On May 17, 2011, at 11:35 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is starting up fine without any drmaa configuration. However the galaxy daemon doesn't start properly when I add drmaa configuration lines as shown below. I have set SGE_ROOT and DRMAA_LIBRARY_PATH variables properly. Am I missing something important here?
Could you provide the output of starting Galaxy with the drmaa options enabled? You may want to start it in the foreground (without --daemon) to capture any messages which are not output to paster.log
It's working now. I hadn't set SGE_QMASTER_PORT env variable earlier. I am guessing galaxy-start process got hung while attempting to connect with 'unknown/null' SGE port. I didn't see any error related to SGE_QMASTER_PORT in the log file, however I did notice that galaxy checks for SGE_ROOT variable value. We are using a fresh SGE submit host install here and hence we may see some initial environment configuration issues. Another community member Ross Lazarus suggested me to try sge as job_runner setting instead of pbs or drmaa. This printed out error message related to SGE_QMASTER_PORT in the logs. I set this variable and then tried drmaa setting again which worked fine this time. Thanks for the help Ross and Nate. -- Shantanu.