CRAY XC40 Using the Batch System

Introduction

The only way to start a parallel job on the compute nodes of this system is to use the batch system. The installed batch system is based on

• the resource management system torque and
• the scheduler moab

Additional you have to know on CRAY XE6/XC30 the user applications are always launched on the compute nodes using the application launcher, aprun, which submits applications to the Application Level Placement Scheduler (ALPS) for placement and execution.

Detailed information for CRAY XE6 about how to use this system and many examples can be found in Cray Application Developer's Environment User's Guide and Workload Management and Application Placement for the Cray Linux Environment.

Detailed information for CRAY XC30 about how to use this system and many examples can be found in Cray Programming Environment User's Guide and Workload Management and Application Placement for the Cray Linux Environment.

• ALPS is always used for scheduling a job on the compute nodes. It does not care about the programming model you used. So we need a few general definitions :
  • PE : Processing Elements, basically an Unix ‘Process’, can be a MPI Task, CAF image, UPC tread, ...
  • numa_node The cores and memory on a node with ‘flat’ memory access, basically one of the 2 Dies on the Intel and the direct attach memory.
  • Thread A thread is contained inside a process. Multiple threads can exist within the same process and share resources such as memory, while different PEs do not share these resources. Most likely you will use OpenMP threads.

• aprun is the ALPS (Application Level Placement Scheduler) application launcher
  • It must be used to run application on the XC compute nodes interactively and in a batch job
  • If aprun is not used, the application is launched on the MOM node (and will most likely fail)
  • aprun man page contains several useful examples at least 3 important parameter to control:
    • The total number of PEs: -n
    • The number of PEs per node: -N
    • The number of OpenMP threads: -d (the 'stride' between 2 PEs in a node
• qsub is the torque submission command for batch job scripts.

Writing a submission script is typically the most convenient way to submit your job to the batch system. You generally interact with the batch system in two ways: through options specified in job submission scripts (these are detailed below in the examples) and by using torque or moab commands on the login nodes. There are three key commands used to interact with torque:

• qsub
• qstat
• qdel

Check the man page of torque for more advanced commands and options

 man pbs