GF3DF

Fortran extraction tool for Specfem and GF3D generated Green function database subset files. The main intent of this repo to include 3D Green functions in the GCMT project's CMT inversion routine.

Quickstart

git clone [email protected]:lsawade/GF3DF.git
cd /path/to/gf3df/
cmake -S . -B build
cmake --build build

Usage in your package

An example of an external program that uses GF3D to extract seismograms from the database is given in ./external_program/test_gf3d.F90. Make sure you have compiled gf3d before jumping to this. To compile the external usage software

cd path/to/GF3DF/external_program
gfortran test_gf3d.F90 -o test-get-sdp -L../build/lib -I../build/include -lgf3d

and to use it simply run

path/to/GF3DF/external_program/test-get-sdp <fortran_subset.h5> <itypsokern>

This extracts seismograms for the same event and corresponding kernel 10 times and computes the average extraction time.

Dependencies

• Fortran compiler -- Tested only gfortran so far; most recently GNU Fortran 13.1.0. Have not tried any other setups.
• CMake -- currently I'm running with Cmake 3.26.4, and I haven't really tested any other cmake setups. The package is not really using any "crazy" CMake functionalities, so I'm not too worried about the whole thing.
• HDF5 -- I have tested with a few different HDF5 packages, but since the function that I'm using are pretty basic reading functions it has been working with all of them (1.10, 1.12, 1.14).

Random tests that worked as well:

• Using a parallel hdf5 implementation

Optimization flags

To get a speed increase of 3x, please use the following environment variable before making.

export FFLAGS="-O3"

executables are larger do to unrolled loops and other global optimizations. I tried using both -O4 and -O5, as well. There is no advantage in -O4 and the aggressive option -O5 is running even slower. Since extraction time for 17 stations is at 0.65 seconds for a 4h seismogram. I will leave it at that for now. I could to some advanced profiling later on.

Usage in your own module

For using the modules in your own package add /path/to/gf3df/build/include to your compilation and in fortran you should be able to just use gf3d. An example use is shown in ./app/gf3d-get-sdp-demo

Shared library

If you want to build a shared library, please use the -fPIC flag

export CFLAGS="-fPIC"
export FFLAGS="-fPIC"

HDF5

Whether you use your own built parallel HDF5 or a cluster non-mpi HDF5, both should work fine! Just make sure that the compilers are the same so that there are no issues. In general, cmake will automatically find the include dirs and libraries related to the HDF5 installation. However, sometimes it's not quite the best at setting the link paths. If that's the case simply set.

export HDF5_ROOT=/path/to/hdf5

If that does not work, see below in the Known Issues section.

Debugging setep

export HDF5_ROOT="/home/lsawade/ph5py-testing/hdf5/build/phdf5"

# For now add some debugging flags
export FFLAGS="-Og -g -Wall -Wextra -pedantic -fimplicit-none -fcheck=all -fba
cktrace"

# Remove build completely and rebuild.
rm -rf build && \
    cmake -S . -B build && \
    cmake --build build && \
    ./build/bin/gf3df-get-sdp-demo single_element.h5 3

---

Notes on code structure

Organization of the code could be better. I'm not quite sure whether the going down the submodule route is the right thing, I did however start changing the library into something that is a set of submodules with interfaces -- if needed -- in the main module. I'll try to rearrange the software a little more.

Known Issues

• CMake does sometimes not find HDF5 correctly. I had a lot of trouble getting it right on my Mac. And eventually, I created a fix in the CMake file. Should you have trouble. Instead of updating the ./CMakeLists.txt, I would start with setting all the HDF5 paths like so

  export HDF5_ROOT=<path/to/hdf5>
  export HDF5_LIBRARIES="${HDF5_ROOT}/lib"
  export HDF5_INCLUDE_DIRS="${HDF5_ROOT}/include"
  export PATH="${HDF5_ROOT}/bin:${PATH}"

  Then try to compiles it again. If that should also fail, you could manually link HDF5 using the HDF5 fortran compiler wrapper as a reference:

  export FFLAGS=${FFLAGS} $(echo "${FFLAGS}" $(h5fc -show | cut -w -f '2-60'))

  If you end up doing this, make sure to remove all lines with find_package(HDF5 ...)

• Only really tested with gfortran. There maybe portability issues with INQUIRE routine.