Soledge3X

https://soledge3x.onrender.com
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Soledge3X is an edge plasma simulation code designed to model the complex physics of tokamak edge...
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### Example config.toml configuration

Source: https://soledge3x.onrender.com/getting_started/configuration

A comprehensive example of the configuration options available in config.toml for the soledge3x theme.

```toml
# Source Code repository section
description = "put your description"
github_repository = "https://github.com/thingsym/hugo-theme-techdoc"
version = "0.9.0"

# Documentation repository section
# documentation repository (set edit link to documentation repository)
github_doc_repository = "https://github.com/thingsym/hugo-theme-techdoc"

# Analytic section
google_analytics_id = "" # Your Google Analytics tracking id
tag_manager_container_id = "" # Your Google Tag Manager container id
google_site_verification = "" # Your Google Site Verification for Search Console

# Open Graph and Twitter Cards settings section
# Open Graph settings for each page are set on the front matter.
# See https://gohugo.io/templates/internal/#open-graph
# See https://gohugo.io/templates/internal/#twitter-cards
title = "Hugo Techdoc Theme"
images = ["images/og-image.png"] # Open graph images are placed in `static/images`

# Theme settings section
# Theme color
# See color value reference https://developer.mozilla.org/en-US/docs/Web/CSS/color
custom_font_color = ""
custom_background_color = ""

# Documentation Menu section
# Menu style settings
menu_style = "open-menu" # "open-menu" or "slide-menu"

# Date format
dateformat = "" # default "2 Jan 2006"
# See the format reference https://gohugo.io/functions/format/#hugo-date-and-time-templating-reference

# path name excluded from documentation menu
menu_exclusion = [
    "archives",
    "archive",
    "blog",
    "entry",
    "post",
    "posts",
]

# Algolia site search section
# See https://www.algolia.com/doc/
algolia_search_enable = true
algolia_indexName = "hugo-demo-techdoc"
algolia_appId = "7W4SAN4PLK"
algolia_apiKey = "cbf12a63ff72d9c5dc0c10c195cf9128" # Search-Only API Key
```

--------------------------------

### Example ccmake configuration

Source: https://soledge3x.onrender.com/getting_started/installation

A sample view of the ccmake interface for editing build options.

```text
CHIP native
CMAKE_BUILD_TYPE Release
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_TOOLCHAIN_FILE /ccc/work/cont003/gen1
COMPILER_REPORTS OFF
ENABLE_UTESTS OFF
HDF5_Fortran_LIBRARY_dl /usr/lib64/libdl.so
HDF5_Fortran_LIBRARY_hdf5 /ccc/products/hdf5-1.12.0/intel--20.0
HDF5_Fortran_LIBRARY_hdf5_fort /ccc/products/hdf5-1.12.0/intel-20.0
HDF5_Fortran_LIBRARY_m /usr/lib64/libm.so
HDF5_Fortran_LIBRARY_pthread /usr/lib64/libpthread.so
HDF5_Fortran_LIBRARY_z /usr/lib64/libz.so
JsonFortran_INCLUDE_DIR JsonFortran_INCLUDE_DIR-NOTFOUND
JsonFortran_LIBRARY JsonFortran_LIBRARY-NOTFOUND
PRECISION double
PRODUCTION_RUN OFF
S3X_USE_AGMG OFF
S3X_USE_MUMPS OFF
S3X_USE_PASTIX OFF
S3X_USE_PETSC ON
USE_EIRENE OFF
USE_GPU NONE
```

--------------------------------

### Load environment modules on IRENE

Source: https://soledge3x.onrender.com/getting_started/installation

Example of loading required libraries and compiler modules on the IRENE supercomputer.

```bash
module purge
module load flavor/buildcompiler/intel
module load flavor/buildmpi/intelmpi
module load mpi/intelmpi
module load feature/system/thp_always
module load flavor/hdf5/parallel
module load hdf5
module load petsc/3.15.0
```

--------------------------------

### Specify manual library paths

Source: https://soledge3x.onrender.com/getting_started/installation

Format for providing paths to manually installed libraries in the configuration.

```text
libs/<libname>/include
libs/<libname>/lib/lib<-->.a
```

