Re: [netcdfgroup] performance issues

• To: Ted Mansell <ted.mansell@xxxxxxxx>
• Subject: Re: [netcdfgroup] performance issues
• From: Karsten Bolding <karsten@xxxxxxxxxxxxxxxxxxxx>
• Date: Wed, 18 Jan 2012 15:21:23 +0000

from the 4.2 simulation

// global attributes:
                :title = "GOTM Simulation" ;
                :history = "Created by GOTM v. 4.1.0" ;
                :Conventions = "COARDS" ;
                :_Format = "classic" ;


On Wed, Jan 18, 2012 at 09:15:34 -0600, Ted Mansell wrote:
> Does the recompile switch on netcdf4 features, or is it still writing a 
> classic nc3 file using the nc4 libs?  Just to clarify -- Not that I know if 
> that makes a difference.
> 
> -- Ted
> 
> On Jan 18, 2012, at 2:10 AM, Karsten Bolding wrote:
> 
> > 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.
> > 
> > 
> > -- 
> > ----------------------------------------------------------------------
> > Karsten Bolding                    Bolding & Burchard ApS
> > Strandgyden 25                     Phone: +45 64422058
> > DK-5466 Asperup                    Fax:   +45 64422068
> > Denmark                            Email: karsten@xxxxxxxxxxxxxxxxxxxx
> > 
> > http://www.findvej.dk/Strandgyden25,5466,11,3
> > 
> > Q: What is irony?
> > A: Almost the same as goldy and bronzy - just made of iron ...
> > (from Blackadder)
> > ----------------------------------------------------------------------
> > 
> > _______________________________________________
> > netcdfgroup mailing list
> > netcdfgroup@xxxxxxxxxxxxxxxx
> > For list information or to unsubscribe,  visit: 
> > http://www.unidata.ucar.edu/mailing_lists/ 
> 
> 

-- 
----------------------------------------------------------------------
Karsten Bolding                    Bolding & Burchard ApS
Strandgyden 25                     Phone: +45 64422058
DK-5466 Asperup                    Fax:   +45 64422068
Denmark                            Email: karsten@xxxxxxxxxxxxxxxxxxxx

http://www.findvej.dk/Strandgyden25,5466,11,3

Q: What is irony?
A: Almost the same as goldy and bronzy - just made of iron ...
(from Blackadder)
----------------------------------------------------------------------

• References:
  • [netcdfgroup] performance issues
    • From: Karsten Bolding
  • Re: [netcdfgroup] performance issues
    • From: Ted Mansell