more pages - initial commit

+[SBGrid Wiki](http://example.com/ "Title")

+* [Supported Operating Systems](operatingsystems.md)

+* [Software Installation](installation_admin.md)

+* [Managing your Installation](managing_install.md)

+

+====== 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.

+

+======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.

+====== 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.

+====== 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.