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Complete rework and formatting
It turned out, that on other computers the original installation instructions did't work. So I tried to overcome the respective caveats. Further I did some better formatting with GitHub Flavored Markdown.
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‎_docs/Cygwin-Build-for-Windows.md‎

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@@ -25,65 +25,176 @@ At the package selection step, search for the following terms and select the ass
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* cpp: all debug, pre-processor, regular expression packages.
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#### Example SU2 installation on WINDOWS 10 using 64-bit Cygwin
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The shell used for all command line steps is the the default Cygwin bash shell.
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1) Install CYGWIN (64-bit version)
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a) Download and run https://www.cygwin.com/setup-x86_64.exe
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b) Install development tools (also 64-bit versions):
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i) gcc, gfortran, python3.7, openmpi, automake, libtools, autoconf, etc.
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ii) python-configobj needs to be installed for the same python version
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(Python module for handling config files)
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often there are installation problems (not yet figured out when and why)
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after installation it should reside in the folder /usr/bin as shown below
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iii) folder /usr/bin as it should be for python3.7 and python-config
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lrwxrwxrwx 1 Andreas None 14 17. Mrz 19:29 /usr/bin/python3.7 -> python3.7m.exe
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-rwxr-xr-x 1 Andreas None 3,3K 17. Mrz 19:46 /usr/bin/python3.7-config
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-rwxr-xr-x 1 Andreas None 9,1K 15. Feb 10:05 /usr/bin/python3.7m.exe
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-rwxr-xr-x 1 Andreas None 3,3K 17. Mrz 19:46 /usr/bin/python3.7m-config
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2) Set Python version for the installation process
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export PYTHON=/usr/bin/python3.7
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3) Goto folder where the SU2 source distribtution has been unzipped
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a) download the SU2 source installation file for version 6.2.0
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https://github.com/su2code/SU2/archive/v6.2.0.tar.gz
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b) unzip and untar
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c) change into the folder where files were untarred
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NOTE: this is later (see step 7) the folder where the SU2_HOME variable points to
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3a) ./bootstrap
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4) Launch following configure command:
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NOTE: didn't get tecio working, therefore disabled with --disable-tecio
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NOTE: "--enable-mpi-cxx" instead of "--enable-mpi"
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(see http://cygwin.1069669.n5.nabble.com/libmpi-cxx-dll-a-missing-td142324.html)
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./configure --prefix=path_where_you_want_the_Executables --disable-tecio --enable-mpi-cxx CXXFLAGS=-O3
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5) Compile and link using:
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make
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6) Not really needed (if a setup like in 7 is used)
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make install
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7) Add the $SU2_HOME and $SU2_RUN environment variables to ~/.bashrc (and "source ~/.bashrc")
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export SU2_RUN="path_where_you_want_the_Executables" (use same folder here as in the configure command above)
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export SU2_HOME="/d/software/CFD/SU2/SU2-6.2.0" <-- UPDATE THIS folder to your environment
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export PATH=$PATH:$SU2_RUN
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export PYTHONPATH=$PYTHONPATH:$SU2_RUN
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8) cd to the QuickStart folder and try serial and parallel versions
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SERIAL command:
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SU2_CFD.exe inv_NACA0012.cfg
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PARALLEL command:
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(mpirun and mpiexec should be the same; mpiexec recommended as standard command)
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(-oversubscribe allows more processes than cores)
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(although I have 8 cores, even with "-n 6" I had to use the option)
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(otherwise I got: There are not enough slots available in the system ...)
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mpiexec -n 6 -oversubscribe SU2_CFD.exe inv_NACA0012.cfg
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The CYGWIN `bash` shell is used for all steps on the command line. It is automatically available after the first installation step (typically to be launched via the CYGWIN desktop icon).
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1. Install CYGWIN (64-bit version) and development packages
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* Download and run:
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[setup-x86_64.exe](https://www.cygwin.com/setup-x86_64.exe)
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Inside the Cygwin Setup GUI use `C:\cygwin64` for both `Root Directory` and `Local Package Directory`. `Chose a Download Site` close to you (also http mirrors often work better). Continue to complete the bare minimum installation. This will end with a desktop icon named `Cygwin64 Terminal`. Double-click this to open the shell and launch further commands from there.
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For detailed informations on how to install CYGWIN and selected packages see [CYGWIN Installation](https://cygwin.com/install.html).
