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

This software benchmarks the performance of PnetCDF method implementing the I/O kernel of Global Cloud Resolving Model (GCRM) simulation codes. GCRM was developed at the Colorado State University (http://kiwi.atmos.colostate.edu/gcrm). GCRM's I/O module, called GIO library, was developed at Pacific Northwest National Laboratory (https://svn.pnl.gov/gcrm). GCRM and GIO are written in Fortran90.

This software package extracts the I/O kernel from GCRM and converts it into C for more flexible parameter settings (e.g. number of MPI processes, max level) and dynamic memory allocation for buffer management.

Note on memory requirement

GCRM is a memory-intensive parallel application which allocates a significant amount of memory per process when running. This software preserves such characteristics to reflect its high demands on memory space. For detailed information about the variable sizes and the amount of memory required, please refer to documents in directory ./doc.

Software requirements

  1. MPI compiler
  2. PnetCDF version 1.4.0 or later

Build instructions

Run commands below.

./configure --with-pnetcdf=/path/to/PnetCDF MPICC=your_MPI_C_compiler
make

It creates an executable file named gcrm_io under directory ./run.

Run Instructions

Several input parameter files are available under directory ./inputs which should be copied over to directory .run. The parameter file can be customized to run different problem sizes.

The executable gcrm_io takes one command-line argument which is the input parameter file name that contains all the parameters settings. If no command-line argument is given, it reads the file named zgrd.in. The following parameter files are provided, each specifying a particular problem size.

zgrd.in.r6     - refine level ==  6, corresponding to grid size 112    Km
zgrd.in.r7     - refine level ==  7, corresponding to grid size  55.9  Km
zgrd.in.r8     - refine level ==  8, corresponding to grid size  27.9  Km
zgrd.in.r9     - refine level ==  9, corresponding to grid size  14.0  Km
zgrd.in.r10    - refine level == 10, corresponding to grid size   6.98 Km
zgrd.in.r11    - refine level == 11, corresponding to grid size   3.49 Km

Parameters determine the number of solution variables

Parameter io_desc_file points to file ZGrd.desc, which describes all GCRM variables, including all grid and field variables with information about their size, type, and dimension.

Parameter io_config_file points to a file describing the I/O configuration.

Parameter physics_mode indicates if additional physics variables will be added to the benchmark. Enabling this mode will demand more memory space on each MPI process.

Four pre-defined configurations are provided in ./inputs.

ZGrd.LZ.fcfg.nophys      writes 11 solution variables, one variable per file,
                         no physics variables. Use it for testing only.
ZGrd.CP.lyr.fcfg         writes 38 solution variables, one per netCDF file.
                         It can only be used when physics_mode is enabled.
ZGrd.CP.lyr.fcfg.groups  writes 38 solution variables in 12 netCDF files,
                         some variables that are often accessed together are
                         saved in the same file. It can only be used when
                         physics_mode is enabled.
ZGrd.CP.lyr.fcfg.one*    writes 38 solution variables in one netCDF file, all
                         variables are saved in the same file. It can only be
                         used when physics_mode is enabled.

Parameter for setting refine level

level_max

Parameter for setting frequency of writes

The following 4 parameters determine/mimic the length of simulation:

  • end_days
  • end_hours
  • end_minutes
  • end_seconds

Together with parameter cdf_output_frequency, the number of writes is determined. For example, if the length of simulation is set to 1 minutes (end_minutes == 1) and cdf_output_frequency is set to 60 (seconds), then there will be 2 writes (including one at the initial dump).

Please note that cdf_output_frequency is the amount of time advanced in each simulation iteration. Depending on the value of level_max, set cdf_output_frequency correspondingly. Below is the possible value pairs.

for level_max        =   3,   4,  5,  6,  7, 8, 9, 10, 11, 12
cdf_output_frequency = 900, 120, 60, 30, 15, 8, 4,  2,  1,  1

Parameters specify the directories to store the output files

Users should edit the input parameter file and change the following two parameters output_path and cdf_output_path to the locations where the output files are to be saved.

parameter "output_path"     points to the path for miscellaneous outputs
parameter "cdf_output_path" points to the path for netcdf output files

Note on restart options

Although restart options are provided (see the bottom of file zgrd.in), not all of them are supported in this release, in particular, reading part is not completed. The only options taking effect are

  • restart_interval
  • restart_output
  • restart_overwrite

I/O methods

Currently there are four I/O options (parameter iotype):

  • nonblocking_collective
  • nonblocking_independent
  • blocking_collective
  • blocking_independent

which correspond to using PnetCDF nonblocking APIs with collective flush, nonblocking APIs with independent flush, blocking collective APIs, and blocking independent APIs, respectively. The original GCRM has two additional options namely direct and interleaved, but they are not implemented in this benchmark.

