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intro story DELWAQ

DELWAQ

DELWAQ is the engine of the D-Water Quality and D-Ecology programmes of the Delft3D suite. It is based on a rich library from which relevant substances and processes can be selected to quickly put water and sediment quality models together.

The processes library covers many aspects of water quality and ecology, from basic tracers, dissolved oxygen, nutrients, organic matter, inorganic suspended matter, heavy metals, bacteria and organic micro-pollutants, to complex algae and macrophyte dynamics. High performance solvers enable the simulation of long periods, often required to capture the full cycles of the processes being modelled.

The finite volume approach underlying DELWAQ allows it to be coupled to both the structured grid hydrodynamics of the current Delft3D-FLOW engine and the upcoming D-Flow Flexible Mesh engine (1D-2D-3D) of the Delft3D Flexible Mesh Suite (or even other models such as TELEMAC).

'DELWAQ in open source' is our invitation to all leading experts to collaborate in further development and research in the field of water quality, ecology and morphology using Delft3D. Feel free to post your DELWAQ related questions or comments in this dedicated forum space. If you are new to DELWAQ, the tutorial (in the user manual) is a good place to start. A list of DELWAQ related publications is available here.

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Sub groups
D-Flow Flexible Mesh
DELWAQ

Cohesive sediments & muddy systems

 


Message Boards

Long computation times while writting to netCDF.

JL
João Lencart e Silva, modified 8 Months ago.

Long computation times while writting to netCDF.

Padawan Posts: 70 Join Date: 3/30/11 Recent Posts

Hi All,

 

I've been compiling in Ubuntu the brand new (for me at least) r7545 and when I test writing to netCDF with the provide examples I get ~12x longer computation run times than with the standard NEFIS files.
Is this what is expected or do I need to change my netCDF compiling options?

I'm still on Ubuntu 14.04 and using the netCDF library out of the main repo ( 1:4.1.3-7ubuntu2).

Cheers,

 

João.

JL
João Lencart e Silva, modified 5 Months ago.

RE: Long computation times while writting to netCDF.

Padawan Posts: 70 Join Date: 3/30/11 Recent Posts

Still no answer on this. Has anyone tested the speed of outputting to netCDF ( FlNcdf = #map his#)?

 

João.

Adri Mourits, modified 5 Months ago.

RE: Long computation times while writting to netCDF.

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi João,

example_01(Nefis), CentOS: 2.09 sec
example_01(Nefis), Windows10: 2.27 sec

example_11(NetCDF), CentOS: 1.94 sec
example_11(NetCDF), Windows10: 1.47 sec

I used revision 63032 and 63014.

So without compression, producing NetCDF files seems to be faster than producing Nefis files.

Regards,

Adri

 

JL
João Lencart e Silva, modified 5 Months ago.

RE: Long computation times while writting to netCDF.

Padawan Posts: 70 Join Date: 3/30/11 Recent Posts

Thanks Adri,

I'll try your revisions. With r62538 I get:

example_01 (Nefis): 1.27s

example_01 (neCDF): 13.44s

example_11 (netCDF): 29.14 s

and it prints an extra line outputting to the screen for both examples using netCDF:

Time to finish   0s,   97.7% completed, time steps left  7
           4           9          12           9

instead of the usual

Time to finish   0s,   97.0% completed, time steps left  9

It may be my build of libnetcdf. I'm using it from the Ubuntu 14.04 repo. Do you build you're own? What version and switches?

Adri Mourits, modified 5 Months ago.

RE: Long computation times while writting to netCDF.

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi João,

That additional line does not ring a bell.

We compiled the NetCDF library ourself. Below is our build script, including version numbers.

#! /bin/bash

module load intel/16.0.3
module load hdf5/1.10.1_intel_16.0.3

module list
echo "$LD_LIBRARY_PATH"

export FC=ifort
export F77=$FC
export CC=icc
export CXX=icpc
export H5DIR="/opt/hdf5/1.10.1_intel_16.0.3"
export NETCDFROOT="/opt/netcdf/v4.6.1_v4.4.0_intel_16.0.3"

CPPFLAGS=-I$NETCDFROOT/include LDFLAGS=-L$NETCDFROOT/lib LD_LIBRARY_PATH=$NETCDFROOT/lib:$LD_LIBRARY_PATH ./configure --prefix=/opt/netcdf/v4.6.1_v4.4.0_intel_16.0.3 --disable-dap

make
make install

Regards,

Adri