOWTOs: SBGrid Installation Notes======

-

-===== Site Configuration =====

-The SBGrid Software Suite is designed to be installed on a single computer at your site, which will then share that installation with all the workstations on your network via NFS.

-We refer to this computer as the site "master" server.

-

-The master server will require at least 250 GB of free disk space on a case-sensitive file system and must run some variety of UNIX. The installation script will download the software branches you select, and then install a cron job that will run regularly to check for updates.

-

-Click on the following image for a graphic detailing the common configuration of an SBGrid member laboratory:

-

-{{howtos:site_diagram.png?250}}

-

-===== Pre-Installation =====

-^ Installation Requirements ^^

-|Hard Drive Space|250 GB required|

-|Operating System|Linux, OS X and other UNIX|

-|Privileges | Root account (Linux) or Administrator account (Mac)|

-

-Email [[accounts@sbgrid.org]] to request the installation script for the software. Be sure to include the following information in your email:

- * Lab Name

- * Types of computers on site: Linux, OS X Intel, OS X PowerPC, IRIX

- * The names and email addresses of lab members that will use the software. One user may be designated to receive the majority of our correspondence if you would prefer not to hear from us too often.

-

-Once the email has been received and your information has been entered into our system, we will email you a script you will run that will begin the remote installation process. Instructions for running the script will be included in that email, and are reproduced below for reference.

-

-===== Installation =====

- - Create an 'sbgrid' user on the machine that will host your software installation. This should be a normal, unprivileged user account.

- - Log in as this 'sbgrid' user.

- - Download the installation script from the URL provided in the account creation email.

- - Make it executable: <code>chmod +x sbgrid-admin</code>

- - Run the script: <code>./sbgrid-admin -i</code>

- - The script will walk you through configuring your installation, downloading the software and installing a cron job that will keep the software updated at your site. You will need the **site name** and **install key** provided in the account creation email. The installation may take anywhere from several hours to a day, depending on your network and the number of applications available to your site.

-

-===== Post-Installation Steps =====

- - Add a symlink in the root directory of each machine that wants to use the software. The installation script will print the suggested syntax for the command.<code>ln -s /path/to/sbgrid/installation /programs</code>

- - Any user that wishes to use the software needs to configure their shell to initialize the SBGrid shell environment. For bash and other sh-compliant shells, add the following line to your ~/.bash_profile or ~/.bashrc: <code>. /programs/sbgrid.shrc</code> For csh and tcsh, add the following line to your ~/.cshrc: <code>source /programs/sbgrid.cshrc</code>

- - For some linux distributions, the shipped version of tcsh does not support shell variables longer than 4096 characters. Since the current PATH in our default shell initialization is larger than that, you will need to update tcsh. RPMs for Red Hat 4/5 and CentOS 4/5 are provided at /programs/i386-linux/system/RPMS.

-

-

-===== SGI IRIX Software Branch ======

-Since the IRIX software branch is frozen and no longer receiving updates, it is not installed and updated in the same manner as the active software branches. In order to install the IRIX software branch, please run: <code>./sbgrid-admin -s</code>

-

-Note that the IRIX branch is only compatible with //tcsh//; there is no sh-compatible configuration for this branch.

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

-

-//Last update: October 12, 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. [[http://www.nvidia.com/object/3d-vision-displays.html|Click here to access their list]].

-

-\\

-

-**Notes on select 120Hz monitors:**

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

-

-\\

-

-** Required graphics cards:**

- * [[http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html|NVidia Quadro FX 3700 or higher graphics card]]. 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:**

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

-

-\\

-===== 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:**

- * [[http://www.zalman.com/eng/product/Product_Read.php?Idx=391|Zalman ZM-M240W]] - 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:**

-

- - 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.

- - CRT display capable of at least 100Hz refresh rate @ 1280x1024+. 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 "[[http://shop.ebay.com/?_nkw=sgi+061-0061-001|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.

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

-

-

-\\

-=====Software configuration required=====

-

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

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

- * Edit the "Screen" section of /etc/X11/xorg.conf to include: <code>Option "Stereo" "3"

-Option "AllowDFPStereo" "1"

-Option "UBB" "1"</code>

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

- * Edit the "Screen" section of /etc/X11/xorg.conf to include: <code>Option "Stereo" "10"

-Option "AllowDFPStereo" "1"

-Option "UBB" "1"</code>

- - Add the following to the end of your xorg.conf:<code>

-Section "Extensions"

- Option "Composite" "Disable"

-EndSection</code>

-

-\\

-

-=====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]]

-====== People ======

-

-The people we deal with on a consistent basis will be included here for reference. Notes specific to our relationships with these contacts, as well as all available contact information should be included

-

-===== Dmitry Filonov (FiL) =====

-FiL is the sysadmin at [[Site Notes::Children's Hospital|Enders]] for HHMI

-^ {{fil.png}} ||

-|[[fil@tchlab.org]]|

-|617-355-4398 (office)|

-

-===== John Chow =====

-John is the local sysadmin at the [[Site Notes::East Quad]] cluster.

