I've just added a new feature to the dev version of recon-all to help you manage your processes.
When you launch recon-all, it will create a file called IsRunning.lh+rh in your subject/scripts folder. When recon-all finishes (with or without errors), this file will be deleted. So, the presence of this file indicates that recon-all is being run on this subject.
This file may also exist if recon-all died in a way that it could not clean up (eg, control-C). The contents of the file indicate information about the process that will allow you to determine whether it is still running or not:
date Thu Jul 19 19:24:30 EDT 2007 processid 10196 hemi lh rh host icebox user greve Linux icebox 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux
You can then ssh to the host and use the unix 'ps' command to check for the existence of the process.
If you run recon-all on this subject again while this file exists, it will exit indicating that the subject is already being processed or recon-all died uncleanly.
If you want it to run regardless, then add -no-isrunning to the command-line. It will not delete the IsRunning file, just ignore it.
When you run the hemispheres separately (ie, -hemi lh or -hemi rh), it will create a IsRunning.lh or IsRunning.rh file. This allows you to run recon-all for both hemis in parallel. If this file exists or IsRunning.lh+rh exists, then again recon-all will exit telling you that the subject is already being processed or recon-all died uncleanly.
doug