Jagamisviis:

Create HPC Pack Linux RDMA Cluster in Azure

  • Artikkel

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 https://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