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

Compilation error in Fedora-25: gfortran: error: unrecognized command line.

ME
MD WASIF E ELAHI, modified 11 Months ago.

Compilation error in Fedora-25: gfortran: error: unrecognized command line.

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Hi, I am trying to compile delft3d in fedora-25 by following the steps of ubuntu installaions. 

I ran $ ./autogen.sh

./Configure

...................

checking for MPI_Init in -lmpichf90... no
checking for MPI_Init in -lmpi... (cached) no
checking for MPI_Init in -lmpich... (cached) no
gfortran: error: unrecognized command line option '-showme:link'; did you mean '--force-link'?
gfortran: fatal error: no input files

compilation terminated.
configure: creating ./config.lt
config.lt: creating libtool
checking for the extension of Delft3D plugins... .so
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating engines_gpl/d_hydro/Makefile
config.status: creating engines_gpl/d_hydro/packages/d_hydro/Makefile
...............................................................................................................

config.status: creating utils_lgpl/ods/Makefile
config.status: creating utils_lgpl/ods/packages/Makefile
config.status: creating utils_lgpl/ods/packages/ods/Makefile
config.status: creating utils_lgpl/ods/packages/ods/srcf/Makefile
config.status: creating utils_lgpl/ods/packages/ods/src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
 

<<<end of configure>>>

then i ran

Make

 

libtool: compile:  gfortran -DHAVE_CONFIG_H -I. -I../../../../.. -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I/include -DWITH_DELFTONLINE -O2 -ffree-line-length-none -cpp -c io_netcdf_version.F90  -fPIC -o .libs/io_netcdf_version.o
f951: Warning: Nonexistent include directory ‘/include’ [-Wmissing-include-dirs]
libtool: compile:  gfortran -DHAVE_CONFIG_H -I. -I../../../../.. -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I/include -DWITH_DELFTONLINE -O2 -ffree-line-length-none -cpp -c io_netcdf_version.F90 -o io_netcdf_version.o >/dev/null 2>&1
/bin/sh ../../../../../libtool  --tag=FC   --mode=compile gfortran -DHAVE_CONFIG_H -I. -I../../../../..     -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I/include -DWITH_DELFTONLINE   -O2  -ffree-line-length-none -cpp -c -o netcdf_utils.lo netcdf_utils.F90
libtool: compile:  gfortran -DHAVE_CONFIG_H -I. -I../../../../.. -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I/include -DWITH_DELFTONLINE -O2 -ffree-line-length-none -cpp -c netcdf_utils.F90  -fPIC -o .libs/netcdf_utils.o
f951: Warning: Nonexistent include directory ‘/include’ [-Wmissing-include-dirs]
netcdf_utils.F90:33:4:

 use netcdf^M
    1
Fatal Error: Can't open module file ‘netcdf.mod’ for reading at (1): No such file or directory
compilation terminated.

Makefile:537: recipe for target 'netcdf_utils.lo' failed
make[5]: *** [netcdf_utils.lo] Error 1
make[5]: Leaving directory '/home/Elahi/delft3d_repository/src/utils_lgpl/io_netcdf/packages/io_netcdf/src'
Makefile:488: recipe for target 'install-recursive' failed
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory '/home/Elahi/delft3d_repository/src/utils_lgpl/io_netcdf/packages/io_netcdf'
Makefile:488: recipe for target 'install-recursive' failed
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory '/home/Elahi/delft3d_repository/src/utils_lgpl/io_netcdf/packages'
Makefile:488: recipe for target 'install-recursive' failed
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory '/home/Elahi/delft3d_repository/src/utils_lgpl/io_netcdf'
Makefile:498: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory '/home/Elahi/delft3d_repository/src/utils_lgpl'
Makefile:548: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
 

<<<end of configure>>>

 

Please help me out. How to solve these issues?

Any help would be highly appreciated.
 

Wasif

ME
MD WASIF E ELAHI, modified 11 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

After following all the steps of "build_ubuntu.16.04LT.readme", above errors are solved. However, now I am getting new errors related to uuid library. uuid package is already installed, but don't know why make cannot find -luuid. Errors are given below:

..................................................................
../../../../../engines_gpl/part/packages/utils_f/src/.libs/libutils_f.a ../../../../../engines_gpl/part/packages/kernel_f/src/.libs/libkernel_f.a ../../../../../engines_gpl/part/packages/io_f/src/.libs/libio_f.a ../../../../../engines_gpl/part/packages/data_f/src/.libs/libdata_f.a -lpthread -luuid -ldl -lrt -lexpat -lstdc++ -pthread -fopenmp -Wl,-rpath -Wl,/home/Elahi/delft3d_repository/src/lib -Wl,-rpath -Wl,/home/Elahi/Downloads/libraries/netcdf_4.4/lib -Wl,-rpath -Wl,/home/Elahi/Downloads/libraries/hdf5-1.8.13/lib
/usr/bin/ld: cannot find -luuid                  (* but uuid package is there in same directory)
collect2: error: ld returned 1 exit status
Makefile:631: recipe for target 'delwaq1' failed
make[6]: *** [delwaq1] Error 1
make[6]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1/src'
Makefile:755: recipe for target 'install' failed
make[5]: *** [install] Error 2
make[5]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1/src'
Makefile:488: recipe for target 'install-recursive' failed
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1'
Makefile:496: recipe for target 'install-recursive' failed
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages'
Makefile:488: recipe for target 'install-recursive' failed
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq'
Makefile:493: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl'
Makefile:548: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

<<<end>>>>

I have attached the log files. I have been trying to compile for a long time. Now I am getting frustrated and losing hope. Any kind of help or suggestion will be highly appreciated.

Adri Mourits, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi Wasif,

Yes, compiling on Linux can really be a pain. The good news is that once you have it compiling, the process is very stable. And you are already quite far.

The error "cannot find -luuid" is caused because the package "uuid-dev" is not installed on your machine, see the prerequisites.

Regards,

Adri

ME
MD WASIF E ELAHI, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Hi Adri,

Thank you for your response. I am still struggling with the same issue. uuid-dev is already installed in the same directory "/usr/bin/", . Am I missing something? should I change any directory for uuid-dev anywhere?  Please help me out.

 

Kind regards,

Wasif 

Adri Mourits, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi Wasif,

When uuid-dev is installed in the normal way, then the library "libuuid.so.1" is located in directory "/lib64". Can you check that?

Automake should add directory "/lib64" to the search paths when looking for libraries.  It's difficult to find out why that goes wrong on your system.

Can you try the following: Before compiling, execute the following command:
export LD_LIBRARY_PATH=/lib64:$LD_LIBRARY_PATH

Regards,

Adri

ME
MD WASIF E ELAHI, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Hi Adri,

Thanks for your qucik response. I checked the location of "libuuid.so.1" is located in "/lib64'. Before compiling, I applied your given command as "export LD_LIBRARY_PATH=/lib64:$LD_LIBRARY_PATH ".

In cofigure.log i found an error line as given below:

.......................

checking for MPI_Init... yes
checking for mpi.h... yes
checking for openmpif77... no
checking for mpif77... mpif77
checking for mpif.h... yes
checking for openmpif90... /home/Elahi/Downloads/libraries/mpich-3/bin/mpif90
checking for mpif.h... yes
gfortran: error: unrecognized command line option '-showme:link'; did you mean '--force-link'?   (any suggestion regarding this please?)
configure: creating ./config.lt
config.lt: creating libtool
checking for the extension of Delft3D plugins... .so
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating engines_gpl/d_hydro/Makefile
config.status: creating engines_gpl/d_hydro/packages/d_hydro/Makefile
.............. (lots of line without any error)

config.status: creating utils_lgpl/ods/packages/ods/src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

<<<end of configure.log>>>

 

In make.log error remains the same:

............

libtool: compile:  /home/Elahi/Downloads/libraries/mpich-3/bin/mpif90 -DHAVE_CONFIG_H -I. -I../../../../.. -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib -lnetcdff -DWITH_DELFTONLINE -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib -lnetcdff -I/home/Elahi/Downloads/libraries/netcdf_4.4/include -O2 -ffree-line-length-none -cpp -c ec_module_version.F90  -fPIC -o .libs/ec_module_version.o
f951: Warning: Nonexistent include directory ‘-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib’ [-Wmissing-include-dirs] ( it seems like generated from the error in configure?)))
f951: Warning: Nonexistent include directory ‘-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib’ [-Wmissing-include-dirs]

libtool: compile:  /home/Elahi/Downloads/libraries/mpich-3/bin/mpif90 -DHAVE_CONFIG_H -I. -I../../../../.. -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib -lnetcdff -DWITH_DELFTONLINE -I../../../../../utils_lgpl/deltares_common/packages/deltares_common/src -I-L/home/Elahi/Downloads/libraries/netcdf_4.4/lib -lnetcdff -I/home/Elahi/Downloads/libraries/netcdf_4.4/include -O2 -ffree-line-length-none -cpp -c ec_module_version.F90 -o ec_module_version.o >/dev/null 2>&1
........

