Citing FIDASIM Source Code
Along with the FIDASIM paper, please cite the source code.
@article{FIDASIMpaper,
author = {Benedikt Geiger and Luke Stagner and William W Heidbrink and Ralph Dux and Rainer Fischer and Yutaka Fujiwara and Alvin Garcia and Asger Schou Jacobsen and Anton Jansen vanVuuren and Alexander N Karpushov and Deyong Liu and Philip Adrian Schneider and Igor Sfiligoi and Peter Zsolt Poloskei and Markus Weiland},
title = {Progress in modelling fast-ion D-alpha spectra and neutral particle analyzer fluxes using FIDASIM},
journal = {Plasma Physics and Controlled Fusion},
url = {http://iopscience.iop.org/10.1088/1361-6587/aba8d7},
year = {2020}
}
@misc{FIDASIMcode,
author = {Stagner, L. and Geiger, B. and Heidbrink, W.W.},
title = {{FIDASIM: A Neutral Beam and Fast-ion Diagnostic Modeling Suite}},
doi = {10.5281/zenodo.1341369},
url = {https://doi.org/10.5281/zenodo.1341369}
}
User Documention
Click here for full user documentation.
Developer Documentation
Contributing Guidelines
If you would like to add code to FIDASIM please follow these guidelines
- Use spaces to indent code not tabs
- Don't push directly to
master. All new work should be on a feature branch prefixed with your initials, e.g.ls/newfeature. When you think you are done open a pull request so it can undergo code review. - Add inline documentation as you go. Follow existing documentation format.
- Be as general as possible. This makes it easier to add new features down the line.
Common Makefile Options
FIDASIM has a few different makefile options
make DEBUG=y #Turns off all optimizations and OpenMP. Turns on bounds checking and floating point exceptions. Default: n
make USE_OPENMP=n #Turns off OpenMP but leaves other optimizations. Default: y
make PROFILE=y #Turns on gprof profiling. Turns off OpenMP. Default: n
make USE_MPI=y #Turns on MPI parallelization. Default: n
make ARCH=<TARGET> #Compile code optimized for <TARGET> e.g. ARCH=haswell/CORE-AVX2/native. Options differ depending on compiler. Generated code may not run on different architectures. Default: n
Run make help for all the available options
Profiling
You can profile FIDASIM by building with the PROFILE=y build option.
With profiling enabled FIDASIM will output a gmon.out file.
To turn this into a profile report run
gprof ./fidasim gmon.out > fidasim.profile
This will create a report that looks something like this
Flat profile:
Each sample counts as 0.01 seconds.
% cumulative self self total
time seconds seconds calls s/call s/call name
34.38 240.02 240.02 106095199 0.00 0.00 __eigensystem_MOD_hqr2
13.75 336.04 96.01 106095199 0.00 0.00 __eigensystem_MOD_matinv
9.62 403.18 67.14 106095199 0.00 0.00 __libfida_MOD_get_rate_matrix
6.39 447.82 44.64 106095199 0.00 0.00 __eigensystem_MOD_hqrvec
4.40 478.53 30.72 5049752 0.00 0.00 __libfida_MOD_interpol2d_2d_arr
3.66 504.10 25.56 5049752 0.00 0.00 __parallel_rng_MOD_randind_w_2
3.48 528.41 24.31 106095199 0.00 0.00 __eigensystem_MOD_balance
3.11 550.11 21.71 116519743 0.00 0.00 __libfida_MOD_store_fida_photons
3.07 571.58 21.47 482016993 0.00 0.00 __libfida_MOD_in_plasma
2.99 592.48 20.90 106095199 0.00 0.00 __eigensystem_MOD_elmhes
1.87 605.53 13.05 636571194 0.00 0.00 __eigensystem_MOD_outerprod
1.53 616.19 10.66 5049520 0.00 0.00 __libfida_MOD_track.constprop.9
1.47 626.45 10.26 1 10.26 696.97 __libfida_MOD_fida_f
...
This can be difficult to parse so it sometimes helpful to use a profile visualization tool like gprof2dot or the online tool Profiler Visualizer 2000
Documentation Website
The documentation is built using FORD.
FORD takes inline documentation, prefixed by !+, and the markdown files located in docs/user_guide and wraps them all up in a pretty website.
The documentation website is automatically updated whenever a commit is added to the master branch. This is done through Travis-CI.
To build the documentation locally run
make docs
This will build the documentation website in the docs/html directory.
The above command will also check the website for dead links which requires linkchecker to be installed.
This functionality can be disabled by passing the CHECK_LINKS=n build option to the make docs command.