### Install GeoCubit using setup.py

Source: https://github.com/specfem/specfem3d/blob/master/CUBIT_GEOCUBIT/README.md

Install GeoCubit by running the setup script. Alternatively, you can add the GeoCubit directory to your PYTHONPATH and PATH.

```bash
python setup.py install
```

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

### Navigate to Example Directory

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Change the working directory to the Gmsh_simple_box_hex27 example folder and list its contents.

```python
%cd /content/specfem3d
%cd EXAMPLES/applications/Gmsh_simple_box_hex27
! ls -al
! ls -al ./bin
```

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

### Install and Run SPECFEM3D

Source: https://github.com/specfem/specfem3d/blob/master/README.md

Commands to configure, compile, and run a default example of SPECFEM3D. Ensure you have Fortran and C compilers available.

```bash
./configure FC=gfortran CC=gcc
make all
./run_this_example.sh
```

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

### Build and Install Git from Source

Source: https://github.com/specfem/specfem3d/wiki/Using-Git-for-SPECFEM

Commands to download, compile, and install a recent version of Git.

```bash
$ cd $HOME
$ mkdir bin/git src
$ cd src
$ git clone git://git.kernel.org/pub/scm/git/git.git
$ sudo apt-get remove git-core
$ cd git
$ make prefix=/usr/local all
$ sudo make install prefix=/usr/local
```

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

### Run SPECFEM3D Noise Tomography Example

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/09_noise_simulations

Execute the pre-processing script for the noise tomography example. This script is designed for a specific workstation setup but outlines a universal procedure.

```bash
./pre-processing.sh
```

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

### Configure and Run Example

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Modify the Par_file to set the simulation steps and disable GPU mode, then execute the example script.

```python
! sed -i "s:^NSTEP .*:NSTEP = 500:" DATA/Par_file
! sed -i "s:^GPU_MODE .*:GPU_MODE = .false.:" DATA/Par_file
! ./run_this_example.sh
```

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

### Configure Command Example

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/C_troubleshooting

Example of specifying Fortran compiler and MPI wrapper during configuration to resolve compiler mixing issues. Ensure these paths are correct for your system.

```bash
> ./configure FC=gfortran MPIF90=/usr/local/openmpi-gfortran/bin/mpif90
```

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

### Navigate to Example Directory

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Change the current working directory to the specific Gmsh example folder within the SPECFEM3D project.

```python
%cd /content/specfem3d
%cd EXAMPLES/applications/Gmsh_simple_box_hex27
! ls -al
```

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

### Install Matlab GUI

Source: https://github.com/specfem/specfem3d/blob/master/external_libs/README_how_to_use_hybrid_specfem_axisem.txt

Run the installation script within the Matlab environment.

```matlab
INSTALL_MATLAB_GUI_FOR_SPECFEM
```

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

### Install Doxygen and Graphviz

Source: https://github.com/specfem/specfem3d/blob/master/doc/call_trees_of_the_source_code/README.txt

Commands to install the required documentation generation tools on Linux systems.

```bash
sudo apt-get install doxygen
```

```bash
sudo apt-get install graphviz
```

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

### Configure and Run Simulation

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Update the Par_file to set NSTEP to 2000 and enable GPU_MODE, then execute the example script.

```python
! sed -i "s:^NSTEP .*:NSTEP = 2000:" DATA/Par_file
! sed -i "s:^GPU_MODE .*:GPU_MODE = .true.:" DATA/Par_file
! ./run_this_example.sh
```

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

### Push Local Changes to Examples Directory

Source: https://github.com/specfem/specfem3d/wiki/Advanced-Git-Topics

This alias is specifically for pushing committed local changes to the 'examples' directory on GitHub.

```bash
alias gitpushexamples "git push origin master"
```

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

### Install Git Dependencies

Source: https://github.com/specfem/specfem3d/wiki/Using-Git-for-SPECFEM

Install necessary development libraries for building Git from source on various Linux distributions.

```bash
sudo yum install curl-devel expat-devel gettext-devel openssl-devel zlib-devel
```

```bash
sudo apt-get install libcurl4-gnutls-dev libexpat1-dev gettext libz-dev libssl-dev ssh expat zlib1g zlib1g-dev tk python
```

