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

Problem compiling on LinuxD3D ubuntu version 0892

U
Michael O'Shea, modified 9 Years ago.

Problem compiling on LinuxD3D ubuntu version 0892

Hi

I have downloaded version 0892 of the Delft software but still get an error after running ./build.sh, see below.


hmrc@linuxadmin-Vostro-3550:~/Public/delft3d_repository/4.00.07.0892/src$ ./build.sh

20111213.113207 :: Running autoreconf -ivf &> logs/autoreconf.log
20111213.113231 :: Running CFLAGS='-O2 ' CXXFLAGS='-O2 ' FFLAGS='-O2 -DWITH_DELFTONLINE ' FCFLAGS='-O2 ' ./configure --prefix=/home/hmrc/Public/delft3d_repository/4.00.07.0892/src &> logs/configure.log
20111213.113312 :: Running make ds-install &> logs/make.log
20111213.113503 :: Make fails!

hmrc@linuxadmin-Vostro-3550:~/Public/delft3d_repository/4.00.07.0892/src$

any ideas?
Fedor Baart, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Padawan Posts: 44 Join Date: 3/2/11 Recent Posts
Michael O'Shea:
Hi

I have downloaded version 0892 of the Delft software but still get an error after running ./build.sh, see below.


hmrc@linuxadmin-Vostro-3550:~/Public/delft3d_repository/4.00.07.0892/src$ ./build.sh

20111213.113207 :: Running autoreconf -ivf &> logs/autoreconf.log
20111213.113231 :: Running CFLAGS='-O2 ' CXXFLAGS='-O2 ' FFLAGS='-O2 -DWITH_DELFTONLINE ' FCFLAGS='-O2 ' ./configure --prefix=/home/hmrc/Public/delft3d_repository/4.00.07.0892/src &> logs/configure.log
20111213.113312 :: Running make ds-install &> logs/make.log
20111213.113503 :: Make fails!

hmrc@linuxadmin-Vostro-3550:~/Public/delft3d_repository/4.00.07.0892/src$

any ideas?


Hi Michael,

You'll probably want to attach the logs/make.log and the logs/configure.log. There should be some error in the logs/make.log file.

Cheers,

Fedor
U
Michael O'Shea, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Fedor,

Log files attached.

Michael
Fedor Baart, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Padawan Posts: 44 Join Date: 3/2/11 Recent Posts
There's a few things I notice in the log files.


libtool: compile:  ifort -I/opt/mpich2/include -I../../../../../../utils_lgpl/parallel_mpi/include -I../../../../../../utils_lgpl/precision/include -I../../../../../../engines_gpl/flow2d3d/packages/data/include -I../../../../../../utils_lgpl/precision/packages/precision/src -I../../../../../../engines_gpl/flow2d3d/packages/data/src/parallel_mpi -I../../../../../../engines_gpl/flow2d3d/packages/data/src/basics -I../../../../../../utils_lgpl/ec_module/packages/ec_module/src -I../../../../../../utils_lgpl/inifiles/packages/inifiles/src -I../../../../../../utils_lgpl/utils_flow/packages/utils_flow/src -O2 -DDFMPI -fpp -O2 -fopenmp -recursive -reentrancy threaded -traceback -c dfinitmpi.f90  -fPIC -o .libs/dfinitmpi.o
dfinitmpi.f90(46): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [MPI]
    use mpi


It is trying to compile the dfinitmpif.f90 file. To be able to compile this file it needs a fortran module, more specific the mpi module that is part of your mpi distribution. It is trying to look for a file in /opt/mpich2/include named mpi.mod. But it is probably not there.

In the trunk I changed it that this part of the code uses mpif90 as a compiler, but in the 0892 version this was not implemented yet.

