deploy: d7cc20c

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 96cb9f1a4be6e31a218d6fc6f4edf1ca
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/examples/index.md.txt

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+# Examples
+
+```{toctree}
+:maxdepth: 1
+
+```
+
+In `TomoATT/examples` directory, you can find small examples of how to use the library.
+
+inversion_small :
+This is the simplest example which runs inversion on a small problem.
+inversion_small_ASCII :
+This example is the same as inversion_small but uses ASCII in/output file format.
+
+Please read the README.md file in each example directory for more information.

_sources/index.md.txt

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+
+#
+
+<br />
+
+```{image} ./_static/TomoATT_logo_2.png
+:alt: Title logo
+:width: 85%
+:align: center
+```
+
+<br />
+<br />
+<br />
+<br />
+<br />
+
+
+TomoATT is a numerical library for adjoint-state travel-time tomography, which is developed for :
+- computing with a very large and fine forward grid,
+- large number of earthquake sources and stations dataset in
+- an efficient and scalable way on modern HPCs.
+
+The implemented logics are on the following published articles: 
+[Ping Tong (2021)](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JB021818), [Jing Chen et. al.(2022)]()
+and [Miles Detrixhe and Frédéric Gibou (2016)](https://doi.org/10.1016/j.jcp.2016.06.023). 
+
+Thanks to the efficiency of an eikonal equation solver, the computation of the travel-time is very fast and requires less amount of computational resources.
+As an input data for TomoATT is travel times at seismic stations, we can easily prepare a great amount of input data for the computation.
+
+<br />
+<br />
+
+```{image} _static/Esfast_flowchart.drawio.png
+:alt: TomoATT flowchart
+:width: 65%
+:align: center
+```
+
+
+
+```{image} _static/vel_anim.gif
+:alt: TomoATT velocity fitting
+:width: 65%
+:align: center
+```
+
+<br />
+<br />
+
+
+For modeling a very large and fine grid with numerous seismic events, this library applies 3-layer parallelization, which are:
+- layer 1: simulutaneous run parallelization (travel times for multiple seismic sources may be calculated simultaneously)
+- layer 2: subdomain decomposition (If the number of computational nodes requires too large memory, we can separate the domain into subdomains and run each subdomain in a separate compute node)
+- layer 3: sweeping parallelization (in each subdomain, sweeping layers are also parallelized)
+
+The details of the parallelization method applied in this library are described in the paper [Miles Detrixhe and Frédéric Gibou (2016)](https://doi.org/10.1016/j.jcp.2016.06.023).
+
+The image below shows the benchmark result of TomoATT (elapse time for a forward simulation) on a single ~ 64 nodes of Fugaku supercomputer (A64FX processor), which shows a high parallel efficiency. 
+
+<br />
+<br />
+
+```{image} ./_static/Fugaku_benchmark.png
+:alt: Fugaku benchmark re   
+:width: 65%
+:align: center
+```
+
+<br />
+<br />
+
+
+Also, an optionzation for serial computation was also implemented in this library. Currently AVX, AVX2, AVX512 for intel processors and SVE for ARM processors are supported.
+CUDA implementation is now under development, which will be available in the future release.
+
+<br />
+<br />
+
+```{image} ./_static/bench_avx_cuda.png
+:alt: bench avx and cuda
+:width: 65%
+:align: center
+```
+<br />
+<br />
+
+
+Regional events (sources within the global domain) and teleseismic events (sources outside the global domain) may be used for inversion.
+
+
+<br />
+<br />
+<br />
+<br />
+
+
+# Citation
+If you use TomoATT for your own research, please cite at least one of the following articles:  
+- [Ping Tong (2021)](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JB021818), 
+- [Jing Chen et. al.(2023)](https://doi.org/10.1093/gji/ggad093), 
+
+
+
+
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+
+install/index
+tutorial/index
+examples/index
+
+```