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

### Basic Meshing Script with Cubit

Source: https://github.com/specfem/specfem3d/blob/master/CUBIT_GEOCUBIT/README.md

A simple 'hello world' example demonstrating how to initialize Cubit and create a basic mesh. This script uses the `cubit` library to execute commands.

```python
import cubit
cubit.init([""])
cubit.cmd('brick x 10')
cubit.cmd('mesh vol all')
```

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

### Locate build tools

Source: https://github.com/specfem/specfem3d/blob/master/external_libs/scotch_5.1.12b/INSTALL.txt

Use the which command to find the installation path of make, lex, and yacc.

```bash
which make
```

```bash
which lex
which yacc
```

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

### Configure SPECFEM3D for Eiger

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/readme_cuda_cscs.txt

Example ./configure commands for the Eiger cluster.

```bash
./configure --with-cuda FC=mpif90 MPIFC=mpif90 CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include
```

```bash
./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="-O3 -ffree-line-length-none -fopenmp" FLAGS_NO_CHECK="-Ofast -mfpmath=sse -funroll-loops -ffree-line-length-none -fopenmp" CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include
```

```bash
./configure --with-cuda FC=mpif90 MPIFC=mpif90 FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L/apps/eiger/Cuda-4.0/cuda/lib64 MPI_INC=-I/apps/eiger/mvapich2/1.5.1p1/mvapich2-gnu/include
```

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

### Configure SPECFEM3D with CUDA

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/Cray_compiler_information/Daniel_Peter_here_is_how_to_configure_SPECFEM3D_on_Piz_Daint_jan2017.txt

Example configuration command for building with CUDA support on a Cray system.

```bash
MPI_INC="${CRAY_MPICH2_DIR}/include"

./configure \
--with-cuda=cuda5 CUDA_INC="$CUDA_INC" CUDA_LIB="$CUDA_LIB" MPI_INC="$MPI_INC" \
MPIFC=$mpif90 MPICC=$mpicc FC=$f90 CC=$cc CXX=$cc FLAGS_CHECK="$flags" CFLAGS="$cflags"
```

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

### Configure with ADIOS Support

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/02_getting_started

Enable ADIOS library support for parallel I/O during configuration. Ensure ADIOS is installed and its environment variables are set.

```bash
./configure --with-adios ..

```

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

### Example Solver Timestamp File Content

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/05_running_the_solver

Monitor simulation progress and performance using timestamp files. These files provide information on the current time step, elapsed time, and maximum displacement.

```plaintext
Time step #          10000
Time:     108.4890      seconds
Elapsed time in seconds =    1153.28696703911
Elapsed time in hh:mm:ss =     0 h 19 m 13 s
Mean elapsed time per time step in seconds =     0.115328696703911
Max norm displacement vector U in all slices (m) =     1.0789589E-02
```

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

### Locate Compilers

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Verify the installation paths for GCC, GFortran, and NVCC.

```python
! which gcc
! which gfortran
! which nvcc
```

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

### Check GNU Make version

Source: https://github.com/specfem/specfem3d/blob/master/external_libs/scotch_5.1.12b/INSTALL.txt

Verify that GNU Make is installed and accessible in the system path.

```bash
make --version
```

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

### Setup Tracking Branch

Source: https://github.com/specfem/specfem3d/wiki/Advanced-Git-Topics

Creates a local tracking branch for the remote devel branch.

```bash
$ git checkout --track origin/devel
```

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

### Configure SPECFEM3D for Cray

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/Cray_compiler_information/here_are_more_details_on_how_to_successfully_configure_the_code_on_CRAY_machines.txt