You can use the trunk version of Delft3D. Make sure you do a clean checkout or do make clean before you build again.
Or you can update the mpi path in the build.sh script. It should contain some reference to this /opt/mpich2/include directory. You can replace it with the location of mpi.mod on your system (which should be build using ifort). You can check for this directory and the compiler that was used to build it using the command
mpif90 -showme


HTH,

Cheers,

Fedor
U
Michael O'Shea, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Fedor,

The location of the mpi.mod file is /usr/include/mpi but there does not seem to be any reference to this location or the mpi.mod file itself in build.sh, see attached file. Please indicate where the reference to mpi.mod should be included in build.sh and the format of the reference to use.

Thanks for the help,

Michael

Attachments:

Fedor Baart, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

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

I checked but the path to -I/opt/mpich2/include was hard coded in the file
/tags/4.00.07.0892/src/engines_gpl/flow2d3d/packages/data/src/parallel_mpi/Makefile.am
There are also some references to /opt in common.am, those are system specific also.

Since then it was moved to build.sh
You can find a stable copy of that version in:
https://svn.oss.deltares.nl/repos/delft3d/tags/5.00.00.1234

I'd suggest to use the new 5.00 version as it requires less effort to get running on linux.

HTH,

Fedor
U
Michael O'Shea, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Fedor,

Unfortunately there still seems to be problems compiling the Delft software.

The new version 5.00 downloaded successfully with the command "svn checkout https://svn.oss.deltares.nl/repos/delft3d/tags/5.00.00.1234 delft3d_repository".

The download was then compiled with the command "./build.sh -gnu" but this finishes with the message "Make fails". The download was also compiled with the command "./build.sh -gnu -64bit", as specified in src/README but this in turn finishes with the message "Configure fails".

Your advice is much appreciated,

Regards,

Michael
Fedor Baart, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

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

I looked at your log files. I notice the following.

In the autogen.log:

The Delft3D build system is now prepared.  To build here, run:
  ./configure
  make

Running the autogen.sh went fine. You should be able to compile Delft3D using the general commands:

./configure
make


In the configure.log I notice that it can't run the executables that you are creating.

checking whether we are cross compiling... configure: error: in `/home/hmrc/delft3d_repository/src':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.


From the terminal output it appears that you are trying to crosscompile a 64 bit Delft3D on a 32 bit system (using the -m64 FLAG). I haven't tried cross compiling for a while, so this part may contain some errors. For cross compilation I think you should also set the host and target flag in ./configure. There's also a build flag. See http://sourceware.org/autobook/autobook/autobook_17.html#SEC17 for some details.
To find out the target you can look at the MACHTYPE environment variable

# on the target machine
echo $MACHTYPE # this should give you the architecture triplet.
# For me this gives
x86_64-redhat-linux-gnu # on centos
x86_64-apple-darwin10.0 # on OSX


You can then configure something like:

# I am not sure if you need to pass the compiler flags also but just in case, it should be something like:
# export these or put in one line with configure.
CFLAGS="-m64 -march=x86_64"
CXXFLAGS="-m64 -march=x86_64"
FCFLAGS="-m64 -march=x86_64"
FFLAGS="-m64 -march=x86_64"
# use -fPIC also for some 64 bit machines...
./configure --target=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu # I think pc is used instead of redhat on other distros, I think you can leave out the --build option.


That should make a 64 bit executable from on a 32 bit platform (assuming the compiler supports it).

In your makefile.log I notice that it uses the mpif90 compiler from /opt/mpich2


../../../../../../libtool: line 1130: /opt/mpich2-1.4.1-gcc-4.6.2/bin/mpif90: No such file or directory


I think the build.sh sets the MPIFC variable to /opt/mpich..., you might want to check where your mpif90 is located (which mpif90 or locate mpif90) and replace that in build.sh.

HTH,

Fedor



Michael O'Shea:
Fedor,

Unfortunately there still seems to be problems compiling the Delft software.

The new version 5.00 downloaded successfully with the command "svn checkout https://svn.oss.deltares.nl/repos/delft3d/tags/5.00.00.1234 delft3d_repository".

