Installation of Code_Saturne 2.0-rc1 on Ubuntu 10.04 (64 bit)

Based on the previous posts, "Installation of Code_Saturne 2.0.0 on Ubuntu 9.04" and "Installation of Code_Saturne 2.0-rc1 on Ubuntu 9.10", and David's comments, I double checked the installation of Code_Saturne onto Ubuntu 10.04 LTS (long-time support version) and record the procedure here.

1. Install prerequisites

Using apt-get install the packages as

:/$ sudo apt-get install build-essential gfortran libxml2 libxml2-dev libatlas-headers libatlas-base-dev openmpi-bin openmpi-dev libibverbs-dev openssh-server python-qt4 pyqt4-dev-tools swig python-dev

2. Install HDF5 and MED libraries

Thanks to David's help, I used apt-get to install the 2 packages

:/$ sudo apt-get install libhdf5-serial-dev libmedc-dev

On Ubuntu 10.04, this installs HDF5 1.8.4 and MED 2.3.5. What Code_Saturne really needs is a MED 2.3 mesh format, and thus the minimum version of MED required must be 2.3.0.

I am also glad to see that Code_Saturne supports to use HDF5 1.8.x now.

3. Compile METIS

Download a patched version of Metis-4.0 from my link, and extract it. Compile as

# ship into metis-4.0
:/$ make
:/$ sudo cp graphchk kmetis mesh2dual mesh2nodal oemetis onmetis partdmesh partnmesh pmetis /usr/local/bin/
:/$ sudo cp libmetis.a /usr/local/lib/
:/$ sudo cp Lib/*.h /usr/local/include/

Indeed, it is annoying to install METIS due to prototypes redefinition, non-standard directories installation, ... which probably make you don't want to use METIS, even though my patched version. As suggested, you can use the SCOTCH library instead (perhaps a bit less performant for many-processors calculation, but sufficient for standard ones), or only use the internal partioner of Code_Saturne (based on a Space-Filling Curve algorithm, which is good-enough for few-processors calculation, e.g. several-core but mono-processor computers).

4. Configure and compile bft, fvm, ecs and mei sequentially

# ship into bft-1.1.2
:/$ ./configure
:/$ make
:/$ sudo make install

# ship into fvm-0.15.0
:/$ ./configure --with-mpi=/usr/lib/openmpi
...
Configuration options:
 use debugging code: false
 MPI (Message Passing Interface) support: yes
   MPI I/O support: yes
   MPI2 one-sided communication support: yes
 HDF (Hierarchical Data Format) support: yes
 CGNS (CFD General Notation System) support: no
 MED (Model for Exchange of Data) support: yes
...
:/$ make
:/$ sudo make install

# ship into ecs-2.0.0-rc1
:/$ ./configure
...
Configuration options:
 use debugging code: false
 use long integers: false
 ADF support: no
 CCM support: no
 HDF5 (Hierarchical Data Format) support: yes
 CGNS (CFD General Notation System) support: no
 MED (Model for Exchange of Data) support: yes
 METIS (Graph Partitioning) support: yes
 SCOTCH (Graph Partitioning) support: no
...
:/$ make
:/$ sudo make install

MEI is not compulsory, but strongly recommended, as long as you want to define function expressions handily in the GUI.

# ship into mei-1.0.1
:/$ ./configure --with-bft=/usr/local
...
Configuration options:
 use debugging code: false
 Python bindings: true
...
:/$ make
:/$ sudo make install

5. Patch and compile ncs

Extract the patch patches-portability-ncs-20rc1.tgz to the ncs directory.

# ship into ncs-2.0.0-rc1
:/$ tar xzvf ../patch/patches-portability-ncs-20rc1.tgz

Extract the patch rho_mu-tar.gz to a directory. There are 2 files contained, cs_gui.c and FluidCharacteristicsView.py, and copy them accordingly.

# in ncs-2.0.0-rc1
:/$ find . -name cs_gui.c
./src/base/cs_gui.c
:/$ cp ../patch/rho_mu/cs_gui.c src/base/
:/$ find . -name FluidCharacteristicsView.py
./gui/Pages/FluidCharacteristicsView.py
:/$ cp ../patch/rho_mu/FluidCharacteristicsView.py gui/Pages/

Configure and compile ncs, as

# in ncs-2.0.0-rc1
:/$ ./configure --with-mpi=/usr/lib/openmpi --with-prepro=/usr/local --with-mei=/usr/local
...
Configuration options:
 use debugging code: false
 use graphical user interface: yes
 MPI (Message Passing Interface) support: yes
 OpenMP support: no
 BLAS (Basic Linear Algebra Subprograms) support: yes
 Libxml2 (XML Reader) support: yes
 MEI (Mathematical Expressions Interpreter) support: yes
 SYRTHES 3 coupling support: no
 IP socket support (for SYRTHES 3 or CFD_Proxy): yes
 Dynamic loader support (for YACS): yes
...
:/$ make
:/$ sudo make install

6. (optional) Compile latex documents

If you don't use latex, you don't have to bother to compile the documents. I already prepared my compiled documents (pdf files) for you to use directly.

If you want to do it manually, please follow

# for processing LaTeX documents
:/$ sudo apt-get install tetex-bin tetex-base transfig
# in ncs-2.0.0-rc1
:/S cp ~/fullpage.sty ~/lastpage.sty doc/style/
:/$ make pdf
:/$ sudo make install-pdf

7. Run Code_Saturne

After finished the procedure without rebooting the system, I tried to run Code_Saturne but encountered an error as

  ********************************************
    Starting calculation
  ********************************************

Error running the preprocessor.
Check preprocessor log (listpre) for details.

Error running the partitioner.
Check partitioner log (listpart) for details.

  ********************************************
    Error in partitioning stage.
  ********************************************

In listpart it was written that

/usr/local/bin/cs_partition: error while loading shared libraries: libbft.so.1: cannot open shared object file: No such file or directory

Don't worry. Update the dynamic library database to avoid it.

:/$ sudo ldconfig
[sudo] password for salad:
:/$ sudo updatedb