Example configuration script using specific compiler flags and paths for Cray systems.

```bash
mpif90=ftn
mpicc=cc
f90=ftn
cc=cc

# run flags
#flags="-eF -em -rm"
#cflags="-h list=m"

## memory > 2GB
#flags="-eF -em -rm -O3,fp3 -hpic -dynamic"
#cflags="-h list=m -hpic -dynamic"

# debug flags
flags="-g -Rb -eF -rm -eC -eD" # -hfp2"
cflags="-g -h list=m"

###
### CUDA
###
CUDA_INC="${CRAY_CUDATOOLKIT_DIR}/include"
CUDA_LIB="${CRAY_CUDATOOLKIT_DIR}/lib64"

###
### mpi.h / mpif.h
###
MPI_INC="${CRAY_MPICH2_DIR}/include"

./configure \
--with-cuda=cuda5 CUDA_INC="$CUDA_INC" CUDA_LIB="$CUDA_LIB" MPI_INC="$MPI_INC" \
MPIFC=$mpif90 MPICC=$mpicc FC=$f90 CC=$cc CXX=$cc FLAGS_CHECK="$flags" CFLAGS="$cflags"
```

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

### Get Initial Copy of the Code

Source: https://github.com/specfem/specfem3d/wiki/Advanced-Git-Topics

Run this command once to obtain the initial copy of the SPECFEM3D codebase after creating a fork on your GitHub page.

```bash
getinitialcopyofthecode
```

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

### MPI Initialization and Barrier Check

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/C_troubleshooting

A basic Fortran program to verify a working MPI installation. Ensure you can compile and run this to confirm MPI is set up correctly before configuring SPECFEM3D.

```Fortran
program main
include 'mpif.h'
integer, parameter :: CUSTOM_MPI_TYPE = MPI_REAL
integer ier
call MPI_INIT(ier)
call MPI_BARRIER(MPI_COMM_WORLD,ier)
call MPI_FINALIZE(ier)
end
```

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

### Install Trelis for Python 2.6 on MacOSX

Source: https://github.com/specfem/specfem3d/blob/master/CUBIT_GEOCUBIT/README.md

Install Trelis using `setup.py` for a specific Python version (2.6) and installation path on MacOSX. This is relevant for older Trelis versions.

```bash
python2.6 setup.py install --install-lib=/Library/Python/2.6/site-packages/
```

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

### Install GeoCubit for Python 2.5 on MacOSX

Source: https://github.com/specfem/specfem3d/blob/master/CUBIT_GEOCUBIT/README.md

Install GeoCubit using `setup.py` for a specific Python version (2.5) and installation path on MacOSX. This is relevant for older Trelis versions.

```bash
python2.5 setup.py install --install-lib=/Library/Python/2.5/site-packages/
```

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

### Copy Input Files for Figure 4 Example

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/reproducible_study/seismoacoustic_bishop2022/README.md

Copy the input data files for the Figure 4 example (planar halfspace) into the SPECFEM3D/DATA/ directory. Replace DATA_FIG4 with DATA_FIG8 to use the topography example.

```bash
cp -r EXAMPLES/reproducible_study/seismoacoustic_bishop2022/DATA_FIG4/ DATA
```

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

### Load Environment and Configure

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/Cray_compiler_information/Daniel_Peter_here_is_how_to_configure_SPECFEM3D_on_Piz_Daint_jan2017.txt

Standard module loading and configuration command for Piz Daint.

```bash
module load daint-gpu

./configure FC=ftn MPIFC=ftn CC=cc CXX=CC
```

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

### Launch Matlab GUI

Source: https://github.com/specfem/specfem3d/blob/master/external_libs/README_how_to_use_hybrid_specfem_axisem.txt

Initialize the hybrid GUI tools in Matlab.

```matlab
Hybrid_Axisem_Specfem
```

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

### Install VTK in Blender Python

Source: https://github.com/specfem/specfem3d/blob/master/utils/Visualization/Blender/python_blender/README.md

Install the required VTK package directly into the Python environment bundled with Blender.

```bash
/Applications/Blender.app/Contents/Resources/3.6/python/bin/python3.10 -m ensurepip
/Applications/Blender.app/Contents/Resources/3.6/python/bin/python3.10 -m pip install vtk==9.2.6
```

