RE: Problems compiling Delft3D Revision 61494 on Ubuntu 16.04

2018-09-05T19:12:07Z

Hi Jay,

Yes, your assumptions are correct; sorry for the confusion.

Does the manual of NetCDF help you further?

Try using NetCDF without HDF5 support, see the prerequisites; that will make the compilation a lot easier.

Regards,

Adri

Problems compiling Delft3D Revision 61494 on Ubuntu 16.04

2018-08-29T16:01:19Z

Hi Folks,

I am trying to compile the Delft3d - Revision 61494 software on Ubuntu16.04. I am trying to follow the instructions as per the Ubuntu 16.04 README in Revision 61494:Trunk/src. I listed the text from README file below..

I follow the instructions as per the README.

Everything proceeds well

I installed all of the required software using apt
However, I think that there are some text errors in the README regarding teh declarations for the environment variables to path locations.
1. I was able to install Zlib
2. The path variable declarations in the routines for HDF5 and Netcdf seem incorrect:

For example, the statement

export HDF5_DIR="/home/abc/Downloads/libraries/hdf5-${v}"

Question:

I assume that I should change

HDF5_DIR=”/home/abc/…”

HDF5_Dir=”/home/my user name/….”?

I did do this for both HDF5 and the netcdf portions of the declaration

The environment variable declaration for netcdf has another questionable portion of text at the very end.
1. export NETCDF4_DIR="/home/abc/Downloads/libraries/netcdf_4.4

Question:

I assume that I should change

export NETCDF4_DIR=”…./libraries/netcdf_4.4

export NETCDF4_DIR=”…./libraries/netcdf-${v}”?

I made all of the assumed corrections above and followed the compilation instructions for compiling zlib, HDF5, and netcdf-4.

However, I am running into errors trying to compile netcdf so I am not sure about the corrections that I made.

Any help would be appreciated. I have been working on this for several days. Does anyone know of additional compilation instructions that may help?

I cannot compile netcdf properly to create a /bin.

Thanks in advance for your response.

Jay

kramerj@childseng.com

>>>>>>>>>>>>>>> Ubuntu 16.04 README

Delft3d - Revision 61494: /trunk/src

Please check the following sites for additional information:

General information: http://oss.deltares.nl/web/delft3d/source-code

FAQ : http://oss.deltares.nl/web/delft3d/faq

Compile forum : http://oss.deltares.nl/web/delft3d/general/-/message_boards?_19_mbCategoryId=200432

Compiling on Ubuntu.16.04LT Linux

====================

0) Make sure you have a good internet connection.

1) prepare the compiling environment. In your home directory, type in:

sudo apt-get update

sudo apt-get upgrade

sudo apt-get install subversion

sudo apt-get install autoconf

sudo apt-get install libtool

sudo apt-get install flex

sudo apt-get install g++

sudo apt-get install gfortran

sudo apt-get install libstdc++6

sudo apt-get install byacc

sudo apt-get install libexpat1-dev

sudo apt-get install uuid-dev

sudo apt-get install ruby

sudo apt-get install gedit

svn co https://svn.oss.deltares.nl/repos/delft3d/trunk delft3dtrunk

cd ~/delft3dtrunk/src

2) In your home directory, go to Downloads and make a directory, e.g. libraries for installation all the libraries. type in:

cd ~/Downloads

mkdir libraries

cd libraries

3) Download the libraries codes and compile them.

BASHRC="~/.bashrc"

# Install zlib

v=1.2.8

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/zlib-${v}.tar.gz

tar -xf zlib-${v}.tar.gz && cd zlib-${v}

./configure --prefix=/usr/local

#sudo make check install

sudo make install

cd ..

# Install HDF5

v=1.8.13

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-${v}.tar.gz

tar -xf hdf5-${v}.tar.gz && cd hdf5-${v}

echo "# HDF5 libraries for Delft3D"

export HDF5_DIR="/home/abc/Downloads/libraries/hdf5-${v}"

./configure --enable-shared --enable-hl --prefix=$HDF5_DIR

make -j 2 # 2 for number of procs to be used

sudo make install

cd ..

# Install Netcdf

v=4.4.1

wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-${v}.tar.gz

tar -xf netcdf-${v}.tar.gz && cd netcdf-${v}

echo "# NETCDF4 libraries for Delft3D"

export NETCDF4_DIR="/home/abc/Downloads/libraries/netcdf_4.4"

CPPFLAGS=-I$HDF5_DIR/include LDFLAGS=-L$HDF5_DIR/lib ./configure --enable-netcdf-4 --enable-shared --enable-dap --prefix=$NETCDF4_DIR

# make check

make

sudo make install

cd ..

export PATH=$PATH:$NETCDF4_DIR/bin

export LD_LIBRARY_PATH=$NETCDF4_DIR/lib:$LD_LIBRARY_PATH

export PKG_CONFIG_PATH=$NETCDF4_DIR/lib/pkgconfig:$PKG_CONFIG_PATH

# Install Netcdf-fortran

v=4.4.4

wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-${v}.tar.gz

tar -xf netcdf-fortran-${v}.tar.gz && cd netcdf-fortran-${v}

CPPFLAGS=-I$NETCDF4_DIR/include LDFLAGS=-L$NETCDF4_DIR/lib LD_LIBRARY_PATH=$NETCDF4_DIR/lib:$LD_LIBRARY_PATH ./configure --prefix=$NETCDF4_DIR

# make check

make

sudo make install

cd ..

# Install mpi

v=3.2

wget http://www.mpich.org/static/downloads/${v}/mpich-${v}.tar.gz

tar -xzf mpich-${v}.tar.gz

cd mpich-${v}

export MPICH2_3_2_DIR="/home/abc/Downloads/libraries/mpich-${v}"

./configure --prefix=$MPICH2_3_2_DIR

make

sudo make install

cd ..

export PATH=$PATH:$MPICH2_3_2_DIR/bin

export LD_LIBRARY_PATH=$MPICH2_3_2_DIR/lib:$LD_LIBRARY_PATH

export PKG_CONFIG_PATH=$MPICH2_3_2_DIR/lib/pkgconfig:$PKG_CONFIG_PATH

4) Go back to ~/delft3dtrunk/src, build DELFT3D source code,

Check in file ./build_ubuntu1604.sh that all references to libraries, include files, etc. match with the paths on your system, and then type in, for example:

./build_ubuntu1604.sh -gnu -64bits

5) After finishing the compiling, there must be a bin directory in ~/delft3dtrunk. You probably have to copy some mpi libraries to the bin directory.

cp ~/Downloads/libraries/mpich-3.2/lib/* ~/delft3dtrunk/bin/lnx64/flow2d3d/bin

cp ~/Downloads/libraries/mpich-3.2/bin/* ~/delft3dtrunk/bin/lnx64/flow2d3d/bin

cd ~/delft3dtrunk/bin/lnx64/flow2d3d/bin

chmod a+x *

Then it should work!

Running examples without GUI

============================

In directory "examples\01_standard":

- Execute script "run_flow2d3d.sh"

Parallel:

- Depending on your system settings, you might need to change the script "run_flow2d3d_parallel.sh"

- Execute script "run_flow2d3d_parallel.sh"

REMARK:

1) In step 3, you can get the version of libraries of netcdf, netcdf-fortran, mpich2 by changing the v variable .

2) In step 3, if it complains " The install directory can't be the same with the build or src directory", you may have to adjust the directory name and the path accordingly.

24 NOV 2016

qinghua.ye@deltares.nl

adri.mourits@deltares.nl