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.
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.
- MPI compiler
- PnetCDF version 1.4.0 or later
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.
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
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.
level_max
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
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
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
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.
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
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
% 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
email: [email protected]
Copyright (C) 2013, Northwestern University
See COPYRIGHT notice in top-level directory.