intro story Coast / Estuary

Coast / Estuary

Coastal systems are among the most dynamic physical systems on earth and are subject to a large variety of forces. The morphodynamic changes occurring to coastlines worldwide are of great interest and importance. These changes occur as a result of the erosion of sediments, its subsequent transport as bed load or suspended load, and eventual deposition. 
 
Estuaries are partly enclosed water bodies that have an open connection to the coast. Estuaries generally have one or more branching channels, intertidal mudflats and/or salt marshes. Intertidal areas are of high ecological importance and trap sediments (sands, silts, clays and organic matter).
Within the Delft3D modelling package a large variation of coastal and estuarine physical and chemical processes can be simulated. These include waves, tidal propagation, wind- or wave-induced water level setup, flow induced by salinity or temperature gradients, sand and mud transport, water quality and changing bathymetry (morphology). Delft3D can also be used operationally e.g. storm, surge and algal bloom forecasting. 
 
On this discussion page you can post questions, research discussions or just share your experience about modelling coastal and/or estuarine systems with Delft3D FM. 
 

** 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 3 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 3 Years ago.

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

Yoda Posts: 1221 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 3 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 3 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 3 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 3 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 3 Years ago.

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

Yoda Posts: 1221 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 3 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 3 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