-|[[jchow@bwh.harvard.edu]]|

-|(617) 525-6242 |

-//Testing a page//

-

- * List 4

- * List 5

-

-

-----

-====== PlayGround ======

-[[start|Wiki Start Page]]

-

- - SBGrid Consortium Support for Users

- * [[Software::Help|Software Help and New Software Requests]]

- * [[Software::OperatingSystems|Supported Operating Systems]]

- * [[Usage::Versions|Overriding Default Software Versions]]

- * [[Software::LaptopInstall|Install The Software On Your Laptop]]

- - SBGrid Consortium Support for Site Administrators

- * [[howtos::installation_notes|Software Installation]]

- * [[Software:workstation_setup|Preparing Workstations to run the Software]]

- * [[Software::installation_admin|Managing your

-Installation]]

- * [[Software::admin_overrides|Administrator Software Version Overrides]]

- * [[Software::mirrors|SBGrid CentOS/Fedora Mirrors]]

- * [[Software::mailinglist|Admins Mailing List]]

- - SBGrid Consortium Support for Developers

- * [[Developers::support|Resources for Developers]]

- * [[Developers::resources|Build and Test Network]]

- - Hardware Support Notes

- * [[Install::Stereo]]

- * [[Hardware::Recommended]|SBGrid Recommended Hardware]]

-

-\\

-\\

-----

-[[https://sbgrid.org:4443/wiki/sidebar?do=edit&rev=|Edit Sidebar]]

-

-

-==== How to connect to the CMCD VPN ====

-

-=== Mac OS X 10.5 and 10.6 ===

-\\

-\\

-== Step 1. ==

-

-Click on the Apple Menu and select //System Preferences//

-\\

-{{:sitenotes:cmcd:vpn_osx_step1.png|}}

-\\

-\\

-== Step 2. ==

-Click on //Network//

-\\

-{{:sitenotes:cmcd:vpn_osx_step2.png|}}

-\\

-\\

-== Step 3. ==

-Unlock the panel by clicking on the padlock and enter the username and password of an admin user.

-\\

-{{:sitenotes:cmcd:vpn_osx_step3.png|}}

-\\

-\\

-== Step 4. ==

-Click on the {{:sitenotes:cmcd:aqua_plus.png|}} to Create a New Service

-\\

-{{:sitenotes:cmcd:vpn_osx_step4.png|}}

-\\

-\\

-== Step 5. ==

-The //Interface// is VPN,\\

-the //Type// is L2TP over IPSec.\\

-Enter a //Service Name//, ie: **CMCD VPN**\\

-Click on //Create//.

-\\

-{{:sitenotes:cmcd:vpn_osx_step5.1.png|}}\\

-{{:sitenotes:cmcd:vpn_osx_step5.2.png|}}

-\\

-\\

-== Step 6. ==

-Enter the server address **vpn.sbgrid.org**\\

-Enter your username\\

-This is the username you use to connect to crystal, and other CMCD services.\\

-Click on //Authentication Settings//

-\\

-{{:sitenotes:cmcd:vpn_osx_step6.png|}}

-\\

-\\

-== Step 7. ==

-Enter your password under //User Authentication//\\

-Under //Machine Authentication//, enter **sbgridvpn** for the //Shared Secret//\\

-Click //OK//

-\\

-{{:sitenotes:cmcd:vpn_osx_step7.png|}}

-\\

-\\

-== Step 8. ==

-Check the box //Show VPN status in menu bar//\\

-Click //Apply//.

-\\

-{{:sitenotes:cmcd:vpn_osx_step8.png|}}

-\\

-\\

-== Step 9. ==

-To connect to the VPN, open the VPN menu in the menu bar, and select //Connect//.\\

-\\

-{{:sitenotes:cmcd:vpn_osx_step9.1.png|}}

-\\

-\\

-== Step 10. ==

-You'll see the word //Connecting// scroll across, and once the connection is complete a timer will start.\\

-\\

-{{:sitenotes:cmcd:vpn_osx_step9.2.png|}}\\

-{{:sitenotes:cmcd:vpn_osx_step9.3.png|}}

-\\

-\\

-== Step 11. ==

-When you want to disconnect from the VPN, simply open the VPN menu, and select //Disconnect//.

-\\

-{{:sitenotes:cmcd:vpn_osx_step10.png|}}

-==== How to connect to the CMCD VPN ====

-

-=== Windows XP ===

-\\

-\\

-== Step 1. ==

-

-Due to the behavior of WinXP SP2, a registry patch must be applied before connecting to the CMCD VPN.

-Download this registry patch, extract the contents of the zip file, and then double click it to run the patch.

-\\

-[[http://sbgrid.org/downloads/cmcdvpn.zip|{{:sitenotes:cmcd:cmcdvpn.png|}}]]

-\\

-\\

-== Step 2. ==

-Click Yes when prompted.\\

-If the patch was successful, you'll get a message similar to the one below.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step2.1.png|}}\\

-{{:sitenotes:cmcd:vpn_winxp_step2.2.png|}}

-

-\\

-\\

-== Step 3. ==

-**Reboot** your computer after applying the registry patch.

-\\

-\\

-\\

-== Step 4. ==

-Go to the Start Menu, and open the Control Panel.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step4.png|}}

-\\

-\\

-== Step 5. ==

-Open //Network and Internet Connections//.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step5.png|}}

-\\

-\\

-== Step 6. ==

-Select //Create a connection to the network at your workplace.//

-\\

-{{:sitenotes:cmcd:vpn_winxp_step6.png|}}

-\\

-\\

-== Step 7. ==

-Select //Virtual Private Network connection//\\

-Click Next.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step7.png|}}

-\\

-\\

-== Step 8. ==

-Enter a name, ie: CMCD VPN\\

-Click //Next//

-\\

-{{:sitenotes:cmcd:vpn_winxp_step8.png|}}

-\\

-\\

-== Step 9. ==

-Enter the server name **vpn.sbgrid.org**

-\\

-{{:sitenotes:cmcd:vpn_winxp_step9.png|}}

-\\

-\\

-== Step 10. ==

-Check the box //Add a shortcut to this connection to my desktop//\\

-Click Finish.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step10.png|}}

-\\

-\\

-== Step 11. ==

-Open the shortcut that was just created on your desktop.\\

-Click on Properties.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step11.png|}}

-\\

-\\

-== Step 12. ==

-Select the Security tab, and click on //IPSec Settings...//

-\\

-{{:sitenotes:cmcd:vpn_winxp_step12.png|}}

-\\

-\\

-== Step 13. ==

-Check the check-box, and enter the pre-shared key **sbgridvpn**\\

-Click OK.\\

-Click OK again to close the Properties page.\\

-\\

-{{:sitenotes:cmcd:vpn_winxp_step13.png|}}

-\\

-\\

-== Step 14. ==

-Enter your username and password and click //Connect//.\\

-This is the username and password you use to connect to crystal, and other CMCD services.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step15.png|}}

-\\

-\\

-== Step 16. ==

-If everything worked correctly, you'll see the following messages.

