Re: [netcdfgroup] abysmal performance

Is this a netcdf-3 (classic) file or netcdf-4?
=Dennis Heimbigner
 Unidata

On 6/2/2016 1:12 PM, Burlen Loring wrote:
I am working on a climate analysis app. it must scan the dataset,
comprised of many netcdf files to determine the available time steps.
I'm finding that during reading the time axis from the file the
performance is really bad. In one example the dataset is 10k files, each
file has 8 time values, each value is 8 bytes, so 64 bytes are read per
file. the time taken to read these arrays is between 0.3 and 2.2 seconds
which puts the measured performance between 213 bytes per second and 29
bytes per second! I've had dial modems faster than that!

reading other much larger arrays is much much faster, eg reading lon
array with 1152 values only takes 7.7e-5 sec. I don't get it.

I'd like some advise on this. On my workstation the read times of time
values on the same dataset ranges between 1.9e-5 and 4.7e-5 sec. Thus
something seems very wrong with the performance on the cray. btw this is
on the lustre scratch2 file system and files are 433 MB each and striped
across 24 ost's with a stripe size of 1MB.

Burlen

here is the raw data gathered from edison

$/usr/common/graphics/teca/builds/TECA/bin/bin/teca_metadata_probe
--input_regex
/scratch2/scratchdirs/prabhat/TCHero/data/cam5_1_amip_run2'\.cam2\.h2.2005-09-[0-9][0-9]-10800.nc$'

scan_files = 1.1513
open_file = 0.0967366
x_axis_metadata = 7.4109e-05
y_axis_metadata = 7.732e-06
z_axis_metadata = 3.84e-07
t_axis_metadata = 5.418e-06
variables = 0.000824452
read_x_axis = 5.9976e-05
read_y_axis = 1.0444e-05
read_z_axis = 4.294e-06
read_t_axis = 0.368079
open_file = 0.122236
t_axis_metadata = 4.906e-05
read_t_axis = 0.431482
open_file = 0.0953903
t_axis_metadata = 3.4205e-05
read_t_axis = 0.3815
open_file = 0.0853393
t_axis_metadata = 2.9607e-05
read_t_axis = 0.396472
open_file = 0.0664037
t_axis_metadata = 2.8239e-05
read_t_axis = 0.351707
open_file = 0.748844
t_axis_metadata = 3.3047e-05
read_t_axis = 1.03634
open_file = 0.161732
t_axis_metadata = 2.6955e-05
read_t_axis = 0.377919
open_file = 0.0820469
t_axis_metadata = 3.1613e-05
read_t_axis = 0.363014
open_file = 0.0903407
t_axis_metadata = 3.1844e-05
read_t_axis = 0.370521
open_file = 0.092586
t_axis_metadata = 2.9547e-05
read_t_axis = 0.37146
open_file = 0.083997
t_axis_metadata = 4.0095e-05
read_t_axis = 0.396375
open_file = 0.0799897
t_axis_metadata = 2.9833e-05
read_t_axis = 0.386237
open_file = 0.105688
t_axis_metadata = 0.000124456
read_t_axis = 0.481453
open_file = 0.0816038
t_axis_metadata = 3.0969e-05
read_t_axis = 0.355051
open_file = 0.101204
t_axis_metadata = 2.5927e-05
read_t_axis = 0.408186
open_file = 0.108662
t_axis_metadata = 2.6313e-05
read_t_axis = 0.314209
open_file = 0.0916682
t_axis_metadata = 2.9697e-05
read_t_axis = 0.319686
open_file = 0.0812744
t_axis_metadata = 2.7813e-05
read_t_axis = 0.391357
open_file = 0.101898
t_axis_metadata = 2.8607e-05
read_t_axis = 0.305515
open_file = 0.0748274
t_axis_metadata = 1.7247e-05
read_t_axis = 0.69522
open_file = 0.100151
t_axis_metadata = 1.7887e-05
read_t_axis = 0.511695
open_file = 0.0700686
t_axis_metadata = 1.8225e-05
read_t_axis = 2.27155
open_file = 0.121193
t_axis_metadata = 1.9918e-05
read_t_axis = 0.497648
open_file = 0.0734922
t_axis_metadata = 2.1134e-05
read_t_axis = 1.70601
open_file = 0.312652
t_axis_metadata = 1.888e-05
read_t_axis = 0.468489
open_file = 0.0906366
t_axis_metadata = 1.9165e-05
read_t_axis = 0.348474
open_file = 0.0776435
t_axis_metadata = 2.3417e-05
read_t_axis = 0.387956
open_file = 0.157729
t_axis_metadata = 4.9765e-05
read_t_axis = 0.344205
open_file = 0.114566
t_axis_metadata = 2.8431e-05
read_t_axis = 0.374615
open_file = 0.0788776
t_axis_metadata = 2.7865e-05
read_t_axis = 0.381856
collect_t_axis = 19.47
total = 20.72
A total of 240 steps available in 30 files. Using the noleap calendar.
Times
are specified in units of days since 1979-01-01 00:00:00. The available
times
range from 2005-9-1 3:0:0 (9733.12) to 2005-10-1 0:0:0 (9763).

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