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Question

我正在使用AMD 2990WX（Ubuntu 18.04）运行LAMMPS仿真。

当我使用如下所示的mpirun只运行一项LAMMPS作业时。

    #!/bin/sh

    LAMMPS_HOME=/APP/LAMMPS/src
    MPI_HOME=/APP/LIBS/OPENMPI2

    Tf=0.30

    $MPI_HOME/bin/mpirun -np 8 --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.020 -var Tf ${Tf}

我没问题，仿真随心所欲。

但是当我运行下面的脚本时。每个LAMMPS作业几乎是单个LAMMPS作业的三倍。因此，我在并行环境中没有性能提升（因为3个作业以单个作业的1/3的速度运行）

    #!/bin/sh

    LAMMPS_HOME=/APP/LAMMPS/src
    MPI_HOME=/APP/LIBS/OPENMPI2

    Tf=0.30

    $MPI_HOME/bin/mpirun -np 8 --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.020 -var Tf ${Tf} &
    $MPI_HOME/bin/mpirun -np 8 --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.025 -var Tf ${Tf} &
    $MPI_HOME/bin/mpirun -np 8 --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.030 -var Tf ${Tf}

没有主机文件my_host，这是相同的。主机文件如下：

    <hostname> slots=32 max-slots=32

我用--with-cuda安装了openmpi，用--enable-shared安装了fftw，并用了一些软件包安装了LAMMPS。

我尝试过openmpi v1.8，v3.0，v4.0和fftw v3.3.8。 RAM足够，存储也足够。我还检查了平均负载和核心使用情况。它们显示当我运行第二个脚本时，该计算机使用24个内核（或相应的负载）。当我在单独的终端（即每个终端中的sh first.sh）上同时运行第一个脚本的副本时，会发生相同的问题。

我使用bash脚本是否有问题？或mpirun（或LAMMPS）+ Ryzen是否存在任何已知问题？

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我已经测试了以下脚本：

/bin/sh

LAMMPS_HOME=/APP/LAMMPS/src
MPI_HOME=/APP/LIBS/OPENMPI2

Tf=0.30

$MPI_HOME/bin/mpirun --cpu-set 0-7 --bind-to core -np 8 --report-bindings --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.020 -var Tf ${Tf} &
$MPI_HOME/bin/mpirun --cpu-set 8-15 --bind-to core -np 8 --report-bindings --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.025 -var Tf ${Tf} &
$MPI_HOME/bin/mpirun --cpu-set 16-23 --bind-to core -np 8 --report-bindings --hostfile my_host $LAMMPS_HOME/lmp_lmp_mpi -in $PWD/../01_Annealing/in.01_Annealing -var MaxShear 0.030 -var Tf ${Tf}

结果显示如下：

[<hostname>:09617] MCW rank 4 bound to socket 0[core 4[hwt 0-1]]: [../../../../BB/../../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 5 bound to socket 0[core 5[hwt 0-1]]: [../../../../../BB/../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 6 bound to socket 0[core 6[hwt 0-1]]: [../../../../../../BB/../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 7 bound to socket 0[core 7[hwt 0-1]]: [../../../../../../../BB/../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/../../../../../../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB/../../../../../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 2 bound to socket 0[core 2[hwt 0-1]]: [../../BB/../../../../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09617] MCW rank 3 bound to socket 0[core 3[hwt 0-1]]: [../../../BB/../../../../../../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09619] MCW rank 4 bound to socket 0[core 20[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../../../BB/../../../../../../../../../../..]
[<hostname>:09619] MCW rank 5 bound to socket 0[core 21[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../../../../BB/../../../../../../../../../..]
[<hostname>:09619] MCW rank 6 bound to socket 0[core 22[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../../../../../BB/../../../../../../../../..]
[<hostname>:09619] MCW rank 7 bound to socket 0[core 23[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../../../../../../BB/../../../../../../../..]
[<hostname>:09619] MCW rank 0 bound to socket 0[core 16[hwt 0-1]]: [../../../../../../../../../../../../../../../../BB/../../../../../../../../../../../../../../..]
[<hostname>:09619] MCW rank 1 bound to socket 0[core 17[hwt 0-1]]: [../../../../../../../../../../../../../../../../../BB/../../../../../../../../../../../../../..]
[<hostname>:09619] MCW rank 2 bound to socket 0[core 18[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../BB/../../../../../../../../../../../../..]
[<hostname>:09619] MCW rank 3 bound to socket 0[core 19[hwt 0-1]]: [../../../../../../../../../../../../../../../../../../../BB/../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 4 bound to socket 0[core 12[hwt 0-1]]: [../../../../../../../../../../../../BB/../../../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 5 bound to socket 0[core 13[hwt 0-1]]: [../../../../../../../../../../../../../BB/../../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 6 bound to socket 0[core 14[hwt 0-1]]: [../../../../../../../../../../../../../../BB/../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 7 bound to socket 0[core 15[hwt 0-1]]: [../../../../../../../../../../../../../../../BB/../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 0 bound to socket 0[core 8[hwt 0-1]]: [../../../../../../../../BB/../../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 1 bound to socket 0[core 9[hwt 0-1]]: [../../../../../../../../../BB/../../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 2 bound to socket 0[core 10[hwt 0-1]]: [../../../../../../../../../../BB/../../../../../../../../../../../../../../../../../../../../..]
[<hostname>:09618] MCW rank 3 bound to socket 0[core 11[hwt 0-1]]: [../../../../../../../../../../../BB/../../../../../../../../../../../../../../../../../../../..]

我对MPI的了解不多，但是对我来说，它并不显示任何奇怪之处。有什么问题吗？

通过多个并发MPI LAMMPS作业而变慢

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0 个答案: