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https://github.com/fschuch/xcompact3d

New version of our solver for the incompressible Navier-Stokes equations
https://github.com/fschuch/xcompact3d

Last synced: 10 months ago
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New version of our solver for the incompressible Navier-Stokes equations

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## The Xcompact3d code



![Build Status](https://github.com/fschuch/Xcompact3d/workflows/Build/badge.svg)

[![DOI](https://img.shields.io/badge/doi-10.1016%2Fj.softx.2020.100550-blue)](https://doi.org/10.1016/j.softx.2020.100550)



Xcompact3d is a Fortran-MPI based, finite difference high-performance code for solving the

incompressible or low Mach number Navier-Stokes equations with an arbitrary number of scalar transport

equations.



This repository contains a major upgrade in the Xcompact3d code. The new version is faster, more flexible and user friendly.



The main homepage for the original Incompact3d can be found at [incompact3d.com](https://www.incompact3d.com/). You can find a list of the work related to the code.



**This is a Fork from Xcompact3d´s official repository, for more information see the [Changelog](CHANGELOG.md)**.



## Resources



- **Homepage:** 

- **Old Binaries (please try to use the latest Github version instead):** 

- **Discussion section (FORUM):** 

- **Xcompact3d-toolbox**, a set of tools for pre and postprocessing prepared for the high-order Navier-Stokes solver Xcompact3d: 



New users and developers are welcome to join.



### External Resources



- [**Twitter**](https://twitter.com/incompact3d)



### Benchmark test cases for code comparison ###



We established a solid and easy way to run a range of benchmark test cases to verify the

code.

Xcompact3d now supports multiple cases, selectable at runtime in the parameter file input.i3d,

including a user-defined case (note this will require editing the setup in src/BC-User.f90 and

recompiling, check the other setup files src/BC-*.f90 for guidance).

The following cases are set to match the parameters for cases of

reference articles obtained with different codes.



|Code| Flow configuration             | BC File         | Reference | Dataset |

|:----------------:|:----------------:|:----------------:|:----------------:|:----------------:|

|1| Gravity Current              | Lock-exchange    |[Necker et al. (2002)](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.483.5774&rep=rep1&type=pdf)

|2| Taylor-Green Vortices        | TGV              |[Beck et al. (2014)](https://link.springer.com/article/10.1007/s00162-011-0253-7)

|3| Periodic Channel            | Channel-flow     |[Moser, Kim & Mansour (1999)](https://www.researchgate.net/publication/243777258_Direct_Numerical_Simulation_of_Turbulent_Channel_Flow_up_to_Re590)|[Dataset](http://turbulence.ices.utexas.edu/data/MKM/chan180/profiles/)

|5| Flow over a Cylinder         | Cylinder         |[Mittal and Balachandar (1995)](https://www.researchgate.net/publication/252073966_Effect_of_three-dimensionality_on_the_lift_and_drag_of_nominal_two-dimensional_cylinders)



N.B. Other cases are in preparation.



## New compiling FLAGS



   -DDOUBLE_PREC - use double-precision

   -DSAVE_SINGLE - save 3D data in single-precision

   -DDEBG        - debuggin incompact3d.f90



**Note:** In order to compile the code with the appropriate flags you must enter the -D$FLAG, i.e., -DDOUBLE_PREC



# Compiled code performance



Xcompact3d is designed to run on laptops/workstations up to large clusters. We support the gfortran, ifort and ftn compilers

which can be selected at compile time by



   make CMP=gcc

   make CMP=intel

   make CMP=cray



respectively (it will default to gfortran otherwise). Note that we use gfortran for development, therefore not all optimizations are enabled by default - if you want to perform production runs using gfortran, adding -O3 to the FFLAGS for CMP=gcc should provide a significant speed up.



## Source Download and Compilation



First, make sure you have all the [required dependencies](#required-build-tools-and-external-libraries) installed.