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

### CMake Project Configuration for sep_topo

Source: https://github.com/specfem/specfem3d/blob/master/utils/small_utilities/bathy_sep_to_ascii/CMakeLists.txt

Initializes the project, checks for C compiler flags, and sets up build directories and source files.

```cmake
cmake_minimum_required (VERSION 2.6)

### Project Configuration
project(sep_topo)

include(CheckCCompilerFlag)
check_c_compiler_flag(-std=gnu99 HAS_STD_GNU99)

if(HAS_STD_GNU99)
  add_definitions(-std=gnu99)
endif()
file(MAKE_DIRECTORY ./bin)
set(EXECUTABLE_OUTPUT_PATH bin/${CMAKE_BUILD_TYPE})

include_directories(
  ./inc
)

set(sources
    src/sep_header.c
    src/convert_topo.c
    src/parse_sep.c)

add_executable(
  create_ascii_bathy_from_sep_vs
  src/create_ascii_bathy_from_sep_vs.c
  ${sources}
)
```

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

### Example Seismogram Filenames

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/B_channel_codes

Examples of generated seismogram filenames based on different sampling rates defined in the parameter file.

```text
AZ.ASBS.MXZ.semd.sac
```

```text
AZ.ASBS.BXZ.semd.sac
```

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

### Configure SCOTCH with Custom Directory

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/02_getting_started

Use this command to configure the build process when SCOTCH libraries are installed in a non-standard location. Specify the path to your SCOTCH installation using the --with-scotch-dir option.

```bash
./configure FC=ifort MPIFC=mpif90 --with-scotch-dir=/opt/scotch
```

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

### Navigate and List Repository

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Change the working directory to the cloned repository and list its contents.

```python
%cd /content/specfem3d
! ls -al
```

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

### Run Adjoint Simulation

Source: https://context7.com/specfem/specfem3d/llms.txt

Steps for performing adjoint simulations, including forward simulation, adjoint source preparation, and adjoint solver execution.

```bash
# Step 1: Run forward simulation and record seismograms
# Set in DATA/Par_file:
SIMULATION_TYPE                 = 1
SAVE_FORWARD                    = .false.

mpirun -np 4 ./bin/xspecfem3D

# Step 2: Prepare adjoint sources from recorded seismograms
# Create SEM/ directory with adjoint source files
mkdir SEM
# Format: NETWORK.STATION.COMPONENT.adj (same format as seismograms)
# Time-reversal is done internally - provide forward-time adjoint sources

# Step 3: Create STATIONS_ADJOINT file
cp DATA/STATIONS DATA/STATIONS_ADJOINT

# Step 4: Run adjoint simulation
# Modify DATA/Par_file:
SIMULATION_TYPE                 = 2
SAVE_FORWARD                    = .false.
```

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

### Mesh Skewness Histogram Example

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/C_troubleshooting

This output shows a histogram of element skewness values, indicating mesh quality. Lower skewness values (closer to 0) represent better quality elements. This example highlights that 81.8% of elements are well-formed.

```text
... histogram of skewness (0. good - 1. bad):
 0.0000000E+00 - 5.0000001E-02 27648 81.81818 %
 5.0000001E-02 - 0.1000000 0 0.0000000E+00 %
...
```

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

### Locate MPI Tools

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Verify the installation paths for MPI wrappers.

```python
! which mpif90
! which mpirun
```

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

### Check Compiler Versions

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Display version information for the installed compilers.

```python
! gcc --version
! gfortran --version
! nvcc --version
```

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

### Configure with GPU Support (CUDA/HIP)

Source: https://context7.com/specfem/specfem3d/llms.txt

Enable GPU acceleration during configuration. Specify the CUDA or HIP version and target architecture. Compile with 'make all' after configuration.

```bash
# Configure with CUDA support for specific GPU architectures
# cuda5 = Kepler (K20), cuda6 = Kepler (K80), cuda8 = Pascal (P100)
# cuda9 = Volta (V100), cuda10 = Turing (RTX 2080), cuda11 = Ampere (A100)
./configure --with-cuda=cuda11 FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi

# Configure with HIP support for AMD GPUs
# MI8, MI25, MI50, MI100, MI250 specify target architectures
./configure --with-hip=MI250 FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi \
    HIP_FLAGS="-fPIC -ftemplate-depth-2048 -fno-gpu-rdc -std=c++17 -O2"

# Compile with GPU support
make all
```

