Create HPC Pack Linux RDMA Cluster in Azure

Deploy a cluster with ARM Template

Run Intel MPI Benchmark Pingpong

  • Log on head node hpc6267 and take nodes online

    nodes

  • Submit a job to run MPI Pingpong among Linux compute nodes

    job submit /numnodes:2 "source /opt/intel/impi/`ls /opt/intel/impi`/bin64/mpivars.sh && mpirun -env I_MPI_FABRICS=shm:dapl -env I_MPI_DAPL_PROVIDER=ofa-v2-ib0 -env I_MPI_DYNAMIC_CONNECTION=0 -env I_MPI_FALLBACK_DEVICE=0 -f $CCP_MPI_HOSTFILE -ppn 1 IMB-MPI1 pingpong | tail -n30"
    
  • The host file or machine file for MPI task is generated automatically

    • Environment variable $CCP_MPI_HOSTFILE could be used in task command to get the file name

    • Environment variable $CCP_MPI_HOSTFILE_FORMAT could be set to specify the format of host file or machine file

      • The default host file format is like:

        nodename1
        nodename2
        …
        nodenameN
        
      • When $CCP_MPI_HOSTFILE_FORMAT=1, the format is like:

        nodename1:4
        nodename2:4
        …
        nodenameN:4
        
      • When $CCP_MPI_HOSTFILE_FORMAT=2, the format is like:

        nodename1 slots=4
        nodename2 slots=4
        …
        nodenameN slots=4
        
      • When $CCP_MPI_HOSTFILE_FORMAT=3, the format is like:

        nodename1 4
        nodename2 4
        …
        nodenameN 4
        
  • Check task result in HPC Pack 2016 Cluster Manager

    pingpong

Run OpenFOAM workload

Download and install Intel MPI

  • Intel MPI is already installed in the Linux image CentOS_7.4_HPC, but a newer version is needed for building OpenFOAM, which can be downloaded from Intel MPI library

  • Download and silently install Intel MPI with clusrun

    clusrun /nodegroup:LinuxNodes /interleaved "wget http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/l_mpi_2018.3.222.tgz && tar -zxvf l_mpi_2018.3.222.tgz && sed -i -e 's/ACCEPT_EULA=decline/ACCEPT_EULA=accept/g' ./l_mpi_2018.3.222/silent.cfg && ./l_mpi_2018.3.222/install.sh --silent ./l_mpi_2018.3.222/silent.cfg"
    

Download and compile OpenFOAM

  • OpenFOAM packages could be downloaded from OpenFOAM download page

  • Before building OpenFOAM, we need to install zlib-devel and Development Tools on Linux compute nodes(CentOS), to change the value of variable WM_MPLIB from SYSTEMOPENMPI to INTELMPI in OpenFOAM environment settings file bashrc, and to source the Intel MPI environment settings file mpivars.sh and OpenFOAM environment settings file bashrc

  • Optionally, environment variable WM_NCOMPPROCS could be set to specify how many processors to use for compiling OpenFoam, which could accelerate the compilation

  • Use clusrun to achieve all above

    clusrun /nodegroup:LinuxNodes /interleaved "yum install -y zlib-devel && yum groupinstall -y 'Development Tools' && wget https://sourceforge.net/projects/openfoamplus/files/v1806/ThirdParty-v1806.tgz && wget https://sourceforge.net/projects/openfoamplus/files/v1806/OpenFOAM-v1806.tgz && mkdir /opt/OpenFOAM && tar -xzf OpenFOAM-v1806.tgz -C /opt/OpenFOAM && tar -xzf ThirdParty-v1806.tgz -C /opt/OpenFOAM && cd /opt/OpenFOAM/OpenFOAM-v1806/ && sed -i -e 's/WM_MPLIB=SYSTEMOPENMPI/WM_MPLIB=INTELMPI/g' ./etc/bashrc && source /opt/intel/impi/2018.3.222/bin64/mpivars.sh && source ./etc/bashrc && export WM_NCOMPPROCS=$((`grep -c ^processor /proc/cpuinfo`-1)) && ./Allwmake"
    

Create share in cluster

  • Create a folder named openfoam on head node and share it to Everyone with Read/Write permission

  • Create directory /openfoam and mount the share on Linux compute nodes with clusrun

    clusrun /nodegroup:LinuxNodes "mkdir /openfoam && mount -t cifs //hpc6267/openfoam /openfoam -o vers=2.1,username=hpcadmin,dir_mode=0777,file_mode=0777,password='********'"
    

    Remember to replace the username and password in above code when copying.

