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Application Guide - ATK

Introduction

Atomistix ToolKit (ATK) is a commercial computational chemistry software for atomic scale modelling, commercialised by QuantumWise.  ATK can run in parallel on the ARC clusters using the MPICH2 implementation of MPI.

The guide shows how to

  • load the ATK module;
  • prepare a ATK job submission script and
  • submit the ATK job.

 

    Running an ATK job

    First, you need to load the module for the ATK package.  A few versions of ATK may be available, all managed through the modules; use the command: module avail atk to see what versions are available.  The sought version can be specified when loading the module, e.g.

    module load atk/12.8.2

     

    If no version is specified, the default version is loaded.  (The default is normally the latest version available.)  When loaded, the module for atk also loads the appropriate module for mpich2.

    Then, you need to prepare a submission script for the ATK job.  Assume the calculations to run are programmed in the python file atkTest.py, which are to be carried out using atkpython.  The submission script for this job should look something like this:

    #!/bin/bash
     
    #SBATCH --nodes=2
    #SBATCH --ntasks-per-node=16
    #SBATCH --time=01:00:00
    #SBATCH --job-name=atkTest
     
    module purge
    module load atk
     
    . atk.sh
    atkpython_run atkTest

    The setup for the parallel run is prepared automatically by the script atk.sh, which works with both the Torquen and Slurm environment.  Starting from the number of nodes requested (nodes=2 in this case), this script sets

    • the number of parallel MPI processes that each node runs and
    • the number of parallel threads that each process uses.

    Following the recommendations from QuantumWise, the setup uses a number of processes per node equal to the number of cores available (16, currently).  This means there is a one to one correspondence between the MPI processes running on a node and the number of cores available on that node.  For some time, QuantumWise recommended the number of MPI processes be equal to the number of CPU sockets available per node, thus leaving each process multithread on the CPU cores.  They have however reviewed this recommendation, and the general wisdom now is to fully populate the nodes with single-threaded MPI processes.  (Our own tests on the ARC clusters have confirmed this finding.) The default setting reflects that.

    If users with to change the default values, they can do so by setting a couple of variables in the submission script.  For example, a job can be set to use 2 MPI process per node (one process per CPU socket) instead of the default 1 by adding

    export NUM_PROCS_PER_NODE=2
    export NUM_THREADS_PER_PROCESS=8

     

    in the submission script just before the line sourcing the script atk.sh.  The total number of MPI processes in the job depends on the nodes request in the PBS headers but is independent of the ppn value.  Also, the total number of threads, equal to the number of processes multiplied by the number of threads per process, is always set to equal the total number of cores available per job.

      The parallel launch is managed using the function atkpython_run (also defined by atk.sh), which launches atkpython through mpiexec.  The command line argument to this function is the name of the job, i.e. the name of the python script without the .py extension.  The standard output from the ATK run goes to a file with the same name and the extension .out; in the above example, output goes to atkTest.out.

        Finally, supposing the above example submission script is called atkTestRun.sh, the job is sent to the execution queue with the command:

        sbatch atkTestRun.sh

        Example Job

        We have provided an example job environment (based on the scripts above) which you can use to familiarise yourself with the batch system or modify for your own jobs. To extract it:

        cd $DATA
        tar xf /system/software/examples/scripts/atk.tgz

         

        This will create a directory named atk-example, to run the example job:

        cd atk-example
        sbatch atk_slurm.sh

         

        Querying ATK License Server

        The ATK license server can be queried from your laptop, desktop or departmental machine with the command

        lmxendutil -licstat -host grant.arc.ox.ac.uk -port 19876 -network

        lmxendutil is a FlexNet (formerly known as FLEXlm) tool that comes with the ATK license server software.

        Service area: 

        Written by IT Services. Latest revision 28 March 2017