The download was then compiled with the command "./build.sh -gnu" but this finishes with the message "Make fails". The download was also compiled with the command "./build.sh -gnu -64bit", as specified in src/README but this in turn finishes with the message "Configure fails".

Your advice is much appreciated,

Regards,

Michael
U
Michael O'Shea, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Fedor,

Unfortunately there are still errors after using make, see below; ./configure appeared to complete without error. The logs in /src/log do not seem to be updating so they have not been included.

Also, the README file supplied with the new version 5.0 download, see attached file, says to use the command "./build.sh -gnu -64bit" when compiling in Linux. This was why it was used rather than wanting to crosscompile. I dont want to cross compile.


/usr/bin/mpif90: line 370: gfortran: command not found
make[7]: *** [dfparall.lo] Error 1
make[7]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl/flow2d3d/packages/data/src/parallel_mpi'
make[6]: *** [all-recursive] Error 1
make[6]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl/flow2d3d/packages/data/src'
make[5]: *** [all-recursive] Error 1
make[5]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl/flow2d3d/packages/data'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl/flow2d3d/packages'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl/flow2d3d'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/hmrc/delft3d_repository/src/engines_gpl'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/hmrc/delft3d_repository/src'
make: *** [all] Error 2

Attachments:

Adri Mourits, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Michael,

I'm sorry, that's my mistake. "./build.sh -gnu -64bit" is meant as a call example. You have to feed build.sh the flags that are appropriate for your system. So please remove "-64bit" if you have a 32bit system and specify the compiler you want to use. I adapted the README in the trunk, revision 1274.

What do you mean with "The logs in /src/log do not seem to be updating"? When running build.sh the output is written to the logs in src/log. Are you or are you not using build.sh? If you do use build.sh and if the logs are really not being updated, can you execute:
./build.sh <your flags> &>build.log

and post the file build.log being created?

The information in your post is not enough to find out what is going wrong. The relevant log files are necessary.

Regards,

Adri
NO
Niall O'Sullivan, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
I have been working with Michael O'Shea over the past few weeks on compiling Delft3D in Linux.

The log files that you requested are attached.

As mentioned previously compilation was initiated with the command "./build.sh -gnu"; "-gnu" was the only parameter added to the command as it seems from reading the build.sh file that the default platform is 32 bit. Unfortunately compilation failed and ended with the message "Make fails".

The first reference to an error that I can find in make.log follows below :

../../../../../../libtool: line 1130: /opt/mpich2-1.4.1-gcc-4.6.2/bin/mpif90: No such file or directory
make[6]: *** [dfparall.lo] Error 1

Is this an indication that there is an additional package, possibly mpich2-1.4.1-gcc-4.6.2, that has not been installed?

Any comments or suggestions that you may have would be much appreciated.

Best regards,
Niall O'Sullivan
NO
Niall O'Sullivan, modified 9 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Please note that the Delft3D version 5.00 download was repeated and this time compiled with the command "./build.sh -intel12" but the compilation still ends with the message "Make fails", see attached log files.

On this occasion the first error that I have found is as follows "/usr/bin/mpif90: line 370: gfortran: command not found"; this file is also attached.

Is this error consistent with the problems associated with using the gnu compiler or does it suggest that there is some more general problem.

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

I'm sorry that it took so long to answer your questions.

It seems that both your problems with the Gnu compiler and the Intel compiler have the same cause:
After downloading the mpich2 source code, you have to compile it using the same compiler as you use for the Delft3D code. So if you want to compile Delft3D using Intel12.0, you must compile mpich2 also with Intel12.0, resulting in an "mpif90" binary using this specific compiler.

When this problem is cleared, can you first try compiling the latest tagged 5.00-version without using "build.sh". See file "README" in the src directory when checked out.

Regards,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your response and suggestions.