-\\

-{{:sitenotes:cmcd:vpn_winxp_step16.1.png|}}\\

-{{:sitenotes:cmcd:vpn_winxp_step16.2.png|}}\\

-{{:sitenotes:cmcd:vpn_winxp_step16.3.png|}}

-\\

-\\

-== Step 17. ==

-To disconnect from the VPN, right-click on the icon in the system tray, and select //Disconnect//.

-\\

-====== 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/<hostname>**, where **<hostname>** 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 **<hostname.conf>**, where **<hostname>** 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/<hostname.conf>

- * $HOME/.sbgrid.conf

-

-The overrides are reported during shell initialization:

-

-<code>

- 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

-</code>

-

-See [[Usage::Versions#Overriding Default Versions|this page]] for details on the override syntax.

-use ssh -X localhost to launch xlook

-====== Software Help ======

-===== Getting Software Help =====

-

-If you are having a problem with software included in the SBGrid suite or think you've discovered an application bug, please use the [[http://sbgrid.org/bugs|SBGrid Software Bug Report]] to alert us to the problem. You can also email bugs@sbgrid.org with details on the problem, but the web form is the preferred method.

-

-If the problem with the software started after an update, you can configure your SBGrid environment to [[usage::versions|use an older version of the software]].

-

-===== New Software and Software Updates =====

-To request a new software package or an update to an existing package, please use the [[http://sbgrid.org/req|Software Update/Installation Request form]].

-

-We try to accommodate most requests for new software, but we do occasionally run into difficulties. Despite most of our software being free for academics, some developers insist that each lab download and install their own software. We are happy to provide developers with the list of SBGrid members that have access to their software, but that doesn't always satisfy their requirements.

-

-Even when things go smoothly, license requests and working out licensing details with developers can take some time, so please don't wait until the last minute before requesting software you anticipate you may need for your project.

-

-===== Newsletter =====

-SBGrid sends a monthly newsletter with information concerning software updates, upcoming webinars, talks and other items of interest to our community. The archive of previous newsletters is available online at the [[http://sbgrid.org/news/newsletters|SBGrid Newsletter Archive]].

-======Managing Your Software Installation======

-====='sbgrid-admin' Utility=====

-The //sbgrid-admin// utility used to install the software has a few other uses. There is a download link in the initial site set up email, and it is included in the installation itself at ///programs/share/sbgrid/bin/sbgrid-admin//. It includes built-in help:

-<code>

- $ sbgrid-admin -h

-sbgrid-admin: a tool for administering an SBGrid Software suite installation

-

-Usage: sbgrid-admin [-chirstu]

-

- -c Cron mode. Used for automated updates of the software suite.

- -h Help message.

- -i Install the software suite on this machine.

- -p Print a launchd plist for updating the software on OS X machines.

- -r Regenerate sh/csh shell configuration files.

- -s Install the software branch for SGI IRIX.

- -t Test the configuration file.

- -u Force manual update of an existing installation.

-</code>

-

-The most commonly used option is //sbgrid-admin -u// to force a manual update. This will synchronize your local installation with the SBGrid master installation hosted at Harvard Medical School.

-

-The SBGrid software configuration files use both static and dynamically generated files. The main shell initialization files, **/programs/sbgrid.cshrc** and **/programs/sbgrid.shrc** are static files, but the operating-system specific configurations are dynamically generated and customized for the packages available at your site. //sbgrid-admin -r// will regenerate the branch-specific configuration files should you accidentally delete or alter them.

-

-===== Configuration Options =====

-The //sbgrid-admin// script has some additional configuration options to accommodate the installation requirements at different sites.

-

-The ~sbgrid/.sbgridrc configuration file for the //sbgrid-admin// script must contain a sitename and site key. All other configurations are optional.

-

-Options take the form of //OPTION_NAME="setting"//.

-

-|**Option**|**Example**|**Description**|

-|SB_SITENAME|sbgrid-bene|The site name for your installation provided by SBGrid|

-|SB_SITEKEY|xyxyxyxyxyxyxy|The installation key for your site provided by SBGrid|

-|INSTALL_TARGET|/nfs/programs|The installation directory for the software|

-|RSYNC_ARGS|"%%--%%port 8080"|Advanced arguments to rsync. Can be used to workaround blocked rsync ports.|

-|HTTP_PROXY|host.name:port|Proxy hostname and port for use by rsync and curl|

-|POST_UPDATE_SCRIPT|/absolute/path/to/script|Optional script to be run after a successful software update|

-|CRON_SCHEDULE|5 1 * * *|Set a custom cron schedule|

-\\

-

-===== Rsync Transaction Logging =====

-If you want a date-stamped log of all rsync downloads, deletions and updates, you can add a line like this to the ~sbgrid/.sbgridrc file:

-

-<code>

-RSYNC_ARGS="--log-file=$HOME/logs/sbgrid-admin-`date +%Y%m%d`.log"

-</code>

-

-This will create a date-stamped log file any time an actual change to the software tree happens. In general this should not be necessary, but for troubleshooting purposes it can be useful.

-====== Copying the Software Installation ======

-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.

-

-<code>

-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.

-</code>

-

-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:

-

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

-

-Then run the script like this:

-

-<code>

-chmod 755 ~/localsync

-~/localsync yourusername@your.server.name

-</code>

-

-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:

-

-<code>

- $ ./localsync 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:

-

-receiving file list ...