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

### Module definition formatting

Source: https://github.com/specfem/specfem3d/wiki/Best-Practices

Module definitions should start at the beginning of the line.

```fortran
module my_par
  integer :: count
end module
```

```fortran
  module my_par
  integer :: count
  end module
```

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

### Step 1: Generate Wavefields

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/09_noise_simulations

Configure simulation for generating initial wavefields. Set SIMULATION_TYPE to 1 and NOISE_TOMOGRAPHY to 1.

```bash
SIMULATION_TYPE = 1
NOISE_TOMOGRAPHY = 1
SAVE_FORWARD (not used, can be either .true. or .false.)
```

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

### Configure SPECFEM3D for Todi

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/readme_cuda_cscs.txt

Build configuration commands for different compiler environments on Todi.

```bash
# Cray configure
./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include
# GNU configure
./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $GNU_CHECK`" FLAGS_NO_CHECK='`echo $GNU_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include
# Intel convifugre
./configure --with-cuda CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $ICC_CHECK`" FLAGS_NO_CHECK='`echo $ICC_FCFLAGS`' CUDA_LIB=-L$CUDA_HOME/lib64 MPI_INC=-I$MPICH_DIR/include

./configure CC=cc FC=ftn MPIFC=ftn MPICC=cc FLAGS_CHECK="`echo $CRAY_CHECK`" FLAGS_NO_CHECK='`echo $CRAY_FCFLAGS`' MPI_INC=-I$MPICH_DIR/include
```

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

### Subroutine indentation

Source: https://github.com/specfem/specfem3d/wiki/Best-Practices

Start subroutines with an indent, except for module definitions.

```fortran
  subroutine scotch_partitioning()
  implicit none
  ..
```

```fortran
subroutine scotch_partitioning
  implicit none
  ..
```

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

### Check MPI Versions

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Display version information for the installed MPI tools.

```python
! mpif90 --version
! mpirun --version
```

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

### Configure Makefile.inc

Source: https://github.com/specfem/specfem3d/blob/master/external_libs/scotch_5.1.12b/INSTALL.txt

Create the required Makefile.inc file in the src directory using either a symbolic link or a direct copy.

```bash
ln -s Make.inc/Makefile.inc.xxxx_xxx_xxx Makefile.inc
```

```bash
cp Make.inc/Makefile.inc.xxxx_xxx_xxx Makefile.inc
```

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

### Run xcreate_movie_shakemap_AVS_DX_GMT

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/11_graphics

Execute the compiled utility to generate visualization files from SPECFEM3D's binary movie and shakemap output. The program will prompt for necessary input parameters.

```bash
xcreate_movie_shakemap_AVS_DX_GMT
```

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

### Compile and Execute SPECFEM3D Demo Codes

Source: https://github.com/specfem/specfem3d/blob/master/utils/small_SEM_solvers_in_Fortran_and_C_without_MPI_to_learn/README_HOWTO_use_these_demo_codes.txt

Commands to navigate directories, configure build settings, and execute the mesher and solver binaries.

```shell
1/ cd mesher_for_serial

2/ edit the Makefile if needed to change the compiler or compiler options

3/ make clean ; make all

4/ ./xmeshfem3D

5/ cd ..

6/ edit make_all_Fortran.csh and make_all_C.csh if needed to change the compiler or compiler options

7/ ./make_all_Fortran.csh

8/ ./make_all_C.csh

9/ ./xspecfem3D_F90_normal

10/ ./xspecfem3D_F90_faster

11/ ./xspecfem3D_C
```

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

### Enable Screen Output for Solver Messages

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/05_running_the_solver

Uncomment the IMAIN parameter in setup/constants.h to redirect solver messages from files to the standard output (screen).

```fortran
! uncomment this to write messages to the screen
! integer, parameter :: IMAIN = ISTANDARD_OUTPUT
```