Apologies for not responding before now, I will do as you suggest and be in contact again next week.

Best regards,
Niall O'Sullivan
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
The original installation of mpich2 has been removed and re-installed by following the instructions in the readme file included with the MPICH2-1.4.1p1 release. All of this completed without error but compiling Delft3D still fails, see attached file for mpich installation commands.

The above readme file includes instructions on how to disable Fortran support but not on how to specify a particular Fortran compiler to use.

Please indicate how to compile mpich2 using a specific Fortran compiler or suggest a possible source for this information.

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

I never compiled MPICH2 myself. But I found a script named "BUILD" that should help you, see attachment.

Regards,

Adri

Attachments:

NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
I will try the script and be in contact with the outcome.

Best regards,
Niall O'Sullivan
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Mpich2 now appears to work correctly and has been compiled with the Intel 12 Fortran compiler. I signed up to the mpich2 mailing list and following some discussion with the people involved, mpich2 now seems to be operational.

Unfortunately, ./build.sh -intel12 still end with the message "Make fails", see attached log files.

The log files autogen.log and configure.log both seem to have been completed without error but this is not the case for make.log.

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

The good news is: you managed to build both the executable d_hydro.exe and the main dll libflow2d3d.so. The problem you have is related to a minor additional program you are not going to use. The easiest way to solve this is by removing "datsel" (and probably also "kubint" and "lint") from file "...\src\tools_gpl\Makefile.am".

After some googling: http://docs.fedoraproject.org/nl-NL/Fedora/13/html/Release_Notes/sect-Release_Notes-The_GCC_Compiler_Collection.html
I'm afraid this page is in Dutch, but the English version can not be far away.

The solution seems to be to add library libm explicitly during linking. So, in file "...\src\tools_gpl\datsel\packages\datsel\src\Makefile.am", replace "-ldl \" by "-ldl -libm \".

It seems to be a Fedora problem. I can not try it myself.

Regards,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your message.

The two makefile.am files, see attachments, were edited as you suggested and now the build command finishes without displaying an error. The associated log files are attached.

As no errors appear to have been generated does this now mean that the package is ready for use? Are the tutorials in the user guide the simplest way to test the installation?

Best regards,
Niall O'Sullivan
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Unfortunately, there still seems to be some remaining problems; when we enter execute "run_flow2d3d.sh" in the examples subdirectory at a terminal window the response is "command not found". Also, a similar response is obtained on entering delft3d-menu in the src subdirectory.

Are there additional steps required after compiling the source? Could the above errors be connected to the PATH variable and if so what changes should be made?

The current setting of the PATH variable is as follows:

hmrc@linuxadmin-Vostro-3550:~/delft3d_repository/examples/01_standard$ echo $PATH

/opt/intel/composer_xe_2011_sp1.7.256/bin/ia32:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/opt/intel/composer_xe_2011_sp1.7.256/mpirt/bin/ia32

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

Executing "run_flow2d3d.sh" inside directory ".../examples/01_standard" should work when compiling finished correctly. Try executing "./run_flow2d3d.sh", in case directory "." is not in your path.

In case this does not help: try to find out whether the script "run_flow2d3d.sh" can be found and if so, what line in it causes problems. You can do this by adding some write statements to the script like this:
echo "This is the start of run_flow2d3d.sh"

You can also (temporary) remove some lines to find out what causes the error.

Also check that binaries are produced and located where the script expects them. Directory "...bin/lnx/flow2d3d/bin" should contain "deltares_hydro.exe", "d_hydro.exe" and "libflow2d3d.so".

If the script is correct and the binaries are there, may be not all dynamic libraries can be found. Looking to your PATH I expect they can, but to be sure:
Execute "ldd libflow2d3d.so" (and "ldd d_hydro.exe") to see what libraries are needed. Compiler specific libraries can be found using PATH, but to make it more portable the advice is to have all binaries needed available in the two directories "...bin/lnx/flow2d3d/bin" and "...bin/lnx/flow2d3d/lib". If you want/need this, you have to copy compiler specific files to one of these two directories. We are working on a script to automate this.