-</code>

-

-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:

-<code>

-mkdir /programs

-chown -R sbgrid:sbgrid /programs

-</code>

- * 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:

-<code>

-ssh-keygen -d

-</code>

-

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

- * Copy the ssh key to server1:

-<code>

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

-</code>

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

-<code>

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

-</code>

-

-(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.)

-</code>

-chmod 755 localsync

-./localsync sbgrid@server1

-</code>

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

-

- * Test the installation:

-<code>

-tcsh

-source /programs/sbgrid.cshrc

-</code>

- or

-<code>

-bash

-source /programs/sbgrid.shrc

-</code>

-

-(You should get a message like this: )

-<file>

- 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> or

- <http://sbgrid.org/bugs>

- This installation last updated: 20110411

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

- Total time to initialize: 1 second(s)

-</file>

-

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

-<code>

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

-</code>

- * Check the cronjob:

-<code>

-crontab -l

-</code>

-

-You're done!

-====== Mailing List for Site Administrators ======

-We have a small mailing list for technical users and site administrators. Visit the [[https://cmcd.hms.harvard.edu/sympa/info/sbgrid-tech|SBGrid-tech mailing list]] page to sign up.

-====== SBGrid Mirrors ======

-

-For the benefit of the local SBGrid community, we recommend the following to access frequently-used open source software. If you would like for us to add a mirror, please [[help@sbgrid.org|contact us]].

-

-\\

-

-^ Mirror Name ^^ Mirror URL ^

-|{{:software:centos_icon_60.png?nolink}}|[[http://www.centos.org|CentOS]]| [[http://mirrors.med.harvard.edu/centos/]]|

-|{{:software:sl6_logo.jpeg?nolink}}|[[http://www.scientificlinux.org/|Scientific Linux]]| [[http://mirrors.med.harvard.edu/scientificlinux/]]|

-====== Supported Operating Systems ======

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

-

-Last Update: 2014-02-04

-

-===== 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.

-

-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.

-\\

-

-===== OS X Intel =====

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

-

-Currently Supported:

- * OS X Intel 10.7 - 10.10

-

-\\

-

-===== 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

-

-\\

-

-===== General =====

- * You should use a network installation for workstations and servers if at all possible. NFS, SMB and AFP all work for sharing a single installation among multiple machines. The decreased admin overhead, bandwidth and disk savings of sharing a single installation is a significant benefit.

-

-===== Linux =====

- * 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:

-<code>

-/programs/i386-linux/system/RPMs

-/programs/x86_64-linux/system/RPMs

-</code>

- * SELinux must be disabled.

- * 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.

-

-Packages for RHEL 6, and 7 and compatible machines:

-<code>

-yum install glibc.i686 libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 ncurses.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 libXScrnSaver

-</code>

-

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

-<code>apt-get install libc6-i386 lsb tcsh gawk libjpeg62 curl libx11-6:i386 libxext6:i386</code>

-

-===== 3D Stereo on RHEL 7 systems with Gnome 3 =====

-

-Nvidia 3D stereo typically requires disabling the Composite extension in X.org. Unfortunately, this extension is required to run Gnome 3 and the gdm login mangager supplied as the default desktop in CentOS and many other linux distributions.

-

-As of version 337.19 of the nvidia driver, some Quadro configurations can operate with the composite extension enabled, but stereo functionality depends on a stereo-aware composite manager. The Composite manager in CentOS7 Gnome3 is not stereo aware and 3D stereo does not work by default.

-

-In order to use 3D stereo on Gnome3 systems, you can switch from Gnome3/gdm to MATE/lightdm.

-The MATE Desktop Environment is the continuation of GNOME 2 which is the default desktop in CentOS 5 and 6.

-

-To change to MATE on CentOS7 systems, first, install the Extra Packages for Enterprise Linux (EPEL) repo:

-<code>

- yum install epel-release

-</code>

-

-Then install the nvidia drivers from epel

-<code>

- yum install kmod-nvidia

-</code>

-

-You may find you need these packages as well

-<code>

- yum install mesa-libGLU-9.0.0-4.el7.x86_64 libXScrnSaver-1.2.2-6.1.el7.x86_64

-</code>

-

-Next, install lightdm which doesn't require the composite extension.

-<code>

- yum install lightdm

-</code>

-

-From there we do a couple of groupinstalls

-You may have these rpms installed already, but just for good measure

-<code>

- yum group install "X Window System"

-</code>

-

-then

-<code>

- yum groupinstall "MATE Desktop"

-</code>

-

-Toggle from gdm to lightdm in systemd using systemctl.

-To see what you are using as a 'display manager', check this link

- <code>

-ls -l /etc/systemd/system/display-manager.service

-</code>

-

-This is likely pointing to gdm and should be changed to point to lightdm.

-You can change that with systemctl.

-<code>

- systemctl disable gdm

- systemctl enable lightdm

-</code>

-

-And then this will reload you changes, similar to changing runlevels with sysinitV

-<code>

- systemctl isolate graphical.target

-</code>

-

-Make sure to select MATE from the drop menu as your graphical before you login.

-===== Mac OS X ======

- * 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.

-

-===== Laptops ======

- * You can create a local installation to take along with you.

-http://www.sbgrid.org/wiki/software/laptopinstall

-====== SBGrid Software Consortium Wiki ======

-Welcome! This site includes documentation on the features and benefits of your SBGrid membership including information for software users, site administrators and software developers.

-

-If you'd like to help contribute to our wiki, please email [[bugs@sbgrid.org]].

-====== Overriding Software Versions ======

-

-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 Versions =====

-To list the available versions of a software title, you can use the //sbgrid// utility. Running //sbgrid -l// will list the versions for your current platform. From a Linux machine, a search for CCP4 versions looks like this:

-

-<code>

-$ 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

-</code>

-

-Running //sbgrid -L// will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).

