intro story Coast / Estuary

Coast / Estuary

Coastal systems are among the most dynamic physical systems on earth and are subject to a large variety of forces. The morphodynamic changes occurring to coastlines worldwide are of great interest and importance. These changes occur as a result of the erosion of sediments, its subsequent transport as bed load or suspended load, and eventual deposition. 
 
Estuaries are partly enclosed water bodies that have an open connection to the coast. Estuaries generally have one or more branching channels, intertidal mudflats and/or salt marshes. Intertidal areas are of high ecological importance and trap sediments (sands, silts, clays and organic matter).
Within the Delft3D modelling package a large variation of coastal and estuarine physical and chemical processes can be simulated. These include waves, tidal propagation, wind- or wave-induced water level setup, flow induced by salinity or temperature gradients, sand and mud transport, water quality and changing bathymetry (morphology). Delft3D can also be used operationally e.g. storm, surge and algal bloom forecasting. 
 
On this discussion page you can post questions, research discussions or just share your experience about modelling coastal and/or estuarine systems with Delft3D FM. 
 

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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 2 Years 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 1 Year 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 1 Year 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 1 Year 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 1 Year 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