Using SBGrid Programs

All applications are located in /programs directory and are configured to run without additional settings. In most cases, you will easily be able to run any program in the collection by opening up a terminal shell, and typing the name of the program that you want to run. Linux applications are installed in the /programs/i386-linux subdirectory. Mac applications are installed in the /programs/i386-mac subdirectory (for intel macs) or the /programs/powermac subdirectory (for PPC macs).

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. To override the default version, follow these instructions.

Running GUI Programs Remotely

It is currently possible to run programs remotely over SSH through a process called X-forwarding. To accomplish this, you may simply use the -Y flag in your SSH command, like so:

1. [user@host ~]$ ssh -Y user@remote-host

If you have to access your machine through a gateway (i.e., ssh to xtal200.harvard.edu, then to a workstation), you can use a command such as:

1. [user@host ~]$ ssh -t -Y user@remote-host ssh -Y internal-host

After logging in to the remote host, you may launch programs by running the command name in a Terminal. With X-forwarding enabled, programs will launch their user interfaces on your computer, much like they would if you ran the program locally.

NOTE: On Mac OS X, you may need to change your display output in order for certain programs to run correctly. You can do this by opening the X11 preferences, clicking the output tab, and selecting a different option from the 'Colors:' dropdown (the default is "From Display"). 256 Colors will emulate an 8-bit color scheme for running applications such as WEB. IF 256 Colors does not resolve the problem you are seeing, revert the change - for the majority of applications it is not necesssary, and in some cases can be problematic.

If you need to download a newer version of X11 for OS X, you can find the binaries here: http://xquartz.macosforge.org/trac/wiki

To enable GL required by some programs like coot you will need to run this in a terminal from your account on your Mac:

defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

Then stop and restart XQuartz.

The bundle identifer used by the XQuartz project has varied over time - there is an additional bundle identifier of org.xquartz.X11 that should also be set.

Running SBGrid Programs

Running programs from the SBGrid software tree should be as simple as opening a Terminal and typing the name of the application you would like to run. You may see a list of available software packages at: http://sbgrid.org/software/

If you are unable to run programs in this manner, you'll need to add the appropriate lines to your shell configuration. Run echo $SHELL in a terminal to determine which file you should edit.

For tcsh, edit your ~/.cshrc file to contain:

if ( -e /programs/sbgrid.cshrc ) then 
	source /programs/sbgrid.cshrc  
endif

For bash,** **edit your ~/.bashrc file to contain:

if [ -f /programs/sbgrid.shrc ]; then
     	. /programs/sbgrid.shrc
fi

You may also need to create a .bash_profile with the following contents:

if [ -f $HOME/.bashrc ]; then
     	. $HOME/.bashrc
fi