-<code>

-$ 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

-</code>

-

-

-===== Overriding Default Versions =====

-To override the default version of a software title, you 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 placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:

-

-<code>APPLICATION_X=1.2</code>

-

-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|

-|i386-linux|_L|

-|x86_64-linux|_X|

-|i386-mac|_M|

-

-To quickly open the overrides file in your default $EDITOR, you can run //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 sitewide or machine-specific overrides as well.

-

-The example output below shows CCP4 on linux being changed from the default version:

-

-<code>

- Configuration options in effect for this shell:

- Variable Setting Configuration

- CCP4_M 6.3.0 personal

-</code>

-

-===== Disabling a Software Package =====

-To disable a specific software package, set its version to "disable" in your ~/.sbgrid.conf file.

-====== DokuWiki ======

-

-[[doku>wiki:dokuwiki|{{wiki:dokuwiki-128.png }}]] DokuWiki is a standards compliant, simple to use [[wp>Wiki]], mainly aimed at creating documentation of any kind. It is targeted at developer teams, workgroups and small companies. It has a simple but powerful [[wiki:syntax]] which makes sure the datafiles remain readable outside the Wiki and eases the creation of structured texts. All data is stored in plain text files -- no database is required.

-

-Read the [[doku>manual|DokuWiki Manual]] to unleash the full power of DokuWiki.

-

-===== Download =====

-

-DokuWiki is available at http://www.splitbrain.org/go/dokuwiki

-

-

-===== Read More =====

-

-All documentation and additional information besides the [[syntax|syntax description]] is maintained in the DokuWiki at [[doku>|www.dokuwiki.org]].

-

-**About DokuWiki**

-

- * [[doku>features|A feature list]] :!:

- * [[doku>users|Happy Users]]

- * [[doku>press|Who wrote about it]]

- * [[doku>blogroll|What Bloggers think]]

- * [[http://www.wikimatrix.org/show/DokuWiki|Compare it with other wiki software]]

-

-**Installing DokuWiki**

-

- * [[doku>requirements|System Requirements]]

- * [[http://www.splitbrain.org/go/dokuwiki|Download DokuWiki]] :!:

- * [[doku>changes|Change Log]]

- * [[doku>Install|How to install or upgrade]] :!:

- * [[doku>config|Configuration]]

-

-**Using DokuWiki**

-

- * [[doku>syntax|Wiki Syntax]]

- * [[doku>manual|The manual]] :!:

- * [[doku>FAQ|Frequently Asked Questions (FAQ)]]

- * [[doku>glossary|Glossary]]

- * [[http://search.dokuwiki.org|Search for DokuWiki help and documentation]]

-

-**Customizing DokuWiki**

-

- * [[doku>tips|Tips and Tricks]]

- * [[doku>Template|How to create and use templates]]

- * [[doku>plugins|Installing plugins]]

- * [[doku>development|Development Resources]]

-

-**DokuWiki Feedback and Community**

-

- * [[doku>newsletter|Subscribe to the newsletter]] :!:

- * [[doku>mailinglist|Join the mailing list]]

- * [[http://forum.dokuwiki.org|Check out the user forum]]

- * [[doku>irc|Talk to other users in the IRC channel]]

- * [[http://bugs.splitbrain.org/index.php?project=1|Submit bugs and feature wishes]]

- * [[http://www.wikimatrix.org/forum/viewforum.php?id=10|Share your experiences in the WikiMatrix forum]]

- * [[doku>thanks|Some humble thanks]]

-

-

-===== Copyright =====

-

-2004-2010 (c) Andreas Gohr <andi@splitbrain.org>((Please do not contact me for help and support -- use the [[doku>mailinglist]] or [[http://forum.dokuwiki.org|forum]] instead)) and the DokuWiki Community

-

-The DokuWiki engine is licensed under [[http://www.gnu.org/licenses/gpl.html|GNU General Public License]] Version 2. If you use DokuWiki in your company, consider [[doku>donate|donating]] a few bucks ;-).

-

-Not sure what this means? See the [[doku>faq:license|FAQ on the Licenses]].

-====== Formatting Syntax ======

-

-[[doku>DokuWiki]] supports some simple markup language, which tries to make the datafiles to be as readable as possible. This page contains all possible syntax you may use when editing the pages. Simply have a look at the source of this page by pressing the //Edit this page// button at the top or bottom of the page. If you want to try something, just use the [[playground:playground|playground]] page. The simpler markup is easily accessible via [[doku>toolbar|quickbuttons]], too.

-

-===== Basic Text Formatting =====

-

-DokuWiki supports **bold**, //italic//, __underlined__ and ''monospaced'' texts. Of course you can **__//''combine''//__** all these.

-

- DokuWiki supports **bold**, //italic//, __underlined__ and ''monospaced'' texts.

- Of course you can **__//''combine''//__** all these.

-

-You can use _subscript and ^superscript, too.

-

- You can use _subscript and ^superscript, too.

-

-You can mark something as <del>deleted</del> as well.

-

- You can mark something as <del>deleted</del> as well.

-

-**Paragraphs** are created from blank lines. If you want to **force a newline** without a paragraph, you can use two backslashes followed by a whitespace or the end of line.

-

-This is some text with some linebreaks\\ Note that the

-two backslashes are only recognized at the end of a line\\

-or followed by\\ a whitespace \\this happens without it.

-

- This is some text with some linebreaks\\ Note that the

- two backslashes are only recognized at the end of a line\\

- or followed by\\ a whitespace \\this happens without it.

-

-You should use forced newlines only if really needed.

-

-===== Links =====

-

-DokuWiki supports multiple ways of creating links.