--------------------------------

### Google Site Verification meta tag

Source: https://soledge3x.onrender.com/getting_started/configuration

Example of the meta tag used for Google Site Verification.

```html
<meta name="google-site-verification" content="e7-viorjjfiihHIoowh8KLiowhbs" />
```

--------------------------------

### Initialize CMake configuration

Source: https://soledge3x.onrender.com/getting_started/installation

Run CMake from the build directory to configure the project.

```bash
cmake ../soledge3x -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../soledge3x/compilation/cmake_resources/<COMPILER>.toolchain.cmake
```

--------------------------------

### Compile the project

Source: https://soledge3x.onrender.com/getting_started/installation

Build the executable files using CMake.

```bash
cmake --build . --parallel --target all
```

--------------------------------

### Define project directory structure

Source: https://soledge3x.onrender.com/getting_started/installation

Recommended folder structure for organizing source code and build files.

```text
S3XE/
- build # compilation folder
- libs # custom libraries
- soledge3x # S3X source code
- styx # STYX source code
```

--------------------------------

### Checkout latest SOLEDGE3X tag

Source: https://soledge3x.onrender.com/getting_started/installation

Switch the repository to the most recent tagged version.

```bash
cd soledge3x
tag=$(git describe --tags `git rev-list --tags --max-count=1`)
git checkout $tag -b ${tag}_master
cd ..
```

--------------------------------

### Clone STYX source code

Source: https://soledge3x.onrender.com/getting_started/installation

Download the STYX interface for EIRENE simulations.

```bash
git clone git@drf-gitlab.cea.fr:s3xe/styx.git
cd styx
tag=$(git describe --tags `git rev-list --tags --max-count=1`)
git checkout $tag -b ${tag}_master
cd ..
```

--------------------------------

### Clone SOLEDGE3X source code

Source: https://soledge3x.onrender.com/getting_started/installation

Download the SOLEDGE3X repository from GitLab.

```bash
git clone git@drf-gitlab.cea.fr:s3xe/soledge3x.git
```

--------------------------------

### OpenMP COLLAPSE(2) loop over chunks and species

Source: https://soledge3x.onrender.com/features/numerical_scheme

OpenMP collapsed loop over chunks and species (0 to Nspecies) in Soledge3X. The COLLAPSE(2) clause combines the two loops for better parallelization.

```Fortran
!$OMP DO COLLAPSE(2)
do ichunk = 1, Nchunks
   do ispec = 0, Nspecies
      call solveChunk(ichunk,ispec)
   end do
end do
!$OMP END DO

```

--------------------------------

### OpenMP DO loop over chunks

Source: https://soledge3x.onrender.com/features/numerical_scheme

OpenMP parallel loop over chunks in Soledge3X. Each chunk is solved by calling solveChunk(ichunk). The loop is parallelized with OpenMP DO directive.

```Fortran
!$OMP DO
do ichunk = 1, Nchunks
   call solveChunk(ichunk)
end do
!$OMP END DO

```

--------------------------------

### solveChunk subroutine with point loops

Source: https://soledge3x.onrender.com/features/numerical_scheme

Subroutine solveChunk in Soledge3X that loops over points within a chunk for a given species. It uses a pointer to the chunk's species data and triple nested loops over psi, theta, phi indices.

```Fortran
subroutine solveChunk(ichunk,ispec)
	implicit none
	real(kind=dp), dimension(:,:,:), pointer :: A_ptr
	integer*4 :: ipsi, itheta, iphi
!...
! pointing to the chunk+spec data
	A_ptr => chunks(ichunk)%spec(ispec)%A
!...
! loop over points in the chunk
	do ipsi = 1, chunks(ichunk)%Npsi
	   do itheta = 1, chunks(ichunk)%Ntheta
	      do iphi = 1, chunks(ichunk)%Nphi
	      	 A_ptr(iphi,itheta,ipsi) = !...
	      end do
	   end do
   	end do
!...
end subroutine

```
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