If the script "run_flow2d3d.sh" works fine, the next step is to copy the generated binaries into the Delft3D graphical user interface (GUI) directory structure. Then you can use the GUI for calculations and follow the tutorials. Please have a look at http://oss.deltares.nl/web/opendelft3d/source-code#Run a calculation.

Regards,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your response and it is great that we have finally made some progress.

The command "./run_flow2d3d.sh" seems to run correctly, see attached txt file for output; however the command "run_flow2d3d.sh" results in "command not" found being displayed.

Also the directory "...bin/lnx/flow2d3d/bin" contains the files "deltares_hydro.exe", "d_hydro.exe" and "libflow2d3d.so".

Finally as the script "run_flow2d3d.sh" works please provide further details on your next instruction "... the next step is to copy the generated binaries into the Delft3D graphical user interface (GUI) directory structure.". Please indicate the binaries that should be copied and where they should be copied to.

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

If you want to avoid adding the "./" in front of "run_flow2d3d.sh" all the time, you have to add "." to your environment parameter PATH, ideally in a config script that is parsed every time you log on, for example in file "~/.bashrc":
export PATH=".:$PATH"


About copying binaries to the GUI: I updated http://oss.delft3d.nl/source-code#Run a calculation. It's a bit tricky due to temporary solutions and "things to do", I'm sorry for that. Can you try copying the binaries to the GUI and give me feed back about this information page?

Thanks,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your response of Tuesday last.

The script "convert_lnx_to_old_directory_structure_intel.sh" ran correctly and created an "intel" directory along with the subdirectories specified in the script. The only error message seemed to be due to two of the original directories being empty, see output below:

hmrc@linuxadmin-Vostro-3550:~/delft3d_repository/bin$ sh convert_lnx_to_old_directory_structure_intel.sh
Converting 'new' directory structure (lnx) to 'old' directory structure (intel) ...
cp: cannot stat `lnx/flow2d3d/lib/*': No such file or directory
cp: cannot stat `lnx/util/bin/*': No such file or directory
Finished converting.

However, it is not clear to me where the "intel" directory created above should be copied to. Please clarify where the "intel" directory in "myDelft3D\intel" should be.

The "README" file in "src" indicates that the binaries are installed in directory "bin\intel" but unfortunately I have not been able to locate this directory.

The location where the software was downloaded to is "Home\delft3d_repository".

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892 (Answer)

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

Looking back at our posts: I think you missed step zero: obtain the GUI setup and install it.
Please have a look at oss.deltares.nl/web/opendelft3d/source-code while being signed in. At the top is a box with the title "TEMPORARY EXTRA SERVICE". That should clarify it.

I updated oss.deltares.nl/web/opendelft3d/source-code#Run a calculation again.

Thanks.

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your message of 24 May last. The GUI installation files and a license file have been obtained but several issues have arisen as follows:

1. It seems to me that the directory "myDelft3D\intel" is the directory "\opt\intel". This latter directory has 12 folders and one file, whereas the intel directory created by the conversion script has only four folders, so should I copy these four directories into \opt\intel rather than replacing the \opt\intel directory itself?

2. At the beginning of the Matlab Compiler Runtime installation on trying to run "MCRInstaller.bin" I got a permission denied error, this was overcome by issuing the command "chmod +x MCRInstaller.bin" ,see http://www.cs.utsa.edu/~jruan/software/commFinder/faq.htm. Also, the permissions on the directory /opt/MATLAB needed to be changed. The installation then completed without error.

