icui / asdf-library

Adaptable Seismic Data Format

Landing page for all things ASDF: https://seismic-data.org

This is Adaptable Seismic Data Format - if you are looking for the Advanced Scientific Data Format, go here: https://asdf.readthedocs.io/en/latest/

Instruction to install the hdf5 parallel library on mac.

Remove everything hdf5 and mpi related from conda

$ conda uninstall hdf5 h5py mpi4py

Install mpi and parallel hdf5 somehow - on mac i strongly recommend homebrew.

$ brew install open-mpi
$ brew tap homebrew/science
$ brew install hdf5 --with-mpi

Then - with the pip in the conda (environement) Will make sure mpi4py is linked against your systems MPI

$ pip install mpi4py

Download h5py and unpack it and make sure the conda env is active

$ python setup.py configure --mpi
$ python setup.py build
$ python setup.py install

This will then install a parallel h5py version.

Usage

The following instructions are for in-source builds.

$ cmake .
$ make

Finding the correct MPI / HDF5 libraries does not seem to be working all the same on different systems.

If the compilation complains about a missing use mpi, try the following:

$ cmake . -DCMAKE_Fortran_COMPILER=mpif90
$ make

If the compilation still complains about missing hdf5 libraries, try:

$ cmake . -DCMAKE_Fortran_COMPILER=h5pfc
$ make

If you want to get cmake to find your local boost directory, try:

$ cmake -DBoost_NO_BOOST_CMAKE=TRUE \
    -DBoost_NO_SYSTEM_PATHS=TRUE \
    -DBOOST_ROOT:PATHNAME=$TARGET \
    -DBoost_LIBRARY_DIRS:FILEPATH=${TARGET}/lib

It should create a library in lib/ examples programs are in test/ and generated there.

If documentation needs to be generated:

cmake -DBUILD_DOCUMENTATION=ON

You should have doxygen installed. Documentation will be generated in doc/.

For out-of source builds, start with:

$ mkdir build/
$ cd build/

and follow the previous instructions, replacing . with ..

Once build, you may run test with:

$ make test

To install in a nonstandard location (e.g., a user directory without root privileges), you can either set CMAKE_INSTALL_PREFIX during configuration or DESTDIR during install, e.g.,

$ cmake -DCMAKE_INSTALL_PREFIX=/path/to/toplevel/install/directory <options> .
$ make
$ make install

or

$ cmake <options> .
$ make
$ make DESTDIR=/path/to/toplevel/install/directory install

Note that the files end up in $DESTDIR/$CMAKE_INSTALL_PREFIX/*, so it is only necessary to set one of these.

Titan compilation

modules

cmake/2.8.10 (or higher)
PrgEnv-gnu/5.2.40
cray-hdf5-parallel
boost/1.57.0 (or higher)

configuration

cd asdf-library
Uncomment line 27 in CMakeLists.txt (Delete the # symbol)
mkdir build
cd build
cmake .. -DCMAKE_Fortran_COMPILER=ftn -DBoost_NO_SYSTEM_PATHS=TRUE

compilation

make
make doc
make install DESTDIR=</path/to/toplevel/install/directory>