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PnetCDF I/O Benchmark using S3D Application I/O Kernel

This software benchmarks the performance of PnetCDF method implementing the I/O kernel of S3D combustion simulation code. The evaluation method is weak scaling.

S3D is a continuum scale first principles direct numerical simulation code which solves the compressible governing equations of mass continuity, momenta, energy and mass fractions of chemical species including chemical reactions. Readers are referred to the published paper below.

  • J. Chen, A. Choudhary, B. de Supinski, M. DeVries, E. Hawkes, S. Klasky, W. Liao, K. Ma, J. Crummey, N. Podhorszki, R. Sankaran, S. Shende, and C. Yoo. Teras-cale Direct Numerical Simulations of Turbulent Combustion Using S3D. In Computational Science and Discovery Volume 2, January 2009.

I/O pattern:

A data checkpoint is performed at regular time intervals, and its data consist of three- and four-dimensional array variables of type double. At each checkpoint, four global arrays, representing mass, velocity, pressure, and temperature, respectively, are written to a newly created file in the canonical order. Mass and velocity are four-dimensional arrays while pressure and temperature are three-dimensional arrays. All four arrays share the same size of the lowest three spatial dimensions X, Y, and Z, which are partitioned among MPI processes in a block-block-block fashion. See Figure 1 below for an illustration when the number of MPI processes is 64. For the mass and velocity arrays, the length of the fourth dimension is 11 and 3, respectively. The fourth dimension, the most significant one, is not partitioned. As the number of MPI processes increases, the aggregate I/O amount proportionally increases as well. For more detailed description, please refer to:

  • W. Liao and A. Choudhary. Dynamically Adapting File Domain Partitioning Methods for Collective I/O Based on Underlying Parallel File System Locking Protocols. In the Proceedings of International Conference for High Performance Computing, Networking, Storage and Analysis, Austin, Texas, November 2008.

Figure 1. S3D I/O data partitioning pattern. (a) For 3D arrays, the sub-array of each process is mapped to the global array in a fashion of block partitioning in all X-Y-Z dimensions.(b) For 4D arrays, the lowest X-Y-Z dimensions are partitioned the same as the 3D arrays while the fourth dimension is not partitioned. This example uses 64 processes and highlights the mapping of process P41's sub-array to the global array.

To compile:

Edit file Makefile and adjust the following variables:

    MPIF90         - MPI Fortran 90 compiler
    FCFLAGS        - compile flags
    PNETCDF_DIR    - the path of PnetCDF library (1.4.0 and higher is required)

For example:

    MPIF90      = /usr/bin/mpif90
    FCFLAGS     = -O2
    PNETCDF_DIR = ${HOME}/PnetCDF

To run:

The command-line arguments are shown below, which can also be obtain by command ./s3d_io.x -h.

Usage: s3d_io.x nx_g ny_g nz_g npx npy npz method restart dir_path

There are 9 command-line arguments:

       nx_g     - GLOBAL grid size along X dimension
       ny_g     - GLOBAL grid size along Y dimension
       nz_g     - GLOBAL grid size along Z dimension
       npx      - number of MPI processes along X dimension
       npy      - number of MPI processes along Y dimension
       npz      - number of MPI processes along Z dimension
       method   - 0: using PnetCDF blocking APIs, 1: nonblocking APIs
       restart  - restart from reading a previous written file (True/False)
       dir_path - the directory name to store the output files

To change the number of checkpoint dumps (default is set to 5), edit file param_m.f90 and set a different value for i_time_end:

       i_time_end = 5   ! number of checkpoints (also number of output files)

When the I/O method is set to PnetCDF blocking APIs, each checkpoint has a total of 4 x i_time_end collective PnetCDF write calls, one for each variable. If restart is set to True, the number of read collective calls is 4, one per variable, regardless of the number of checkpoints, as read only performs once at the beginning of the run. When the I/O method is set to PnetCDF nonblocking APIs, each checkpoint has 4 nonblocking PnetCDF write calls, one per variable, followed by a call to nfmpi_waitall to flush the write requests. Thus, the total number of calls to nfmpi_waitall is equal to i_time_end. For read, there are a total of 4 nonblocking PnetCDF read calls and a single call to nfmpi_waitall for read requests.

The contents of all variables written to netCDF files are randomly generated numbers. This setting can be disabled by commenting out the line below in file solve_driver.f90. Commenting it out can reduce the benchmark execution time.

       call random_set

Example run command:

For a test run with small data size and a short return time, here is an example command for running on 4 MPI processes.

   mpiexec -n 4 ./s3d_io.x 10 10 10 2 2 1 1 F .

The example command below runs a job on 4096 MPI processes with the global array of size 800 x 800 x 800 and local arrays of size 50 x 50 x 50, output directory /scratch1/scratchdirs/wkliao/FS_1M_96 using nonblocking APIs, and without restart.

   mpiexec -l -n 4096 ./s3d_io.x 800 800 800 16 16 16 1 F /scratch1/scratchdirs/wkliao/FS_1M_96

Example output from screen:

 ++++ I/O is done through PnetCDF ++++
 I/O method          : nonblocking APIs
 Run with restart    : False
 No. MPI processes   :    4096
 Global array size   :     800 x    800 x    800
 output file path    : /scratch1/scratchdirs/wkliao/FS_1M_96
 file striping count :      96
 file striping size  : 1048576 bytes
 -----------------------------------------------
 Time for open       :        0.11 sec
 Time for read       :        0.00 sec
 Time for write      :       18.04 sec
 Time for close      :        0.02 sec
 no. read  calls     :        0    per process
 no. write calls     :       20    per process
 total read  amount  :        0.00 GiB
 total write amount  :      305.18 GiB
 read  bandwidth     :        0.00 MiB/s
 write bandwidth     :    17318.78 MiB/s
 -----------------------------------------------
 total I/O   amount  :      305.18 GiB
 total I/O   time    :       18.17 sec
 I/O   bandwidth     :    17201.53 MiB/s

Example metadata of the output file.

% ncdump -h pressure_wave_test.0.000E+00.field.nc

netcdf pressure_wave_test.0.000E+00.field {
dimensions:
        x = 800 ;
        y = 800 ;
        z = 800 ;
        nsc = 11 ;
        three = 3 ;
variables:
        double yspecies(nsc, z, y, x) ;
        double u(three, z, y, x) ;
        double pressure(z, y, x) ;
        double temp(z, y, x) ;

// global attributes:
                :time = 0. ;
                :tstep = 0. ;
                :time_save = 100000. ;
}

Questions/Comments:

email: wkliao@eecs.northwestern.edu

Copyright (C) 2013, Northwestern University

See COPYRIGHT notice in top-level directory.