[netcdfgroup] performance issues

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] performance issues
• From: Karsten Bolding <karsten@xxxxxxxxxxxxxxxxxxxx>
• Date: Wed, 18 Jan 2012 08:10:55 +0000

Hello

I'm working on a 1D ocean model that stores its output in NetCDF.

With NetCDF4 I've experienced some performance issues as shown in the
timings below for a specific model run:

NetCDF4:
real    0m42.940s
user    0m3.630s
sys     0m0.110s

NetCDF 3.6.3:
real    0m1.838s
user    0m1.820s
sys     0m0.000s

Its run on the same system only recompiling the executable to link
either NetCDF 3 or 4.

Disk performance is not an issue:
/dev/sda:
 Timing buffered disk reads: 344 MB in  3.02 seconds = 114.06 MB/sec

as the resulting file is only 10MB.

I'm using the 4.2 release candidate configured as follows:

C:
CPPFLAGS=-I/opt/hdf5/include LDFLAGS=-L/opt/hdf5/lib  ./configure
--prefix=/opt/netcdf-${netcdf_ver}_IFORT 

Fortran:
FFLAGS="-O3" FC=ifort F77=ifort CPPFLAGS=-I/opt/hdf5/include CFLAGS="-O3" 
LDFLAG S=-L/opt/hdf5/lib  ./configure --prefix=/opt/netcdf-${netcdf_ver}_IFORT

i.e. no specific optimisation. 

Netcdf 3.6.3 is also compiled without specific optimisation.

Any ideas anyone?

Karsten

PS: I've done the above simulations a number of times with consistent
results.


-- 
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Karsten Bolding                    Bolding & Burchard ApS
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A: Almost the same as goldy and bronzy - just made of iron ...
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