3. As I do not have a dongle a dongle driver was not installed.

4. Delft3D system itself is supplied as an rpm file but, as far as I am aware, this is not suitable for Ubuntu which I am using, where a deb file is required. Conversion from rpm to deb was achieved using the package alien via the command sudo alien Delft3D-openhydromorpho-4.00.01-02.i386.rpm and the installation was then initiated by sudo dpkg -i delft3d-openhydromorpho_4.00.01-3_i386.deb. The resulting response, which seems to be without any error messages was:

Selecting previously deselected package delft3d-openhydromorpho.
(Reading database ... 144600 files and directories currently installed.)
Unpacking delft3d-openhydromorpho (from delft3d-openhydromorpho_4.00.01-3_i386.deb) ...
Setting up delft3d-openhydromorpho (4.00.01-3) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place

Please confirm that this approach is correct.

5. Should the FLEXnet license manager software be obtained independently as I do not seem to have received these items?

6. Is it necessary to set the environment variables manually as at this stage these have not been set in accordance with p27 of the installation manual?

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

The answer to point 1. is "yes, copy the intel directory (with 4 subdirectories) into \opt\intel (with 12 subdirectories), replacing a few files, leaving a lot of files and directories unchanged".

I'll ask a colleague to answer your questions about .rpm, .deb, FLEX net and environment variables.

Regards,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your response of June 1 last.

As suggested the intel subdirectory was copied into /opt/intel. The /opt/intel subdirectory now has an additional intel subdirectory, a directory listing follows below:

hmrc@linuxadmin-Vostro-3550:/opt/intel$ ls
ActivationTool composer_xe_2011_sp1 intel licenses
bin composer_xe_2011_sp1.7.256 intel_sdp_products.db man
composerxe include lib mkl
hmrc@linuxadmin-Vostro-3550:/opt/intel$

Please confirm that this is correct.

Also, the document at http://oss.deltares.nl/web/opendelft3d/source-code#Run%20a%20calculation gives the following instructions for starting the Delft3D-menu :

Linux: "Dot" the profile and start the menu, using the following two commands:
. /myDelft3D/etc/profile.d/delft3d.sh
delft3d-menu

Unfortunately, in the directory /opt/intel, which we have agreed is equivalent to myDelft3D/intel does not contain an etc directory.

Please indicate where delft3d.sh should be located.

Best regards,
Niall O'Sullivan
AT
Aaron Tran, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 1 Join Date: 5/30/12 Recent Posts
I am not Adri, but I think delft3d.sh is located in /etc/profile.d/delft3d.sh. And, /opt/intel looks like it contains files for the Intel Fortran compiler; it may be /opt/delft3d/intel instead. My disclaimer is that I've tried these respectively and have not gotten the GUI working yet!

Thank you all for this thread - it has been very helpful in trying to install Delft3D.
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Thank you for your response and I am glad that you found the thread of use.

As my delft3d.sh file is located in /etc/profile.d, as you suggested, I changed the recommended command to that shown below and succeeded in getting the GUI to appear to operate, see attached file

hmrc@linuxadmin-Vostro-3550:~$ . /etc/profile.d/delft3d.sh
hmrc@linuxadmin-Vostro-3550:~$ delft3d-menu

We will do some further tests in the coming days to establish how much of the package is actually working.

Best regards,
Niall O'Sullivan
Adri Mourits, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Yoda Posts: 1221 Join Date: 1/3/11 Recent Posts
Hi Niall,

I'm sorry, but we only support RedHat/CentOS. For other operating systems, we try to answer questions as long as the effort is small.

Please put as much relevant information as possible on this forum to help other Ubuntu users.

Thanks,

Adri
NO
Niall O'Sullivan, modified 8 Years ago.

RE: Problem compiling on LinuxD3D ubuntu version 0892

Youngling Posts: 18 Join Date: 9/16/11 Recent Posts
Adri,
Thank you for your response of June 15 last and for your help since we started in December last.

It seems to me that at this stage it may be best to change from Ubuntu to CentOS and start the installation again.

Best regards,
Niall O'Sullivan