-

-==== External ====

-

-External links are recognized automagically: http://www.google.com or simply www.google.com - You can set the link text as well: [[http://www.google.com|This Link points to google]]. Email addresses like this one: <andi@splitbrain.org> are recognized, too.

-

- DokuWiki supports multiple ways of creating links. External links are recognized

- automagically: http://www.google.com or simply www.google.com - You can set

- link text as well: [[http://www.google.com|This Link points to google]]. Email

- addresses like this one: <andi@splitbrain.org> are recognized, too.

-

-==== Internal ====

-

-Internal links are created by using square brackets. You can either just give a [[pagename]] or use an additional [[pagename|link text]].

-

- Internal links are created by using square brackets. You can either just give

- a [[pagename]] or use an additional [[pagename|link text]].

-

-[[doku>pagename|Wiki pagenames]] are converted to lowercase automatically, special characters are not allowed.

-

-You can use [[some:namespaces]] by using a colon in the pagename.

-

- You can use [[some:namespaces]] by using a colon in the pagename.

-

-For details about namespaces see [[doku>namespaces]].

-

-Linking to a specific section is possible, too. Just add the section name behind a hash character as known from HTML. This links to [[syntax#internal|this Section]].

-

- This links to [[syntax#internal|this Section]].

-

-Notes:

-

- * Links to [[syntax|existing pages]] are shown in a different style from [[nonexisting]] ones.

- * DokuWiki does not use [[wp>CamelCase]] to automatically create links by default, but this behavior can be enabled in the [[doku>config]] file. Hint: If DokuWiki is a link, then it's enabled.

- * When a section's heading is changed, its bookmark changes, too. So don't rely on section linking too much.

-

-==== Interwiki ====

-

-DokuWiki supports [[doku>Interwiki]] links. These are quick links to other Wikis. For example this is a link to Wikipedia's page about Wikis: [[wp>Wiki]].

-

- DokuWiki supports [[doku>Interwiki]] links. These are quick links to other Wikis.

- For example this is a link to Wikipedia's page about Wikis: [[wp>Wiki]].

-

-==== Windows Shares ====

-

-Windows shares like [[\\server\share|this]] are recognized, too. Please note that these only make sense in a homogeneous user group like a corporate [[wp>Intranet]].

-

- Windows Shares like [[\\server\share|this]] are recognized, too.

-

-Notes:

-

- * For security reasons direct browsing of windows shares only works in Microsoft Internet Explorer per default (and only in the "local zone").

- * For Mozilla and Firefox it can be enabled through different workaround mentioned in the [[http://kb.mozillazine.org/Links_to_local_pages_do_not_work|Mozilla Knowledge Base]]. However, there will still be a JavaScript warning about trying to open a Windows Share. To remove this warning (for all users), put the following line in ''conf/local.protected.php'':

-

- $lang['js']['nosmblinks'] = '';

-

-==== Image Links ====

-

-You can also use an image to link to another internal or external page by combining the syntax for links and [[#images_and_other_files|images]] (see below) like this:

-

- [[http://www.php.net|{{wiki:dokuwiki-128.png}}]]

-

-[[http://www.php.net|{{wiki:dokuwiki-128.png}}]]

-

-Please note: The image formatting is the only formatting syntax accepted in link names.

-

-The whole [[#images_and_other_files|image]] and [[#links|link]] syntax is supported (including image resizing, internal and external images and URLs and interwiki links).

-

-===== Footnotes =====

-

-You can add footnotes ((This is a footnote)) by using double parentheses.

-

- You can add footnotes ((This is a footnote)) by using double parentheses.

-

-===== Sectioning =====

-

-You can use up to five different levels of headlines to structure your content. If you have more than three headlines, a table of contents is generated automatically -- this can be disabled by including the string ''<nowiki>~~NOTOC~~</nowiki>'' in the document.

-

-==== Headline Level 3 ====

-=== Headline Level 4 ===

-== Headline Level 5 ==

-

- ==== Headline Level 3 ====

- === Headline Level 4 ===

- == Headline Level 5 ==

-

-By using four or more dashes, you can make a horizontal line:

-

-----

-

-===== Images and Other Files =====

-

-You can include external and internal [[doku>images]] with curly brackets. Optionally you can specify the size of them.

-

-Real size: {{wiki:dokuwiki-128.png}}

-

-Resize to given width: {{wiki:dokuwiki-128.png?50}}

-

-Resize to given width and height((when the aspect ratio of the given width and height doesn't match that of the image, it will be cropped to the new ratio before resizing)): {{wiki:dokuwiki-128.png?200x50}}

-

-Resized external image: {{http://de3.php.net/images/php.gif?200x50}}

-

- Real size: {{wiki:dokuwiki-128.png}}

- Resize to given width: {{wiki:dokuwiki-128.png?50}}

- Resize to given width and height: {{wiki:dokuwiki-128.png?200x50}}

- Resized external image: {{http://de3.php.net/images/php.gif?200x50}}

-

-

-By using left or right whitespaces you can choose the alignment.

-

-{{ wiki:dokuwiki-128.png}}

-

-{{wiki:dokuwiki-128.png }}

-

-{{ wiki:dokuwiki-128.png }}

-

- {{ wiki:dokuwiki-128.png}}

- {{wiki:dokuwiki-128.png }}

- {{ wiki:dokuwiki-128.png }}

-

-Of course, you can add a title (displayed as a tooltip by most browsers), too.

-

-{{ wiki:dokuwiki-128.png |This is the caption}}

-

- {{ wiki:dokuwiki-128.png |This is the caption}}

-

-If you specify a filename (external or internal) that is not an image (''gif, jpeg, png''), then it will be displayed as a link instead.

-

-For linking an image to another page see [[#Image Links]] above.

-

-===== Lists =====

-

-Dokuwiki supports ordered and unordered lists. To create a list item, indent your text by two spaces and use a ''*'' for unordered lists or a ''-'' for ordered ones.

