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

 

Message Boards

PetscInitialize() must be called before PetscFinalize() (SOLVED)

MS
michael schaferkotter, modified 2 Years ago.

PetscInitialize() must be called before PetscFinalize() (SOLVED)

Youngling Posts: 15 Join Date: 9/6/16 Recent Posts

compiled r8765 with petsc-3.4.5 using MPI 

 

(simple) partition the domain using:

 

$DFM_DIR/dflowfm --partition:ndomains=$NDOMAINS:icgsolver=6 $MDUFILE

 

results in the creation of: 

 

${AREA_NAME}_0000.mdu,  ${AREA_NAME}_0001.mdu, ..., ${AREA_NAME}_$NDOMAINS-1.mdu

and the corresponding ${AREA_NAME}_*_net.nc files.

 

 

however, a log message appears:

PetscInitialize() must be called before PetscFinalize()

 

https://lists.mcs.anl.gov/pipermail/petsc-users/2016-August/030221.html

 

indicates that the error code for PetscInitialize() was _not_ checked, the program continued running util it reached PetscFinalize(), where it could not handle the state since PETSc was not properly initialized.

 

the dflowfm code:

 

 src/engines_gpl/dflowfm/packages/dflowfm_kernel/src/solve_petsc.F90

 

  79 !> initialze PETSc

  80    subroutine startpetsc()

  81 #ifdef HAVE_PETSC

  82       use m_petsc

  83       use m_flowparameters, only: Icgsolver

  84       implicit none

  85       PetscErrorCode :: ierr = PETSC_OK

  86

  87       if ( icgsolver.eq.6 ) then

  88          call PetscInitialize(PETSC_NULL_CHARACTER,ierr)

  89          call PetscLogBegin(ierr)

  90       end if

  91 #endif

  92  

  93  

  94       return

  95    end subroutine startpetsc

  99 !> initialze PETSc

 100    subroutine stoppetsc()

 

 101 #ifdef HAVE_PETSC

 102       use m_petsc

 103       use m_flowparameters, only: Icgsolver

 104       implicit none

 105       PetscErrorCode :: ierr = PETSC_OK

 106

 107       if (Icgsolver.eq.6) then

 108          call killSolverPETSC()

 109          call PetscFinalize(ierr)

 110       end if

 111 #endif

 112       return

 113    end subroutine stoppetsc

 

recommendations?

MS
michael schaferkotter, modified 2 Years ago.

RE: PetscInitialize() must be called before PetscFinalize()

Youngling Posts: 15 Join Date: 9/6/16 Recent Posts

PROBLEM SOLVED:

the issue seemed to be with the optimization level -O3 in the PrgEnv-gnu (cray xc40).

debugging with valgrind elicited an 'unrecognized instruction'.

vi ./src/utils_lgpl/deltares_common/packages/deltares_common/src/geometry_module.f90 +370

370          csphi = dcos(0.5d0*(yy1+yy2))

review of other issues of this ilk, coupled with experience, led to review of the optimization levels.

http://valgrind.org/docs/manual/quick-start.html

Compile your program with -g to include debugging information so that Memcheck's error messages include exact line numbers. Using -O0 is also a good idea, if you can tolerate the slowdown. With -O1 line numbers in error messages can be inaccurate, although generally speaking running Memcheck on code compiled at -O1 works fairly well, and the speed improvement compared to running -O0 is quite significant. Use of -O2 and above is not recommended as Memcheck occasionally reports uninitialised-value errors which don't really exist.

after reducing the optimization level and a recompile, this issue did not occur.

further study is needed:

1. determine the maximum optimization level tolerated with this programming environment

2. compile under other PrgEnv-intel, PrgEnv-cray

XW
Xiaohui Wang, modified 2 Years ago.

RE: PetscInitialize() must be called before PetscFinalize() (SOLVED)

Youngling Posts: 1 Join Date: 10/2/18 Recent Posts

Hi,

I also meet the problem with PetscInitialize() must be called before PetscFinalize() when I try to parallel run the model. Do I understand correctly that you changed the dflowfm code to correct the error? How can I do that I don't have the source code?

 

Best wishes

Xiaohui