Prepare the environment setting file for running MPI tasks

  • Create file settings.sh in the share with code:

    #!/bin/bash
    # impi
    source /opt/intel/impi/2018.3.222/bin64/mpivars.sh
    export MPI_ROOT=$I_MPI_ROOT
    export I_MPI_FABRICS=shm:dapl
    export I_MPI_DAPL_PROVIDER=ofa-v2-ib0
    export I_MPI_DYNAMIC_CONNECTION=0
    # openfoam
    source /opt/OpenFOAM/OpenFOAM-v1806/etc/bashrc
    

    Be care of the line endings if the file is edited on head node, which should be \n rather than \r\n

Prepare sample data for OpenFOAM job

  • Copy the sample sloshingTank3D in OpenFOAM tutorials directory to the share openfoam

  • Optionally, modify the value of deltaT from 0.05 to 0.5 and the value of writeInterval from 0.05 to 0.5 in /openfoam/sloshingTank3D/system/controlDict to accelerate data processing

  • Modify the file /openfoam/sloshingTank3D/system/decomposeParDict in terms of the core number to use, more refer to OpenFOAM User Guide: 3.4 Running applications in parallel

    /*--------------------------------*- C++ -*----------------------------------*\
    | =========                 |                                                 |
    | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
    |  \\    /   O peration     | Version:  v1806                                 |
    |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
    |    \\/     M anipulation  |                                                 |
    \*---------------------------------------------------------------------------*/
    FoamFile
    {
        version     2.0;
        format      ascii;
        class       dictionary;
        object      decomposeParDict;
    }
    // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
    
    numberOfSubdomains 32;
    
    method          hierarchical;
    
    coeffs
    {
        n           (1 1 32);
        //delta       0.001; // default=0.001
        //order       xyz;   // default=xzy
    }
    
    distributed     no;
    
    roots           ( );
    
    // ************************************************************************* //
    
  • Prepare sample data in /openfoam/sloshingTank3D. Below code could be used when performing it manually on Linux compute node:

    cd /openfoam/sloshingTank3D
    source /openfoam/settings.sh
    source /home/hpcadmin/OpenFOAM/OpenFOAM-v1806/bin/tools/RunFunctions
    m4 ./system/blockMeshDict.m4 > ./system/blockMeshDict
    runApplication blockMesh
    cp ./0/alpha.water.orig ./0/alpha.water
    runApplication setFields
    
  • Submit a job to achieve all above

    set CORE_NUMBER=32
    job submit "cp -r /opt/OpenFOAM/OpenFOAM-v1806/tutorials/multiphase/interFoam/laminar/sloshingTank3D /openfoam/ && sed -i 's/deltaT          0.05;/deltaT          0.5;/g' /openfoam/sloshingTank3D/system/controlDict &&  sed -i 's/writeInterval   0.05;/writeInterval   0.5;/g' /openfoam/sloshingTank3D/system/controlDict && sed -i 's/numberOfSubdomains 16;/numberOfSubdomains %CORE_NUMBER%;/g' /openfoam/sloshingTank3D/system/decomposeParDict && sed -i 's/n           (4 2 2);/n           (1 1 %CORE_NUMBER%);/g' /openfoam/sloshingTank3D/system/decomposeParDict && cd /openfoam/sloshingTank3D/ && m4 ./system/blockMeshDict.m4 > ./system/blockMeshDict && source /opt/OpenFOAM/OpenFOAM-v1806/bin/tools/RunFunctions && source /opt/OpenFOAM/OpenFOAM-v1806/etc/bashrc && runApplication blockMesh && cp ./0/alpha.water.orig ./0/alpha.water && runApplication setFields"
    

Create job containing MPI tasks to process date

  • Create a job and add 4 tasks with dependence

    Task name Dependent task Cores Command Environment variable
    task1 N/A 1 source /openfoam/settings.sh && decomposePar -force N/A
    task2 task1 32 source /openfoam/settings.sh && mpirun -machinefile $CCP_MPI_HOSTFILE interFoam -parallel CCP_MPI_HOSTFILE_FORMAT=1
    task3 task2 1 source /openfoam/settings.sh && reconstructPar N/A
    task4 task3 32 source /openfoam/settings.sh && mpirun -machinefile $CCP_MPI_HOSTFILE foamToEnsight -parallel CCP_MPI_HOSTFILE_FORMAT=1
  • Set the working directory to /openfoam/sloshingTank3D and standard output to ${CCP_JOBID}.${CCP_TASKID}.log of each task

  • Achieve all above with commands:

    set CORE_NUMBER=32
    job new
    job add !! /workdir:/openfoam/sloshingTank3D /name:task1 /stdout:${CCP_JOBID}.${CCP_TASKID}.log "source /openfoam/settings.sh && decomposePar -force"
    job add !! /workdir:/openfoam/sloshingTank3D /name:task2 /stdout:${CCP_JOBID}.${CCP_TASKID}.log /depend:task1 /numcores:%CORE_NUMBER% /env:CCP_MPI_HOSTFILE_FORMAT=1 "source /openfoam/settings.sh && mpirun -machinefile $CCP_MPI_HOSTFILE interFoam -parallel"
    job add !! /workdir:/openfoam/sloshingTank3D /name:task3 /stdout:${CCP_JOBID}.${CCP_TASKID}.log /depend:task2 "source /openfoam/settings.sh && reconstructPar"
    job add !! /workdir:/openfoam/sloshingTank3D /name:task4 /stdout:${CCP_JOBID}.${CCP_TASKID}.log /depend:task3 /numcores:%CORE_NUMBER% /env:CCP_MPI_HOSTFILE_FORMAT=1 "source /openfoam/settings.sh && mpirun -machinefile $CCP_MPI_HOSTFILE foamToEnsight -parallel"
    job submit /id:!!
    

Get result

  • Check job result in HPC Pack 2016 Cluster Manager

    openfoam

  • The result of sample sloshingTank3D is generated as file \\hpc6267\openfoam\sloshingTank3D\EnSight\sloshingTank3D.case, which could be viewed by Ensight