-

- * This is a list

- * The second item

- * You may have different levels

- * Another item

-

- - The same list but ordered

- - Another item

- - Just use indention for deeper levels

- - That's it

-

-<code>

- * This is a list

- * The second item

- * You may have different levels

- * Another item

-

- - The same list but ordered

- - Another item

- - Just use indention for deeper levels

- - That's it

-</code>

-

-Also take a look at the [[doku>faq:lists|FAQ on list items]].

-

-===== Text Conversions =====

-

-DokuWiki can convert certain pre-defined characters or strings into images or other text or HTML.

-

-The text to image conversion is mainly done for smileys. And the text to HTML conversion is used for typography replacements, but can be configured to use other HTML as well.

-

-==== Text to Image Conversions ====

-

-DokuWiki converts commonly used [[wp>emoticon]]s to their graphical equivalents. Those [[doku>Smileys]] and other images can be configured and extended. Here is an overview of Smileys included in DokuWiki:

-

- * 8-) %% 8-) %%

- * 8-O %% 8-O %%

- * :-( %% :-( %%

- * :-) %% :-) %%

- * =) %% =) %%

- * :-/ %% :-/ %%

- * :-\ %% :-\ %%

- * :-? %% :-? %%

- * :-D %% :-D %%

- * :-P %% :-P %%

- * :-O %% :-O %%

- * :-X %% :-X %%

- * :-| %% :-| %%

- * ;-) %% ;-) %%

- * ^_^ %% ^_^ %%

- * :?: %% :?: %%

- * :!: %% :!: %%

- * LOL %% LOL %%

- * FIXME %% FIXME %%

- * DELETEME %% DELETEME %%

-

-==== Text to HTML Conversions ====

-

-Typography: [[DokuWiki]] can convert simple text characters to their typographically correct entities. Here is an example of recognized characters.

-

--> <- <-> => <= <=> >> << -- --- 640x480 (c) (tm) (r)

-"He thought 'It's a man's world'..."

-

-<code>

--> <- <-> => <= <=> >> << -- --- 640x480 (c) (tm) (r)

-"He thought 'It's a man's world'..."

-</code>

-

-The same can be done to produce any kind of HTML, it just needs to be added to the [[doku>entities|pattern file]].

-

-There are three exceptions which do not come from that pattern file: multiplication entity (640x480), 'single' and "double quotes". They can be turned off through a [[doku>config:typography|config option]].

-

-===== Quoting =====

-

-Some times you want to mark some text to show it's a reply or comment. You can use the following syntax:

-

- I think we should do it

-

- > No we shouldn't

-

- >> Well, I say we should

-

- > Really?

-

- >> Yes!

-

- >>> Then lets do it!

-

-I think we should do it

-

-> No we shouldn't

-

->> Well, I say we should

-

-> Really?

-

->> Yes!

-

->>> Then lets do it!

-

-===== Tables =====

-

-DokuWiki supports a simple syntax to create tables.

-

-^ Heading 1 ^ Heading 2 ^ Heading 3 ^

-| Row 1 Col 1 | Row 1 Col 2 | Row 1 Col 3 |

-| Row 2 Col 1 | some colspan (note the double pipe) ||

-| Row 3 Col 1 | Row 3 Col 2 | Row 3 Col 3 |

-

-Table rows have to start and end with a ''|'' for normal rows or a ''^'' for headers.

-

- ^ Heading 1 ^ Heading 2 ^ Heading 3 ^

- | Row 1 Col 1 | Row 1 Col 2 | Row 1 Col 3 |

- | Row 2 Col 1 | some colspan (note the double pipe) ||

- | Row 3 Col 1 | Row 3 Col 2 | Row 3 Col 3 |

-

-To connect cells horizontally, just make the next cell completely empty as shown above. Be sure to have always the same amount of cell separators!

-

-Vertical tableheaders are possible, too.

-

-| ^ Heading 1 ^ Heading 2 ^

-^ Heading 3 | Row 1 Col 2 | Row 1 Col 3 |

-^ Heading 4 | no colspan this time | |

-^ Heading 5 | Row 2 Col 2 | Row 2 Col 3 |

-

-As you can see, it's the cell separator before a cell which decides about the formatting:

-

- | ^ Heading 1 ^ Heading 2 ^

- ^ Heading 3 | Row 1 Col 2 | Row 1 Col 3 |

- ^ Heading 4 | no colspan this time | |

- ^ Heading 5 | Row 2 Col 2 | Row 2 Col 3 |

-

-You can have rowspans (vertically connected cells) by adding '':::'' into the cells below the one to which they should connect.

-

-^ Heading 1 ^ Heading 2 ^ Heading 3 ^

-| Row 1 Col 1 | this cell spans vertically | Row 1 Col 3 |

-| Row 2 Col 1 | ::: | Row 2 Col 3 |

-| Row 3 Col 1 | ::: | Row 2 Col 3 |

-

-Apart from the rowspan syntax those cells should not contain anything else.

-

- ^ Heading 1 ^ Heading 2 ^ Heading 3 ^

- | Row 1 Col 1 | this cell spans vertically | Row 1 Col 3 |

- | Row 2 Col 1 | ::: | Row 2 Col 3 |

- | Row 3 Col 1 | ::: | Row 2 Col 3 |

-

-You can align the table contents, too. Just add at least two whitespaces at the opposite end of your text: Add two spaces on the left to align right, two spaces on the right to align left and two spaces at least at both ends for centered text.

-

-^ Table with alignment ^^^

-| right| center |left |

-|left | right| center |

-| xxxxxxxxxxxx | xxxxxxxxxxxx | xxxxxxxxxxxx |

-

-This is how it looks in the source:

-

- ^ Table with alignment ^^^

- | right| center |left |

- |left | right| center |

- | xxxxxxxxxxxx | xxxxxxxxxxxx | xxxxxxxxxxxx |

-

-Note: Vertical alignment is not supported.