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

### Run xdecompose_mesh

Source: https://github.com/specfem/specfem3d/wiki/USER_MANUAL/03_mesh_generation

Synopsis for executing the mesh partitioner, which requires the number of partitions and input/output directories.

```bash
./bin/xdecompose_mesh nparts input_directory output_directory
```

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

### Define ADIOS integer scalar subroutine

Source: https://github.com/specfem/specfem3d/wiki/Best-Practices

Example signature for defining an ADIOS integer scalar.

```fortran
subroutine define_adios_integer_scalar(adios_group, group_size_inc, path, name, var)
  ..
```

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

### Clone and Configure Repository

Source: https://github.com/specfem/specfem3d/wiki/Using-Git-for-SPECFEM

Commands to clone a repository, switch to the development branch, and apply the configuration script.

```bash
$ git clone SPECFEM/specfem3d
```

```bash
$ cd specfem3d
$ git checkout -b devel origin/devel
```

```bash
$ config_repo your_github_name
```

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

### SPECFEM3D configuration output

Source: https://github.com/specfem/specfem3d/blob/master/EXAMPLES/notebooks/specfem3d-colab-example.ipynb

Sample output generated by the configure script during the environment setup process.

```text
## ---------------------------- ##
## setting up compilation flags ##
## ---------------------------- ##
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gfortran... gfortran
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU Fortran... yes
checking whether gfortran accepts -g... yes
configure: running /bin/bash ./flags.guess
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/local/cuda/lib64/stubs -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag needed to accept free-form source... none
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking for Fortran flag to compile preprocessed .F90 files... none
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
## ------ ##
## SCOTCH ##
## ------ ##
```

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

### Check Git Version

Source: https://github.com/specfem/specfem3d/wiki/Using-Git-for-SPECFEM

Verify the installed version of Git to ensure it meets the minimum requirement of 1.8.

```bash
$ git --version
```

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

### Configure with ADIOS/HDF5 for Large-Scale I/O

Source: https://context7.com/specfem/specfem3d/llms.txt

Enable parallel I/O libraries like ADIOS or HDF5 for large simulations. Configure with the appropriate flags and paths. SCOTCH can be used for mesh partitioning.

```bash
# Configure with ADIOS support
./configure --with-adios FC=ifort CC=icc MPIFC=mpif90 --with-mpi

# Configure with HDF5 support
./configure --with-hdf5 HDF5_INC="/opt/homebrew/include" \
    HDF5_LIBS="-L/opt/homebrew/lib" FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi

# With SCOTCH mesh partitioning library
./configure FC=ifort MPIFC=mpif90 CC=icc --with-scotch-dir=/opt/scotch
```

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

### Render Visualization with Blender

Source: https://github.com/specfem/specfem3d/blob/master/utils/Visualization/Blender/python_blender/README.md

Execute the rendering script with the specified VTK input file.

```bash
./plot_with_blender.py --vtk_file=OUTPUT_FILES/AVS_shaking_map.inp
```

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

### Linker Error Log

Source: https://github.com/specfem/specfem3d/blob/master/utils/infos/Cray_compiler_information/here_are_more_details_on_how_to_successfully_configure_the_code_on_CRAY_machines.txt

