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

Parallel in more than one node in linux?

JF
Jose Manuel Fernandez Jaramillo, modified 7 Years ago.

Parallel in more than one node in linux?

Youngling Posts: 5 Join Date: 4/26/11 Recent Posts
Hi everybody,

I am trying to use Delft3d in a linux cluster using Fedora 17 64b and mpich2 compiled with gcc/gcc-gfortran . I have had success to execute manually a task requesting the environmental variables of the nodes and the variable PMI_RANK is available and working in all the nodes of the cluster. This is one of the environmental variables that are tested in the file engines_gpl/flow2d3d/packages/data/src/parallel_mpi/dfinitmpi.F90 to know if a cluster is running or not.

When I execute the Delft3d script, it executes all the tasks in a single node and with a message telling: "MPI process number 000 has host unknown and is running on processor node1" and this for every one of the executed processes.

In one of the FAQs it is mentioned that multiple nodes are not availables for windows but not mention to linux. May be it works only for intel, or what could be the problem?

I don't know if it is important to mention here, but when I execute on linux the scripts with deltares_hydro.exe calling the ini file, I get no outputs at all, no xml (using the flag to keep it) or even an error message, for this reason I have changed the parallel script to use d_hydro.exe and the xml file (I am creating it under windows).

Thanks, Jose Manuel
Adri Mourits, modified 7 Years ago.

RE: Parallel in more than one node in linux?

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Jose Manuel,

On Linux, you can use multiple nodes for parallel calculations. You have to create a machinefile containing a list of machines and how much partitions must be started on each. Have a look at the comments inside file "...\examples\01_standard\run_flow2d3d_parallel.sh".

The way this machinefile is created may depend on some queueing tool used on a Linux cluster. An example based on SGE is "...\examples\01_standard\run_flow2d3d_parallel_sge.sh".

I tried it on Windows too, but that didn't work. I didn't manage to solve that problem.

"deltares_hydro.exe" is a precompiled, 32-bit executable based on the Tcl script "...\src\scripts_lgpl\deltares_hydro\deltares_hydro.tcl". I know there are problems on 64-bit Linux systems, may be related to not being enabled to execute 32-bit binaries. We are working on a solution for this, based on removing "deltare_hydro.exe" with it's INI-file input and switching to an XML-file as input for "d_hydro.exe". The format will be different than the currently used, intermediate XML-file.

Regards,

Adri
JF
Jose Manuel Fernandez Jaramillo, modified 7 Years ago.

RE: Parallel in more than one node in linux?

Youngling Posts: 5 Join Date: 4/26/11 Recent Posts
Hi Adri,

Thanks for your help. My cluster is a prototype to evaluate the settings for the optimal design to build a real one very soon. The problem was in our case that the example script defines NPART equal to NHOSTS and "--ncpus=2", and we have only two machines with one processor each one (they are virtual machines). I just change manually "mpdboot -n 2 ..." and "mpirun -np 4 ..." and now it splits the task among both machines.

Best regards, Jose Manuel