Troubleshooting Jobs on Quest

This page contains steps to help you determine if something is wrong with your job on Quest and how to go about fixing it.

There are two common issues with jobs on Quest: a job isn't running or a job ended before you expected. This page has some tips for figuring out what may be going wrong. For additional help, contact quest-help@northwestern.edu.

Why isn't my job running?

Common reasons why a job or jobs may not be running are:

  • Your allocation is expired or it has been used extensively in the recent past beyond your "fair" share of the resources. Use the checkproject utility to check your allocation resources. See this example of output from such a situation for more details.
  • You requested more resources (memory or cores) per node than are available on Quest. The scheduler will reject your submission and let you know which resource request is out of bounds according to system configuration and architecture. See Managing Jobs for the checkjob command, and Checking Processor and Memory Utilization for Jobs to check the resources used by your job.
  • You submitted a large number of jobs, and some are listed as "PENDING". This is normal. You can submit up to 5000 jobs to the scheduler and 1000 of these can run concurrently. The pending jobs will wait until running jobs complete and resources become available.
  • Quest is busy.
    • If you are running under a general access Research Allocation I or Research Allocation II, you are using shared resources. If you can keep your jobs under four hours of walltime, your jobs will have access to more nodes than jobs submitted to normal or long partitions.
    • If you are running under a full access allocation with dedicated nodes, see Full Access Allocation Management for commands to check your nodes and jobs. Make sure you have specified the appropriate buyin partition (queue) when submitting your job.
    • To see an estimate of how long it will take for your job to start, use the --test-only option with sbatch:
      sbatch --test-only <job_submission_script.sh>
      This command will return an estimate of when this job would start if it were submitted:
      sbatch: Job 123456 to start at 2019-03-01T07:23:54
      Note this does not actually submit your job.
  • For interactive jobs, see Why won't my interactive job start?

Check the Output File

The first place to look is the output/error file for your job. See Checking the Job Output File for an example. The job output file will be in the directory from which you submitted your job. Even if you directed output from your script/program to another location, there is still an output file with information about the job itself. By default, the output file is named slurm-<jobID>.out and it contains both the standard output and error. You can use the cat command to print the contents to the terminal, or open the file in your preferred text editor.

Another important hint can be obtained from the job's exit code. checkjob <jobID> command will provide this code. The ExitCode field in checkjob report contains two values delineated by a colon (:). The first value is the exit code and the second value will indicate the unix termination signal if a signal was responsible for the termination of the job. An "ExitCode=0:0" means a successfully completed job (as far as the scheduler is concerned). Any other value indicates a potential error. The exit value comes from Slurm and standard unix signals. The list of codes is fairly cryptic, but you can contact quest-help@northwestern.edu for assistance deciphering a non-zero exit code.

The Slurm job state also provides information about the possible issues you may encounter. If you encounter "FAILED" or "NODE_FAIL" job states, there is a strong possibility that your job was not successfully completed. We recommend checking the output for irregularities in these cases.

Job State SLURM Code Description
PENDING PD Job is queued; waiting to run
PREEMPTED PR Job terminated due to preemption
CONFIGURING CF Job has been allocated resources, but is waiting for them to become ready
RUNNING R Job has allocation and is running
COMPLETING CG Job is in the process of completing; some nodes may still be active
COMPLETED CD Job has terminated all processes succesfully
CANCELLED CA Job was explicitly cancelled by user or administrator before or during running
SUSPENDED S Job has allocation, but execution has been suspended
TIMEOUT TO Job has reached its time limit
FAILED F Job terminated with non-zero exit code or other failure condition
NODE_FAIL NF Job terminated due to failure of one or more allocated nodes

If you have an exit code of 0:0 and a COMPLETED state but still think your job ended early or had a problem, there may have been an error in your program code/script. Check any additional output and files you may have written from your code if there isn't additional information in the job output/error file.

Resources Exceeded

Besides errors in your script or hardware failure, your job may be aborted by the system if it is still running when the walltime limit you requested (or the upper walltime limit for the partition) is reached. You will see TIMEOUT state for these jobs.

If you use more cores than you requested, the system will again stop the job. This can happen with programs that are multi-threaded. Similarly, if the job exceeds the requested memory, the job will be terminated. Due to this, it is important to profile your code for the memory requirement.

If you do not set the number of nodes/cores, memory or time in your job submission script, the default values will be assigned by the scheduler.

Out of Disk Space

Your job could also fail if you exceed your storage quote in your home or projects directory.

Check how much space you are using in your home directory with

homedu

or

du -h --max-depth=0 ~

Check how much space is used in your projects directory with

checkproject <allocationID>

Examples

See Also:




Keywords:Quest, msub, Moab, checkjob, batch   Doc ID:70711
Owner:Research Computing .Group:Northwestern
Created:2017-02-15 15:29 CSTUpdated:2019-07-10 15:09 CST
Sites:Northwestern
CleanURL:https://kb.northwestern.edu/troubleshooting-jobs-on-quest
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