Re: [galaxy-dev] debugging jobs in 'new' state
Hi, you didn't specify what clustering method u r using. Are u using drmaa or pbs? With Regards, Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi pa...@uab.edu wrote: We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] debugging jobs in 'new' state
Thanks for the reply Ambarish. We are using SGE cluster and job submission is done using drmaa. -- Shantanu. On Jul 28, 2011, at 7:24 PM, ambarish biswas wrote: Hi, you didn't specify what clustering method u r using. Are u using drmaa or pbs? With Regards, Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi pa...@uab.edumailto:pa...@uab.edu wrote: We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] debugging jobs in 'new' state
hi, can you paste the configuration from your *universe_wsgi.ini* file. With Regards, Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Jul 29, 2011 at 12:31 PM, Shantanu Pavgi pa...@uab.edu wrote: Thanks for the reply Ambarish. We are using SGE cluster and job submission is done using drmaa. -- Shantanu. On Jul 28, 2011, at 7:24 PM, ambarish biswas wrote: Hi, you didn't specify what clustering method u r using. Are u using drmaa or pbs? With Regards, Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi pa...@uab.edu wrote: We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