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* Install development tools (dependencies on these packages will be automatically selected by CYGWIN)
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> NOTE: A single command installing all required packages in one is given below this list
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1. General build environment tools
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* autoconf
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* autoconf2.5
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* autogen
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* automake
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* automake1.15
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* libtool
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* make
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1. Compilers
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* gcc-g++
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* mingw64-x86_64-gcc-core
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* mingw64-x86_64-gcc-g++
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1. Python
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* python37
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* python37-devel
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* python3-configobj
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1. OpenMPI
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* libopenmpi-devel
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* openmpi
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1. Miscellaneous
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* vim (or any other editor in order to be able to edit files)
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* wget (to be able to download from the command line)
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* zlib-devel
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* All-in-one installation of packages (after the initial minimum installation):
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> NOTE: Prepend path to `setup-x86_64.exe` (depending where it has been downloaded)
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```bash
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setup-x86_64.exe -q -P autoconf,autoconf2.5,autogen,automake,automake1.15,libtool,make,gcc-g++,mingw64-x86_64-gcc-core,mingw64-x86_64-gcc-g++,python37,python37-devel,python3-configobj,libopenmpi-devel,openmpi,vim,wget,zlib-devel
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```
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1. Configure CYGWINs default mount point (optional, but following steps use a syntax relying on this)
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```bash
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mount -c / -o binary,noacl,posix=0
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mount -m > /etc/fstab
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```
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1. Configure OpenMPI
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Because in OpenMPI the C++ interface was removed, the option `-lmpi_cxx` has to be removed from the linker defaults. We need to check if this option is contained in the wrapper control file. This depends on the installed OpenMPI libraries.
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Assuming the 64-bit CYGWIN is installed in `C:\cygwin64` and `/etc/fstab` has been modified as in the previous step:
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```bash
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cat /c/cygwin64/usr/share/openmpi/mpic++-wrapper-data.txt | grep lmpi_cxx
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```
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If the option is set, then the following lines would be the result of the above `grep`command:
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libs=-lmpi_cxx -lmpi
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libs_static=-lmpi_cxx -lmpi -lopen-rte -lopen-pal -lm -lgdi3
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> NOTE: If `-lmpi_cxx` was not found, skip the next step
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If this is the case, edit `mpic++-wrapper-data.txt` and remove the `-lmpi_cxx` options so that the respective lines look like this:
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libs=-lmpi
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libs_static=-lmpi -lopen-rte -lopen-pal -lm -lgdi3
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1. Set the Python version for the installation process (for permanent setting add this line to `~/.profile`)
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```bash
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export PYTHON=/usr/bin/python3.7
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```
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1. Get the SU2 source code:
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* Download following file for SU2 version 6.2.0
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```bash
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wget https://github.com/su2code/SU2/archive/v6.2.0.tar.gz
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```
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* Extract files and change into the folder where the files were extracted to:
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```bash
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tar -xzvf v6.2.0.tar.gz
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cd SU2-6.2.0
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```
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> NOTE: This is later the folder where the SU2_HOME variable points to
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1. Run the utility for autoconf/automake toolchain setup:
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```bash
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./bootstrap
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```
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1. Create Makefiles:
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NOTE: didn't yet get `tecio` working, therefore disabled with `--disable-tecio`<br>
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NOTE: Removed `-DHAVE_EXECINFO_H` from metis cppflags (potentially could be solved via [gnulib](https://www.gnu.org/software/gnulib/manual/html_node/execinfo_002eh.html))
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```bash
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./configure --prefix=/home/Andreas/SU2-6.2.0 -enable-mpi --with-cc=/usr/bin/mpicc --with-cxx=/usr/bin/mpicxx --disable-tecio --with-metis-cppflags="-D_FILE_OFFSET_BITS=64 -DNDEBUG -DNDEBUG2 -DHAVE_GETLINE"
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```
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1. Compile and link using:
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```bash
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make
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```
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1. Distribute executables, etc. to their intended locations:
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```bash
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make install
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```
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1. Add the `$SU2_HOME` and `$SU2_RUN` environment variables to `~/.bashrc` (and `source ~/.bashrc`)
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```bash
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export SU2_RUN="path_where_you_want_the_Executables" (use same folder here as in the configure command above)
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export SU2_HOME="/d/software/CFD/SU2/SU2-6.2.0" <-- UPDATE THIS folder according to your environment
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export PATH=$PATH:$SU2_RUN
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export PYTHONPATH=$PYTHONPATH:$SU2_RUN
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```
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1. Test serial and parallel versions:
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```bash
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cd $SU2_HOME/QuickStart
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```
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SERIAL command (due to the previous step `SU2_CFD.exe` should now be available in the path):
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```bash
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SU2_CFD.exe inv_NACA0012.cfg
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```
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PARALLEL command:
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Both `mpirun` and `mpiexec` do the same; `mpiexec` is recommended as the standard command.
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```bash
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mpiexec -n 4 SU2_CFD.exe inv_NACA0012.cfg
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```
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If more processes are requested than cores are available an error will be thrown:
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> There are not enough slots available in the system.
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On WINDOWS this can be if hyperthreading is active. A system physically having 4 CPUs (cores), would show 8 CPUs in case of hyperthreading. Oversubscribe allows more processes than cores (which not necessarily is faster).
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```bash
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mpiexec -n 8 -oversubscribe SU2_CFD.exe inv_NACA0012.cfg
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```
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or
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```bash
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mpiexec --use-hwthread-cpus -n 8 SU2_CFD.exe inv_NACA0012.cfg
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```

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