intro story D-Flow FM

 

D-Flow Flexible Mesh

D-Flow Flexible Mesh (D-Flow FM) is the new software engine for hydrodynamical simulations on unstructured grids in 1D-2D-3D. Together with the familiar curvilinear meshes from Delft3D 4, the unstructured grid can consist of triangles, pentagons (etc.) and 1D channel networks, all in one single mesh. It combines proven technology from the hydrodynamic engines of Delft3D 4 and SOBEK 2 and adds flexible administration, resulting in:

  • Easier 1D-2D-3D model coupling, intuitive setup of boundary conditions and meteorological forcings (amongst others).
  • More flexible 2D gridding in delta regions, river junctions, harbours, intertidal flats and more.
  • High performance by smart use of multicore architectures, and grid computing clusters.
An overview of the current developments can be found here.
 
The D-Flow FM - team would be delighted if you would participate in discussions on the generation of meshes, the specification of boundary conditions, the running of computations, and all kinds of other relevant topics. Feel free to share your smart questions and/or brilliant solutions! 

 

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We have launched a new website (still under construction so expect continuous improvements) and a new forum dedicated to Delft3D Flexible Mesh.

Please follow this link to the new forum: 
/web/delft3dfm/forum

Post your questions, issues, suggestions, difficulties related to our Delft3D Flexible Mesh Suite on the new forum.

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** PLEASE TAG YOUR POST! **

 

 

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 1 Year 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: 1224 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: 1224 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