_sources/install/Use_on_HPCs.md.txt

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+# use on HPCs
+
+This page shows how to compile TomoATT on a few HPCs which we have been using.  
+If you have any experience on compiling TomoATT on other HPCs, your contribution on this page is highly appreciated. So please feel free to contact us.
+
+## Gekko @ NTU
+
+### 1. Load necessary modules and select GNU compilers
+```bash
+module purge && module load cmake gnu/gcc-9.3.0
+```
+
+### 2. compiler openmpi and HDF5 with parallel option
+`./install_mpi_and_hdf5_local.sh`  
+will create openmpi and hdf5 executables in external_libs/local_mpi_hdf5/bin
+
+### 3. Compile TomoATT
+```bash
+# make a build directory
+mkdir build
+
+# compile TomoATT
+cd build
+CC=/usr/local/gcc-9.3.0/bin/gcc CXX=/usr/local/gcc-9.3.0/bin/g++ cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
+
+make -j16
+```
+
+Then the executable TOMOATT is created in the build directory.
+
+
+## Fugaku @ RIKEN
+
+
+### 0. start interactive job on Fugaku (for accessing arch64 environment)
+
+```bash 
+pjsub --interact -g hp<project_id> -L "node=1" -L "rscgrp=int" -L "elapse=1:00:00" --mpi "max-proc-per-node=12" --sparam "wait-time=600" -x PJM_LLIO_GFSCACHE=/vol0004 --no-check-directory     
+```
+
+
+### 1. Load necessary modules 
+```bash
+# prepare spack env
+. /vol0004/apps/oss/spack/share/spack/setup-env.sh
+# load Fujitsu mpi
+spack load /jfzaut5
+# or load gnu 11.2.0
+spack load /nphnrhl /cvur4ou
+```
+
+
+
+### 2. Download hdf5 source code and compile it
+```bash
+
+# every file will be placed in external_libs
+cd ./external_libs
+
+# make a local install pass
+mkdir local_mpi_hdf5
+
+# download hdf5 source
+wget https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/v112/hdf5-1.12.2-1.tar.gz
+
+#Extract the downloaded directory
+tar -xvf hdf5-1.12.2-1.tar.gz && cd hdf5-1.12.2-1
+
+# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
+CC=mpifcc CFLAGS="-Nclang" CXX=mpiFCC CXXFLAGS="-Nclang" ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
+
+# make
+make -j12 && make install
+
+# now hdf5 executables are in external_libs/local_mpi_hdf5/bin
+```
+
+or with gnu 11.2.0
+```bash
+
+# download hdf5 source
+wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/hdf5-1.13.2.tar.gz
+#Extract the downloaded directory
+tar -xvf hdf5-1.13.2.tar.gz
+cd hdf5-1.13.2
+# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
+CC=mpicc CXX=mpic++ ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
+# make
+make -j12 && make install
+
+```
+
+
+### 3. Compile TomoATT
+```bash
+# cd to TomoATT directory
+cd ../..
+
+# make a build directory
+mkdir build
+
+# compile TomoATT
+cd build
+
+CC=mpifcc CXX=mpiFCC cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
+# or for gnu 11.2.0
+cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
+
+make -j12
+```
+
+### 4. terminalte interactive job
+`Ctrl + D`
+
+
+
+
+<!--
+## ASPIRE 1 @ NSCC
+
+### 0. load necessary modules
+```bash
+module purge
+export PATH=/app/gcc/9.5.0/bin:$PATH && export LD_LIBRARY_PATH=/app/gcc/9.5.0/lib:$LD_LIBRARY_PATH
+module load intel/19.0.0.117
+```
+
+### 1. Download hdf5 source code and compile it
+```bash
+
+# download openmpi and hdf5 source code on your LOCAL MACHINE
+wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz
+
+# then upload it to NSCC (for example)
+scp -rC hdf5-1.13.3.tar.gz aspire1:~/(where TomoATT placed)/external_libs/
+
+# on ASPIURE 1
+cd external_libs
+
+mkdir local_mpi_hdf5
+
+# extract tar file and cd to the directory
+tar -xvf hdf5-1.13.3.tar.gz && cd hdf5-1.13.3
+
+# configure the code
+CC=mpiicc  CXX=mpiicpc \
+./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
+
+# make and install to the prefix
+make -j16 && make install
+
+```
+
+### 2. Compile TomoATT
+```bash
+# cd to TomoATT directory
+cd ../..
+
+# make a build directory
+mkdir build
+
+# compile TomoATT
+cd build
+CC=icc CXX=icpc cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
+
+make -j16
+```
+-->