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

Problems running mormerge

GS
George Schramkowski, modified 7 Years ago.

Problems running mormerge

Youngling Posts: 7 Join Date: 4/12/11 Recent Posts
Hi everyone,

A colleague of me is trying to work with the mormerge functionality.
To this end, he uses the tagged Delft3D version 5.00.00.1234 (64 bits),
compiled with Intel Fortran v 11.1 and mpich2 v. 1.4.1p1. Mormerge is
called by using the mormerge.tcl script.

Initially we had a problem to use the torque queueing system (mormerge
appears to use SGE by default) but this has been resolved.

However when doing a test run with mormerge, we end up with the following
error statements:

ERROR: ld.so: object '/opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/../lib/libgfortran.so.3' from LD_PRELOAD cannot be preloaded: ignored.
/opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/mormerge.exe: error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory

Both of these errors are strange to me. For instance, why would mormerge.tcl
want to find a libgfortran library file when the Delft3D version is compiled
with Intel Fortran? It will never find it since it simply isn't there.
How can this issue be resolved?

Also, I am bothered by the inablity of mormerge to find libifport.so.5. In
fact, prior to using mormerge.tcl I set the Intel Fortran environment variables
so that libifport.so.5 should be found. Moreover, if I give the command
ldd /opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/mormerge.exe
after setting the enviromenment variables, all libs are found. Does
mormerge.tcl ignore these settings? And if so, why? And how to resolve this?

By the way, do you have any documentation regarding the general use of mormerge?
This could also shed some light on the direct use of mormerge.exe (rather
than mormerge.tcl) which seems to pose less problems in terms of finding
libraries.

Kind regards,

George Schramkowski
Fedor Baart, modified 7 Years ago.

RE: Problems running mormerge

Padawan Posts: 44 Join Date: 3/2/11 Recent Posts
Hi George,

George Schramkowski:
Hi everyone,


ERROR: ld.so: object '/opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/../lib/libgfortran.so.3' from LD_PRELOAD cannot be preloaded: ignored.
/opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/mormerge.exe: error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory



The first error originates from the following line in mormerge.tcl, I think you can safely ignore it, allthough it should not occur.

puts $scriptfile "export LD_PRELOAD=[file join $flowlibdir libgfortran.so.3]"

As an apparently temporary solution this was added by Adri Mourits. I'll ask him what the idea is here.

The second error message, is more serious. The compiled mormerge.exe apparently has a reference to libifport.so.5 which is not in the current path.
This path is usually set by sourcing the ifortvars.sh in the shell where it is running. That will add the appropriate path (where libifport.so.5 is) to the LD_LIBRARY_PATH.

You can do this by


. /path/to/intel/compiler/bin/ifortvars.sh


HTH,

Cheers,

Fedor
Adri Mourits, modified 7 Years ago.

RE: Problems running mormerge

Yoda Posts: 1224 Join Date: 1/3/11 Recent Posts
Hi George,

The LD_PRELOAD statement is necessary when building with the Gnu Fortran compiler and running on some other systems (including our own cluster). It will not harm in the other cases.

The mormerge script is updated in revision 1424. This will probably solve your problem.

Can you please:
  • Use the tagged version 5.00.05.1576
  • Copy all needed compiler/platform libraries to directory "myCode/bin/<platform>/flow2d3d/lib". This is currently not done automatically yet.
  • Check that the directory structure is preserved. Looking at your post, I expect a directory named "flow2d3d" in the path "/opt/delft3d/delft3D-5.00.00.1234_selfcompiled/bin/mormerge.exe"
  • Test step by step: run the relevant example testcases on the build machine, run the relevant example testcases on your cluster, run your own model on the cluster without mormerge and finally with mormerge.


Adding the mormerge documentation to the user manual is on our To Do list. Use it with care.

Regards,

Adri