Number of processes to run and command-line arguments

GCRM runs only on certain numbers of MPI processes, depending on the value of sbdmn_iota. The number of processes must be able to divide evenly

M = 10 x 4 ^ sbdmn_iota

M is the total number of subdomains. This is to ensure the numbers of subdomains assigned to individual MPI processes are the same.

sbdmn_iota is the first index i of array nblocks below such that nblocks[i] is divisible by the number of MPI processes.

int nblocks[10] = {10, 40, 160, 640, 2560, 10240, 40960, 163840, 655360, 2621440};

For example, if the number of MPI processes, nprocs, is 80, then sbdmn_iota will be set to 2, because nblocks[2] will be picked 160 which is the minimum number in nblocks[] divisible by nprocs.

Note that because GCRM is memory intensive, the number of processes to run for a refine level, set in level_max, must be sufficiently large to avoid running out of memory. In doc/data\ summary.pdf, the 3rd page shows a table of the memory usage for various combinations of number of processes and level_max when writing all physics variables is enabled and no restart write is performed. The memory usage will be reported for different settings.

Again, the default input parameter file is zgrd.in (when no command-line argument is given.) Users can specify a different parameters file, such as

mpiexec -n 8 ./gcrm_io zgrd.in.r6

Example output from stdout

Below is the output on screen of an example run on 20 MPI processes using the input files ZGrd.CP.lyr.fcfg, ZGrd.desc, and zgrd.in copied from folder inputs.

% mpiexec -n 20 ./gcrm_io

while loop num_dumps=1 time_ZGrd=0.000000 gio_default_frequency=60
while loop num_dumps=2 time_ZGrd=60.000000 gio_default_frequency=60
GIO: ----------------------------------------------------------
GIO statistics: (cumulative across all MPI processes)
GIO: total_time_in_API                           1566.9720
GIO: time_in_nf_put_var                             0.0000
GIO: time_in_nf_put_var_grid                        6.6997
GIO: time_in_nf_put_att                             0.0336
GIO: time_in_nf_def_dim                             0.0063
GIO: time_in_nf_def_var                             0.0059
GIO: time_in_update_time                            0.0036
GIO: time_in_nf_create                            226.8757
GIO: time_in_nf_open                               30.7878
GIO: time_in_nf_close                               5.6107
GIO: time_in_nf_enddef                              2.1618
GIO: time_in_nf_inq_varid                           0.0612
GIO: time_in_nf_inq_dimlen                          0.0000
GIO: time_in_nf_iput                                4.8521
GIO: time_in_nf_iget                                0.0000
GIO: time_in_nf_wait                             1246.1515
GIO: time_in_API_copy                               1.3175
GIO: time_in_avgs                                   0.1935
GIO: ----------------------------------------------------------
GIO: bytes_API_write (Bytes):                   3654442380
GIO: bytes_API_write (MiB):                      3485.1478
GIO: bytes_API_write (GiB):                         3.4035
GIO: bandwidth for writes (MiB/sec):               44.4826
GIO: bandwidth for writes (GiB/sec):                0.0434
GIO: ----------------------------------------------------------
---- MPI file info used ----
MPI File Info: [ 0] key =     romio_pvfs2_debugmask, value = 0
MPI File Info: [ 1] key =           striping_factor, value = 0
MPI File Info: [ 2] key =             striping_unit, value = 0
MPI File Info: [ 3] key =    romio_pvfs2_posix_read, value = disable
MPI File Info: [ 4] key =   romio_pvfs2_posix_write, value = disable
MPI File Info: [ 5] key =    romio_pvfs2_dtype_read, value = disable
MPI File Info: [ 6] key =   romio_pvfs2_dtype_write, value = disable
MPI File Info: [ 7] key =   romio_pvfs2_listio_read, value = disable
MPI File Info: [ 8] key =  romio_pvfs2_listio_write, value = disable
MPI File Info: [ 9] key =            cb_buffer_size, value = 16777216
MPI File Info: [10] key =             romio_cb_read, value = enable
MPI File Info: [11] key =            romio_cb_write, value = enable
MPI File Info: [12] key =                  cb_nodes, value = 8
MPI File Info: [13] key =         romio_no_indep_rw, value = true
MPI File Info: [14] key =              romio_cb_pfr, value = disable
MPI File Info: [15] key =         romio_cb_fr_types, value = aar
MPI File Info: [16] key =     romio_cb_fr_alignment, value = 1
MPI File Info: [17] key =     romio_cb_ds_threshold, value = 0
MPI File Info: [18] key =         romio_cb_alltoall, value = automatic
MPI File Info: [19] key =        ind_rd_buffer_size, value = 4194304
MPI File Info: [20] key =             romio_ds_read, value = automatic
MPI File Info: [21] key =            romio_ds_write, value = disable
MPI File Info: [22] key =            cb_config_list, value = *:1
MPI File Info: [23] key =      nc_header_align_size, value = 2048
MPI File Info: [24] key =         nc_var_align_size, value = 1
MPI File Info: [25] key = nc_header_read_chunk_size, value = 0
====  gcrm-io-pnetcdf 1.0.0   released on  22 Nov 2013 ====
----  Run-time parameters ---------------------------------
----  Number of processes                            = 20
----  level_max  (global horizontal grid resolution) = 5
----  sbdmn_iota (see grid_params.h)                 = 1
----  level_glbl (see grid_params.h)                 = 2
----  km         (number of vertical layers)         = 256
----  cell_max   (global number of cells)            = 10242
----  im         (local  number of cells along i)    = 18
----  jm         (local  number of cells along j)    = 18
----  nsdm_glbl  (global number of blocks)           = 40
----  nsdm       (local  number of blocks)           = 2
----  using physics variables                        = enabled
----  number of files written                        = 40
----  number of grid  variables written              = 16
----  number of field variables written              = 74
----  number of snapshot dumps                       = 2
---------------------------------------------------------------
Timing results (max among all processes)
init     time=             1.43 sec
Max comp time=             2.23 sec
Max I/O  time=            77.58 sec
finalize time=             0.06 sec
---------------------------------------------------------------
Write  amount=          3654.51 MB      =        3485.22 MiB
Read   amount=             9.08 MB      =           8.66 MiB
I/O    amount=          3663.60 MB      =        3493.88 MiB
             =             3.66 GB      =           3.41 GiB
I/O bandwidth=            47.22 MB/sec  =          45.04 MiB/sec
             =             0.05 GB/sec  =           0.04 GiB/sec
---------------------------------------------------------------
memory MAX usage (among 20 procs) =        315.78 MiB
memory MIN usage (among 20 procs) =        315.48 MiB
memory AVG usage (among 20 procs) =        315.62 MiB

