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! 

 

=======================================================
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.

=======================================================

** PLEASE TAG YOUR POST! **

 

 

Sub groups
D-Flow Flexible Mesh
DELWAQ
Cohesive sediments & muddy systems

 


Message Boards

Linking errors - Intel 2019.4 / CentOS 7

DD
Damir Dezeljin, modified 9 Months ago.

Linking errors - Intel 2019.4 / CentOS 7

Youngling Posts: 2 Join Date: 1/30/20 Recent Posts
Hello,

I'm trying to build Delft3D on latest CentOS 7.x as per 2020-02-12. I'm using Intel Parallel Studio 2019.4.The last step of the build fails with linking problems. The issue is a missing -L/path/to/mpi-libraries. Unfortunately I can't figure out how to add this parameter to libtool.

Here are details on what I'm doing:export CC=icc
export CXX=icc
export F77=ifort
export F90=ifort
export FC=ifort
export CPP=icc
export CXXCPP=icpc

export CFLAGS="-Ofast -I/opt/intel-build-libs/include -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/include"
export CPPFLAGS="-Ofast -I/opt/intel-build-libs/include -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/include"
export CXXFLAGS="-Ofast -I/opt/intel-build-libs/include -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/include"
export FFLAGS="-Ofast -I/opt/intel-build-libs/include -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/include"
export FCFLAGS="-Ofast -I/opt/intel-build-libs/include -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/include"

export LDFLAGS="-L/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/lib/release -L/opt/intel/compilers_and_libraries_2019.4.243/linux/mpi/intel64/lib -L/opt/intel-build-libs/lib"

export LD_LIBRARY_PATH=/opt/intel-build-libs/lib:/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/lib/intel64_lin:$LD_LIBRARY_PATH

source /opt/intel/parallel_studio_xe_2019/bin/psxevars.sh

cd delft3d.trunk/src/
./autogen.sh
cd third_party_open/kdtree2/
./autogen.sh
cd ../../
PETSc_CFLAGS="-I/home/username/delft3d/include/" PETSc_LIBS="-L/home/username/delft3d/lib" MPIFC=mpiifort ./configure --prefix=/home/username/delft3d --with-netcdf --with-mpi --with-metis --with-petsc

make ds-install

The error I'm getting is:
...
 /usr/bin/mkdir -p '/home/user/delft3d/share/man/man3'
 /usr/bin/install -c -m 644 sigwatch.3 '/home/user/delft3d/share/man/man3'
make[3]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/libsigwatch'
make[2]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/libsigwatch'Making install in FLAP
make[2]: Entering directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/FLAP'
Assembling Test_Driver/TEST_DRIVER
ld: cannot find -lmpifort
ld: cannot find -lmpi
make[2]: *** [Test_Driver/TEST_DRIVER] Error 1
make[2]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/FLAP'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open'
make: *** [install-recursive] Error 1


Any help will be appreciated,
Damir Dezeljin
GK
Gert Klopman, modified 9 Months ago.

RE: Linking errors - Intel 2019.4 / CentOS 7

Youngling Posts: 1 Join Date: 2/13/20 Recent Posts
Dear Damir,
Your script has been very helpful for me to compile with Intel Parallel Studio.
I think you have to also set
export MPI_INCLUDE="$I_MPI_ROOT/intel64/include"
export MPILIBS_ADDITIONAL="-L$I_MPI_ROOT/intel64/lib"

Success,
Gert Klopman
DD
Damir Dezeljin, modified 9 Months ago.

RE: Linking errors - Intel 2019.4 / CentOS 7

Youngling Posts: 2 Join Date: 1/30/20 Recent Posts
I'm glad to hear my notes helped you.  Unfortunately I'm still stack with the same error. May I ask you at which point you set the two additional env variables MPI_INCLUDE and MPILIBS_ADDITIONAL?
I set them up before running the first autogen.sh.  Also I had to remove 'intel64' from their path as the ${I_MPI_ROOT} already points to a directory containing include/ and lib/ dirs and the later contains the required libmpifort.so*
As a developer I'm tempted on digging into the build process and update the scripts, but would rather avoid this as it would for sure take me a week of time.Therefore any further hints would be greatly appreciated. 
make[3]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/libsigwatch'
make[2]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/libsigwatch'
Making install in FLAP
make[2]: Entering directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/FLAP'
Assembling Test_Driver/TEST_DRIVER
ld: cannot find -lmpifort
ld: cannot find -lmpi
make[2]: *** [Test_Driver/TEST_DRIVER] Error 1
make[2]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open/FLAP'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/user/delft3d/delft3d.trunk/src/third_party_open'
make: *** [install-recursive] Error 1