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

expat.h in the system but not being found

TS
Tiago Silva, modified 4 Years ago.

expat.h in the system but not being found

Youngling Posts: 8 Join Date: 7/21/15 Recent Posts
Hi,

I am having a problem finding expat.h on running configure.sh. As you can see below the file is in the system on the location defined by $EXPATINCPATH. How can I point configure.sh towards this path?

This is a CentOS 5.5 cluster.

Many thanks,
tiago

$ ./configure.sh
(...)
checking for sys/ipc.h... yes
checking sys/shm.h usability... yes
checking sys/shm.h presence... yes
checking for sys/shm.h... yes
checking for main in -lstdc++... yes
checking for struct shm_info... no
checking expat.h usability... no
checking expat.h presence... no
checking for expat.h... no
configure: error: Compiler can't find <expat.h>
$ module show expat/gcc/2.1.0
-------------------------------------------------------------------
/gpfs/grace/modules/utils/expat/gcc/2.1.0:

module-whatis Adds expat 2.1.0 gcc to your environment
append-path PATH /gpfs/grace/expat-2.1.0-gcc/bin
append-path LD_LIBRARY_PATH /gpfs/grace/expat-2.1.0-gcc/lib
setenv EXPATLIBPATH /gpfs/grace/expat-2.1.0-gcc/lib
setenv EXPATINCPATH /gpfs/grace/expat-2.1.0-gcc/include
-------------------------------------------------------------------

$ echo $EXPATINCPATH
/gpfs/grace/expat-2.1.0-gcc/include
$ ls $EXPATINCPATH/expat.h
/gpfs/grace/expat-2.1.0-gcc/include/expat.h
$

Attachments:

Adri Mourits, modified 4 Years ago.

RE: expat.h in the system but not being found (Answer)

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

You can add the relevant path to parameter STANDARD_C_INCLUDES in common.am. Not the most elegant way, but it should work.

Regards,

Adri
TS
Tiago Silva, modified 4 Years ago.

RE: expat.h in the system but not being found

Youngling Posts: 8 Join Date: 7/21/15 Recent Posts
Thanks Adri, I have rerun autogen --verbose and configure but I get the same error. I wonder if with the log files included will give any hint of why configure can't find the include file.

Cheers
tiago


STANDARD_C_INCLUDES = \
-I$(top_builddir)/engines_gpl/d_hydro/include \
-I$(top_builddir)/engines_gpl/flow2d3d/packages/flow2d3d/include \
-I$(top_builddir)/utils_lgpl/d_hydro_lib/include \
-I$(top_builddir)/utils_lgpl/delftonline/include \
-I$(top_builddir)/utils_lgpl/esmfsm/include \
-I$(top_builddir)/utils_lgpl/deltares_common/packages/deltares_common_c/include \
-I/gpfs/grace/expat-2.1.0-gcc/include


[uck09rvu@login00 ~/delft3d/tag5389/src]$ ls /gpfs/grace/expat-2.1.0-gcc/include
expat_external.h expat.h
TS
Tiago Silva, modified 4 Years ago.

RE: expat.h in the system but not being found

Youngling Posts: 8 Join Date: 7/21/15 Recent Posts
Just a note on this ticket not being "Resolved" as stated on the thread's list.

Thanks,
tiago
Fedor Baart, modified 4 Years ago.

RE: expat.h in the system but not being found (Answer)

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

checking for expat.h... no
configure: error: Compiler can't find <expat.h>
append-path LD_LIBRARY_PATH /gpfs/grace/expat-2.1.0-gcc/lib
setenv EXPATINCPATH /gpfs/grace/expat-2.1.0-gcc/include
$


I would expect the following the work:


$ CPPFLAGS=-I$EXPATINCPATH ./configure


CPPFLAGS is used for C/C++ preprocessor flags, e.g. -I<include dir>.
TS
Tiago Silva, modified 4 Years ago.

RE: expat.h in the system but not being found

Youngling Posts: 8 Join Date: 7/21/15 Recent Posts
Thanks Baart, that did work after I did the same for the expat libraries:

CFLAGS='-O2' CXXFLAGS='-O2' FFLAGS='-O2' FCFLAGS='-O2' CPPFLAGS="-I$EXPATINCPATH -L$EXPATLIBPATH" ./configure --prefix=`pwd`

Unfortunately it is now failing doing "make ds-install" with a data type error: integer (4)

(...)
Generating version number in the ./deltares_common_version.F90
Done, new version number is: 5539
make install-recursive
make[6]: Entering directory `/gpfs/home/uck09rvu/delft3d/delft3trunk/src/utils_lgpl/deltares_common/packages/deltares_common/src'
Making install in rd_token
make[7]: Entering directory `/gpfs/home/uck09rvu/delft3d/delft3trunk/src/utils_lgpl/deltares_common/packages/deltares_common/src/rd_token'
/bin/sh ../../../../../../libtool --tag=F77 --mode=compile mpif77 -DWITH_DELFTONLINE -O2 -ffixed-line-length-none -c -o gettok.lo gettok.f
libtool: compile: mpif77 -DWITH_DELFTONLINE -O2 -ffixed-line-length-none -c gettok.f -fPIC -o .libs/gettok.o
gettok.f: In subroutine `gettok':
gettok.f:50:
integer (4), intent(in ) :: lun !< logical unitnumber input file
1 2
Invalid kind at (2) for type at (1) -- unsupported or not permitted
(...)
Adri Mourits, modified 4 Years ago.

RE: expat.h in the system but not being found

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

Are you using a recent GFortran version, for example GFortran 4.8.4? Problems were reported related to this version. Solving this is on my ToDo list, but will not happen this year. You will have to solve it yourself or switch to a older GFortran version, or switch to the Intel compiler.

Regards,

Adri
TS
Tiago Silva, modified 4 Years ago.

RE: expat.h in the system but not being found

Youngling Posts: 8 Join Date: 7/21/15 Recent Posts
Adri,

Yes, I am using gfortran 4.8.3. I will give up on gfortran for now and try the intel compiler.

Thanks,
tiago
BM
Bradley Monahan, modified 4 Years ago.

RE: expat.h in the system but not being found

Youngling Posts: 2 Join Date: 7/31/14 Recent Posts
Hi Tiago

I am using GFortran 4.8.4

I was having similar issues with Library files, in the end i installed mpich, curl, zlib, szip & netcdf-C and netcdf-fortran in /usr/local and HDF5 to /opt/HDF5

I have uploaded the textfile that I gave to my IT support which provides instructions from a fresh Ubuntu LTS 14.04.03 install.

Some further updates however are needed and I have also switched to MPICH 3.1.2 on my home computer and compiled the latest version of source code (5596). this solved some of the issues that I was having with "dlwq19.f" & "vbstat.f90" source code (i.e. these no longer needed to be edited; lines 117:140)

This section of my text document (lines 163:170) was to test a suggestion that Adri made on a colleagues post:

geany /home/uowadmin/Desktop/source/5425/src/engines_gpl/flow2d3d/packages/kernel/src/general/prterr.f90

###replace line 831 with below:

write (*, '(a)') msg(:msglen)

however all warning messages are printed to the screen a the simulation runs - I have not investigated the cause of my issue, the simulations run so I decided to ignore it for now

My main concern is I am getting mpd errors (I know hydra is the default now) in parallel flow simulations, they seem to run fine however. Also the 10_delwaq-part-tracer does not complete successfully I have uploaded the screen logs of these

any comments or additions are much appreciated.

Thanks, Bradley