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asdf-library
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Adaptable Seismic Data Format
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asdf-library
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[](https://travis-ci.org/SeismicData/asdf-library) Landing page for all things **ASDF**: https://seismic-data.org > This is **A**daptable **S**eismic **D**ata **F**ormat - if you are looking for the **A**dvanced **S**cientific **D**ata **F**ormat, 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. ```bash $ 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: ```bash $ cmake . -DCMAKE_Fortran_COMPILER=mpif90 $ make ``` If the compilation still complains about missing hdf5 libraries, try: ```bash $ cmake . -DCMAKE_Fortran_COMPILER=h5pfc $ make ``` If you want to get cmake to find your local boost directory, try: ```bash $ 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: ```bash $ mkdir build/ $ cd build/ ``` and follow the previous instructions, replacing ``.`` with ``..`` Once build, you may run test with: ```bash $ 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., ```bash $ cmake -DCMAKE_INSTALL_PREFIX=/path/to/toplevel/install/directory <options> . $ make $ make install ``` or ```bash $ 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> ```