..........

ibdata_f.a -lpthread -luuid -ldl -lrt -lexpat -lstdc++ -pthread -fopenmp -Wl,-rpath -Wl,/home/Elahi/delft3d_repository/src/lib -Wl,-rpath -Wl,/home/Elahi/Downloads/libraries/netcdf_4.4/lib -Wl,-rpath -Wl,/home/Elahi/Downloads/libraries/hdf5-1.8.13/lib
/usr/bin/ld: cannot find -luuid
collect2: error: ld returned 1 exit status
Makefile:631: recipe for target 'delwaq1' failed
make[6]: *** [delwaq1] Error 1
make[6]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1/src'
Makefile:755: recipe for target 'install' failed
make[5]: *** [install] Error 2
make[5]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1/src'
Makefile:488: recipe for target 'install-recursive' failed
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages/delwaq1'
Makefile:496: recipe for target 'install-recursive' failed
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq/packages'
Makefile:488: recipe for target 'install-recursive' failed
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl/waq'
Makefile:493: recipe for target 'install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory '/home/Elahi/delft3d_repository/src/engines_gpl'
Makefile:548: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
<<<end>>>>

Adri Mourits, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi Wasif,

Workaround: uuid is only used by WAQ. If you do not need WAQ, you can exclude it from the compilation as follows:
Open file ".../src/engines_gpl/Makefile.am" in an editor and remove the line "     waq \ "

If you do need WAQ: I'm confused: the make.log file attached to your previous post contains the error "cannot find -luuid". But the fragment you posted now contains an error message about NetCDF. Anyway, I'll ask a WAQ-colleague to help with the uuid problem.

Regards,

Adri

Michelle Jeuken, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Jedi Knight Posts: 156 Join Date: 1/21/13 Recent Posts

uuid is used in src\engines_gpl\waq\packages\waq_utils_c\src\getuuid.c

If you can't get the compilation to find uuid, you can modifiy this file, so it will generate a fake uuid. Remove this section:

#ifdef WIN32
#include <windows.h>
#else
#include <uuid/uuid.h>
#endif

End replace the call to generate a uuid:

#ifdef WIN32
    CoCreateGuid( (GUID *)guid );
#else
    uuid_generate( guid );
#endif

with this:

    for (i = 0; i < 16; i++) {
        guid[i] = '0';
    }

Then remove -luuid in both these Makefile.am's

src\engines_gpl\waq\packages\delwaq2\src\Makefile.am

src\engines_gpl\waq\packages\delwaq1\src\Makefile.am

I hope this will avoid the need of the uuid library

 

Michelle

ME
MD WASIF E ELAHI, modified 10 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Hi Adri and Michelle,

Thanks a lot. I have successfully finished the compilation after removing WAQ. I tried by modifying getuuid.c as per Michelle's suggestion. Still, I got some errors related to uuid. However, I will use Delft3d to study wave, wind and sediment process altogether. Hope it could be done without WAQ, right? 

Thanks again. 

Kind regards,

Wasif

 

Adri Mourits, modified 8 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts

Hi Wasif,

Yes, by combining FLOW and WAVE, you can model wave, wind and sediment processes.

Regards,

Adri

Ahmed Elkut, modified 7 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 9 Join Date: 5/20/14 Recent Posts

Hi Wasif

I am trying to install D3D on Ubuntu 16.04LTS and I am experiencing the same problem you had

f951: Warning: Nonexistent include directory ‘/include’ [-Wmissing-include-dirs]
netcdf_utils.F90:33:4:

 use netcdf^M
    1
Fatal Error: Can't open module file ‘netcdf.mod’ for reading at (1): No such file or directory
compilation terminated.

 

Would you please tell me how you have solved this problem.

Thank you

ME
MD WASIF E ELAHI, modified 7 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Hi Ahmed,

You can try below steps that worked for me. 

Workaround: uuid is only used by WAQ. If you do not need WAQ, you can exclude it from the compilation as follows:
Open file ".../src/engines_gpl/Makefile.am" in an editor and remove the line "     waq \ "

Ahmed Elkut, modified 7 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 9 Join Date: 5/20/14 Recent Posts

Dear Wasif

The current problem is not WAQ, it has something with the netcdf library (The first problem you had).

 

f951: Warning: Nonexistent include directory ‘/include’ [-Wmissing-include-dirs]
netcdf_utils.F90:33:4:

 use netcdf^M
    1
Fatal Error: Can't open module file ‘netcdf.mod’ for reading at (1): No such file or directory
compilation terminated.
 

 

I have followed the steps in build_ubuntu.16.04LTS.readme, but still have the same problem.

how did you solve this issue?

Best regards, 

ME
MD WASIF E ELAHI, modified 7 Months ago.

RE: Compilation error in Fedora-25: gfortran: error: unrecognized command l

Youngling Posts: 7 Join Date: 7/27/18 Recent Posts

Dear Ahmed, 

Please start a fresh installation by following the steps of "build_ubuntu.16.04LT.readme" file. Don't miss any linking command of the libraries. Hope that will work.