Then, acquire the source code by cloning the git repository:



    git clone git@github.com:xcompact3d/Incompact3d.git



(If you are behind a firewall, you may need to use the `https` protocol instead of the `git` protocol:



    git config --global url."https://".insteadOf git@



Be sure to also configure your system to use the appropriate proxy settings, e.g. by setting the `https_proxy` and `http_proxy` variables.)



By default you will be building the latest master version of Xcompact3d, to use the release preview you must checkout the release branch



    git checkout release



Now run `make` to build the `Xcompact3d` executable. To perform a parallel build, use `make -j N` and supply the maximum number of concurrent processes. (See [Platform Specific Build Notes] for details.)

This takes a while, but only has to be done once. If the defaults in the build do not work for you, and you need to set specific make parameters, you can save them in `Make.user`. The build will automatically check for the existence of `Makefile` and use it if it exists.

Building Xcompact3d requires very little of disk space and virtual memory.



**Note:** The compiling process



Once it is built, you can run the `Xcompact3d` executable using its full path in the directory created above (the `Xcompact3d` directory).



Now you should be able to run Xcompact3d like this:



    mpirun -n 4 ./xcompact3d ./examples//input.i3d



If a input.i3d file is not provide, xcompact3d will look for it locally (i.e. try to load ./input.i3d).



If everything works correctly, you will see a Xcompact3d banner and an interactive prompt into which you can enter expressions for evaluation. (Errors related to libraries might be caused by old, incompatible libraries sitting around in your PATH. In this case, try moving the `Xcompact3d` directory earlier in the PATH).



### Updating an existing source tree



If you have previously downloaded `incompact3d` using `git clone`, you can update the

existing source tree using `git pull` rather than starting anew:



    cd incompact3d

    git pull && make



Assuming that you had made no changes to the source tree that will conflict

with upstream updates, these commands will trigger a build to update to the

latest version.



#### General troubleshooting



1. Over time, the base library may accumulate enough changes such that the

   bootstrapping process in building the system image will fail. If this

   happens, the build may fail with an error like



   ```sh

    *** This error is usually fixed by running 'make clean'. If the error persists, try 'make cleanall' ***

   ```

   As described, running `make clean && make` is usually sufficient. Occasionally, the stronger cleanup done by `make cleanall` is needed.



## Platform-Specific Notes



### Linux



#### General



* GCC version 4.7 or later is required to compile the code.



We recommended that you remove the limits of the environment (e.g. in `.bash_profile`)



    ulimit -c unlimited

    ulimit -s unlimited



You must exit and re-login from your terminal for the change to take effect



    ulimit -a



#### Architecture Customization



Xcompact3d can be compiled for a non-generic architecture by configuring the `ARCH` Makefile variable. See the appropriate section of `Makefile` for additional customization options, such as `MARCH` and `CPU_TARGET`. You can also set `march=native` for a maximum-performance build customized for the current machine CPU.



#### Ubuntu



In order to compile and execute Xcompact3d in the latest Ubuntu version please install the following packages:



    sudo apt install gfortran libopenmpi-dev



#### Fedora/RHEL/CentOS



On RHEL/CentOS 6 systems:



    sudo dnf install gcc-gfortran



### OS X



You need to have the current Xcode command line utilities installed: run `xcode-select --install` in the terminal.

You will need to rerun this terminal command after each OS X update, otherwise you may run into errors involving missing libraries or headers. You will also need a 64-bit gfortran to compile the code. The gfortran-4.7 (and newer) compilers in Brew, Fink, and MacPorts work for building Xcompact3d. On current systems, we recommend that you install the command line tools as described above. Older systems do not have a separate command line tools package from Apple, and will require a full Xcode install. On these, you will need at least Xcode 4.3.3. In Xcode prior to v5.0, you can alternatively go to Preferences -> Downloads and select the Command Line Utilities.



## GitHub Configuration



To add you SSH key to your GitHub account please follow the steps https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/ or just copy the content of the id_rsa.pub file to your clipboard, go to Personal settings and add a new SSH key:



    cat ~/.ssh/id_rsa.pub