Example of a configuration log showing multiple definition errors during the linking phase on a Cray system.

```text
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o):(.bss+0x13): multiple definition of `FLAG__namespace_do_not_use_directly_use_DECLARE_bool_instead::FLAGS_tcmalloc_abort_on_large_alloc'
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o):(.bss+0x13): first defined here
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o): In function `TCMallocImplementation::GetAllocatedSize(void*)':
tcmalloc.cc:(.text+0x1f0): multiple definition of `TCMallocImplementation::GetAllocatedSize(void*)'
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o):tcmalloc.cc:(.text+0x1f0): first defined here
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o): In function `TCMallocImplementation::MarkThreadBusy()':
tcmalloc.cc:(.text+0xb00): multiple definition of `TCMallocImplementation::MarkThreadBusy()'
/opt/cray/pe/cce/8.5.5/craylibs/x86-64/pkgconfig/..//libtcmalloc_minimal.a(tcmalloc.o):tcmalloc.cc:(.text+0xb00): first defined here
```

```text
configure:4111: checking for dummy main to link with Fortran libraries
configure:4145: cc -o conftest -g -O2   conftest.c -L/opt/cray/cce/8.4.1/CC/x8
6-64/lib/x86-64 -L/opt/gcc/4.8.1/snos/lib64 /opt/cray/cce/8.4.1/craylibs/x86-64/
libmodules.a /opt/cray/cce/8.4.1/craylibs/x86-64/libomp.a /opt/cray/cce/8.4.1/cr
aylibs/x86-64/libopenacc.a -L/opt/cray/dmapp/default/lib64 -L/opt/cray/mpt/7.2.6
/gni/mpich-cray/8.3/lib -L/opt/cray/libsci/13.2.0/CRAY/8.3/x86_64/lib -L/opt/cra
y/rca/1.0.0-2.0502.57212.2.56.ari/lib64 -L/opt/cray/alps/5.2.3-2.0502.9295.14.14
.ari/lib64 -L/opt/cray/xpmem/0.1-2.0502.57015.1.15.ari/lib64 -L/opt/cray/dmapp/7
.0.1-1.0502.10246.8.47.ari/lib64 -L/opt/cray/pmi/5.0.7-1.0000.10678.155.25.ari/l
ib64 -L/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/lib64 -L/opt/cray/udreg/2.3.2-1.0
502.9889.2.20.ari/lib64 -L/opt/cray/atp/1.8.3/libApp -L/opt/cray/cce/8.4.1/crayl
ibs/x86-64 -L/opt/cray/wlm_detect/1.0-1.0502.57063.1.1.ari/lib64 -lAtpSigHandler
 -lAtpSigHCommData -lpthread -lmpichf90_cray -lrt -lugni -lpmi -lsci_cray_mpi_mp
 -lm -lf -lsci_cray_mp -lmpich_cray -lcraymp -lpgas-dmapp -lfi -lu -ldmapp -ludr
eg -lcray-c++-rts -lcraystdc++ -lxpmem -lalpslli -lwlm_detect -lalpsutil -lrca -
lquadmath -lomp -lmodules -lcraymath -lgfortran -lcsup -latomic -ltcmalloc_minim
al -lstdc++ -L/opt/gcc/4.8.1/snos/lib/gcc/x86_64-suse-linux/4.8.1 -L/opt/cray/cc
e/8.4.1/cray-binutils/x86_64-unknown-linux-gnu/lib -L//usr/lib64 >&5
/opt/cray/cce/8.4.1/craylibs/x86-64/libtcmalloc_minimal.a(tcmalloc.o):(.bss+0x13
): multiple definition of `FLAG__namespace_do_not_use_directly_use_DECLARE_bool_
instead::FLAGS_tcmalloc_abort_on_large_alloc'
/opt/cray/cce/8.4.1/craylibs/x86-64/libtcmalloc_minimal.a(tcmalloc.o):(.bss+0x13
): first defined here
/opt/cray/cce/8.4.1/craylibs/x86-64/libtcmalloc_minimal.a(tcmalloc.o): In functi
on `TCMallocImplementation::GetAllocatedSize(void*)':
tcmalloc.cc:(.text+0x1f0): multiple definition of `TCMallocImplementation::GetAl
locatedSize(void*)'
/opt/cray/cce/8.4.1/craylibs/x86-64/libtcmalloc_minimal.a(tcmalloc.o):tcmalloc.c
c:(.text+0x1f0): first defined here
/opt/cray/cce/8.4.1/craylibs/x86-64/libtcmalloc_minimal.a(tcmalloc.o): In functi
on `TCMallocImplementation::MarkThreadBusy()':
```

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

### Visualize Documentation

Source: https://github.com/specfem/specfem3d/blob/master/doc/call_trees_of_the_source_code/README.txt

Command to open the generated documentation in a web browser.

```bash
firefox html/index.html
```