Output files created in the output folder.

% ls -lhgG
total 3.5G
-rw------- 1  21M Jul 18 15:24 cloud_ice_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 cloud_water_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 divergence_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 exner_lyr_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 geopotential_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 graupel_mmr_19010101_000000.nc
-rw------- 1 2.0M Jul 18 15:23 grid.nc
-rw------- 1  21M Jul 18 15:24 heat_flux_vdiff_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 heating_latent_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 heating_lw_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 heating_lw_cs_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 heating_sw_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 heating_sw_cs_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 ke_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 mass_19010101_000000.nc
-rw------- 1  83K Jul 18 15:24 olr_19010101_000000.nc
-rw------- 1  83K Jul 18 15:24 prec_frz_19010101_000000.nc
-rw------- 1  83K Jul 18 15:24 prec_tot_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 pressure_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qci_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qcw_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qgr_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qrw_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qsn_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 qwv_tend_micro_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 rain_mmr_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 rel_vorticity_19010101_000000.nc
-rw------- 1 1.4G Jul 18 15:24 restart.nc19010101_000000.nc
-rw------- 1 1.4G Jul 18 15:25 restart.nc19010101_000100.nc
-rw------- 1  21M Jul 18 15:24 snow_mmr_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 strm_func_19010101_000000.nc
-rw------- 1  83K Jul 18 15:24 swinc_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 temperature_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 vel_pot_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 vorticity_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 water_vapor_19010101_000000.nc
-rw------- 1  61M Jul 18 15:24 wind_19010101_000000.nc
-rw------- 1  41M Jul 18 15:24 wind_crn_ew_19010101_000000.nc
-rw------- 1  41M Jul 18 15:24 wind_crn_ns_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 wtr_flux_vdiff_19010101_000000.nc
-rw------- 1  21M Jul 18 15:24 w_vert_19010101_000000.nc

Questions/Comments:

email: [email protected]

Copyright (C) 2013, Northwestern University

See COPYRIGHT notice in top-level directory.

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