-

-===== No Formatting =====

-

-If you need to display text exactly like it is typed (without any formatting), enclose the area either with ''%%<nowiki>%%'' tags or even simpler, with double percent signs ''<nowiki>%%</nowiki>''.

-

-<nowiki>

-This is some text which contains addresses like this: http://www.splitbrain.org and **formatting**, but nothing is done with it.

-</nowiki>

-The same is true for %%//__this__ text// with a smiley ;-)%%.

-

- <nowiki>

- This is some text which contains addresses like this: http://www.splitbrain.org and **formatting**, but nothing is done with it.

- </nowiki>

- The same is true for %%//__this__ text// with a smiley ;-)%%.

-

-===== Code Blocks =====

-

-You can include code blocks into your documents by either indenting them by at least two spaces (like used for the previous examples) or by using the tags ''%%<code>%%'' or ''%%<file>%%''.

-

- This is text is indented by two spaces.

-

-<code>

-This is preformatted code all spaces are preserved: like <-this

-</code>

-

-<file>

-This is pretty much the same, but you could use it to show that you quoted a file.

-</file>

-

-Those blocks were created by this source:

-

- This is text is indented by two spaces.

-

- <code>

- This is preformatted code all spaces are preserved: like <-this

- </code>

-

- <file>

- This is pretty much the same, but you could use it to show that you quoted a file.

- </file>

-

-==== Syntax Highlighting ====

-

-[[wiki:DokuWiki]] can highlight sourcecode, which makes it easier to read. It uses the [[http://qbnz.com/highlighter/|GeSHi]] Generic Syntax Highlighter -- so any language supported by GeSHi is supported. The syntax is the same like in the code and file blocks in the previous section, but this time the name of the used language is inserted inside the tag. Eg. ''<nowiki><code java></nowiki>'' or ''<nowiki><file java></nowiki>''.

-

-<code java>

-/**

- * The HelloWorldApp class implements an application that

- * simply displays "Hello World!" to the standard output.

- */

-class HelloWorldApp {

- public static void main(String[] args) {

- System.out.println("Hello World!"); //Display the string.

- }

-}

-</code>

-

-The following language strings are currently recognized: //4cs, abap, actionscript-french, actionscript, actionscript3, ada, apache, applescript, asm, asp, autoconf, autohotkey, autoit, avisynth, awk, bash, basic4gl, bf, bibtex, blitzbasic, bnf, boo, c, c_mac, caddcl, cadlisp, cfdg, cfm, chaiscript, cil, clojure, cmake, cobol, cpp, cpp-qt, csharp, css, cuesheet, d, dcs, delphi, diff, div, dos, dot, ecmascript, eiffel, email, erlang, fo, fortran, freebasic, fsharp, gambas, genero, genie, gdb, glsl, gml, gnuplot, groovy, gettext, gwbasic, haskell, hicest, hq9plus, html, icon, idl, ini, inno, intercal, io, j, java5, java, javascript, jquery, kixtart, klonec, klonecpp, latex, lisp, locobasic, logtalk, lolcode, lotusformulas, lotusscript, lscript, lsl2, lua, m68k, magiksf, make, mapbasic, matlab, mirc, modula2, modula3, mmix, mpasm, mxml, mysql, newlisp, nsis, oberon2, objc, ocaml-brief, ocaml, oobas, oracle8, oracle11, oxygene, oz, pascal, pcre, perl, perl6, per, pf, php-brief, php, pike, pic16, pixelbender, plsql, postgresql, povray, powerbuilder, powershell, progress, prolog, properties, providex, purebasic, python, q, qbasic, rails, rebol, reg, robots, rpmspec, rsplus, ruby, sas, scala, scheme, scilab, sdlbasic, smalltalk, smarty, sql, systemverilog, tcl, teraterm, text, thinbasic, tsql, typoscript, unicon, vala, vbnet, vb, verilog, vhdl, vim, visualfoxpro, visualprolog, whitespace, winbatch, whois, xbasic, xml, xorg_conf, xpp, z80//

-

-==== Downloadable Code Blocks ====

-

-When you use the ''%%<code>%%'' or ''%%<file>%%'' syntax as above, you might want to make the shown code available for download as well. You can to this by specifying a file name after language code like this:

-

-<code>

-<file php myexample.php>

-<?php echo "hello world!"; ?>

-</file>

-</code>

-

-<file php myexample.php>

-<?php echo "hello world!"; ?>

-</file>

-

-If you don't want any highlighting but want a downloadable file, specify a dash (''-'') as the language code: ''%%<code - myfile.foo>%%''.

-

-

-===== Embedding HTML and PHP =====

-

-You can embed raw HTML or PHP code into your documents by using the ''%%<html>%%'' or ''%%<php>%%'' tags. (Use uppercase tags if you need to enclose block level elements.)

-

-HTML example:

-

-<code>

-<html>

-This is some <span style="color:red;font-size:150%;">inline HTML</span>

-</html>

-<HTML>

-<p style="border:2px dashed red;">And this is some block HTML</p>

-</HTML>

-</code>

-

-<html>

-This is some <span style="color:red;font-size:150%;">inline HTML</span>

-</html>

-<HTML>

-<p style="border:2px dashed red;">And this is some block HTML</p>

-</HTML>

-

-PHP example:

-

-<code>

-<php>

-echo 'A logo generated by PHP:';

-echo '<img src="' . $_SERVER['PHP_SELF'] . '?=' . php_logo_guid() . '" alt="PHP Logo !" />';

-echo '(generated inline HTML)';

-</php>

-<PHP>

-echo '<table class="inline"><tr><td>The same, but inside a block level element:</td>';