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

symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

U
James Morrison, modified 8 Years ago.

symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

I am attempting to run a flow computation and when the application d_hydro.exe is being run I get the following error:

Starting Delft3D-FLOW computation ...
Executing "/opt/delft3d/intel/flow/bin/d_hydro.exe TMP_config_flow2d3d_3450.xml" ...
--------------------------------------------------------------------------------
Deltares, FLOW2D3D Version 5.00.10.000000, Dec 3 2012, 15:33:45
libflow2d3d.so entry Flow2D3D::Run
--------------------------------------------------------------------------------

Part I - Initialisation Time Dep. Data module...
runid : test

ERROR: /opt/delft3d/intel/flow/bin/d_hydro.exe: symbol lookup error: /opt/delft3d/intel/flow/bin/libflow2d3d.so: undefined symbol: for_array_copy_in
- Starting "d_hydro.exe" may give more information:
- Run "deltares_hydro.exe <INI-inputfile> -keepXML".
- Run "d_hydro.exe TMP_config_flow2d3d_<processId>.xml".

I am running the latest tag version of the source ( 5.00.10.1983 ) and compiled with gcc 4.7.2 and ifort 13.0.1, running on Centos 5.8 32 bit ( kernel - 2.6.18-308.20.1.el5PAE ). I needed to update autoconf and automake to the latest version for the source to compile. I am starting the simulation from the GUI.

I noticed the same error on another forum thread on WIndows - http://oss.deltares.nl/web/opendelft3d/general/-/message_boards/view_message/163530 but I do not see a problem with that particular library.

Would this have anything to do with the 2013 Intel Fortran compiler?

Many Thanks
U
James Morrison, modified 8 Years ago.

RE: symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

I uninstalled 2013 ifort and installed 12.1.3

I now get the following error when running the same flow simulation

Starting Delft3D-FLOW computation ...
Executing "/opt/delft3d/intel/flow/bin/d_hydro.exe TMP_config_flow2d3d_13467.xml" ...
--------------------------------------------------------------------------------
Deltares, FLOW2D3D Version 5.00.10.000000, Dec 4 2012, 15:10:17
libflow2d3d.so entry Flow2D3D::Run
--------------------------------------------------------------------------------

Part I - Initialisation Time Dep. Data module...
runid : test
Part II - Creating intermediate files...
Part III - Initialisation of the Execution module...
Part IV - Reading complete MD-file...

ERROR: d_hydro.exe: oc.c:159: create_nefis_files: Assertion `(BUInt8) -1 == (size_t)(BUInt8) -1' failed.
- Starting "d_hydro.exe" may give more information:
- Run "deltares_hydro.exe <INI-inputfile> -keepXML".
- Run "d_hydro.exe TMP_config_flow2d3d_<processId>.xml".

Any suggestions regarding this problem?
Adri Mourits, modified 8 Years ago.

RE: symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

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

This problem was reported last Friday. It's on our To Do list to solve it. It appears when compiling/running on a 32bit Linux machine. It does not appear on a 64bit Linux machine.
I will post a message when it is solved.

Regards,

Adri
U
James Morrison, modified 8 Years ago.

RE: symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

Hi Adri, thanks for your response. Is there any particular distribution you recommend to build on?

I notice the instructions at the top of the forum were for Ubuntu, but as the gui is an rpm currently, I am building with Centos 5.8 64 bit now.

On the advice for running simulations between multiple machines in Linux, there is a line which says:

Method 1) using several machines is implemented for Linux only and is not supported yet in the open source version. Contact sales to obtain a closed source version supporting this.

Is this still the case that we will need to use this closed source version and is this distributed by the same means as the gui ( rpm )?


Many Thanks
Adri Mourits, modified 8 Years ago.

RE: symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

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

There is only one version/distribution and that is the trunk. The stable, tested versions in the trunk are available via the tagged versions. So nothing is better than the latest tagged version.

There is only one exception: DomainDecomposition calculations using several machines is not working in the current version. It did work in an old version (2010) before we went open source (Linux only). So, if you really want to use this feature, you have to let me know that. Then I will discuss internally if this really is an option or not.

Regards, Adri
GP
gonzalo palomares, modified 7 Years ago.

RE: symbol lookup error libflow2d3d.so: undefined symbol: for_array_copy_in

Youngling Posts: 3 Join Date: 9/3/12 Recent Posts
Hello,

I'm newbbie to Delft and I've been folllowing this forum for quite a while to compile the Delft3d under linux (ubuntu 12.01, 32 bits). Finally I've managed to compile it, but I have the exact same problem James is reporting here, so I can't run example 01. It shows an error: d_hydro.exe: oc.c:159: create_nefis_files: Assertion `(BUInt8) -1 == (size_t)(BUInt8) -1' failed.

I'm using tagged version 5.01.00.2163. Is the problem already solved? Should I use any other version?

I understand I can use the GUI for pre and post processing, even if the GUI was meant for version 4.0? can I build the GUI with the quickplot files downloaded in the tagged version using matlab? In this case I should use windows workstation for pre and post processing, and ubuntu for running calculations ...

This forum is a great support, thank you for sharing your knowledge.

Gonzalo Diz Lois