Common computational problems

Here are some computational problems commonly encountered on the compute servers and cluster and some solutions or workarounds.

  • Your cluster job won't start
    • Your account may not have been given access to the cluster. Please email trouble [at] stat [dot] berkeley [dot] edu.
    • Jobs in the high queue can use at most 36 cores.
    • See also the next common problem listed just below.
  • Your cluster job is stuck at the top of the queue and other jobs start before it
    • Jobs requesting multiple cores may not start because not enough cores become available at once. The SLURM scheduler will try to accumulate sufficient cores for your job to start, but other smaller jobs may start before yours if the scheduler determines that doing so will not delay the start of your job. Unfortunately, because we don't require time limits, SLURM has limited information with which to make this determination. So particularly for jobs requesting many cores, this may happen. 
  • R hangs when using profiling
    • This is likely a conflict between's Rprof() and the threaded BLAS used by R for linear algebra. Solutions include (1) disabling threading (see here for more details) and (2) not using profiling.
  • Matlab won't use more than 12 cores at once