Hi again, Just to let anyone that comes across this message to know that the issue turned out to be a problem with a specific version of the openafs client.
The server is running Debian Wheezy and openafs-client was 1.6.1. Using the backported version 1.6.5 solved the issue. Regards, Renato Quoting Renato Alves on 18-10-2013 03:18: > Hi everyone, > > I'm currently setting up galaxy to run on top of AFS using torque for > handling jobs. > > Everything is setup according to wiki documentation but I'm having a > weird filesystem corruption problem. > > The setup is the following: > > machine A: runs galaxy. Galaxy home folder is on AFS. > machine B: runs torque server and shares Galaxy's home folder. > > When I launch a process via galaxy everything works as expected but the > output file becomes corrupted with 4kb of leading zero bytes (file > NC_010473.tabular). This corruption is reproducible at all times, > regardless of file size. In the attached example, the original file is > NC_010473.faa. > > If I restart the openafs client or flush the AFS file cache the > corruption goes away. However, if I re-run the same script created by > galaxy through torque the corruption doesn't happen. Hence it only > happens if launched via Galaxy. > > I also tried both the DRMAA and the PBS modules but the corruption remained. > > Does anyone know what could be the cause of this? > > Thanks, > Renato >
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