pyasdf and Dependencies¶
pyasdf supports Python version 2.7, 3.4, 3.6, and 3.7 and it depends on the
following Python modules:
dill, and optionally
mpi4py. You can
pyasdf with or without parallel I/O support; the later requires
mpi4py and parallel versions of
pyasdf itself is available on pypi and also as a conda package in the
conda-forge channel (non-parallel only).
If you know what you are doing, install it any way you see fit. Otherwise do yourself a favor and download the Anaconda Python distribution for your chosen Python version.
When to choose the parallel I/O version?
Please note that in most cases it is not worth it to install the parallel I/O version. For one most machines (aside from actual HPC machines) don’t even have the necessary hardware to do actually parallel I/O. Also seismological waveform data is usually not that big in volume so a single reading/writing thread might be sufficient. Furthermore modern SSDs can write at very high speeds.
But if your application does indeed benefit from parallel I/O follow the instructions below.
This is very easy - just execute this one line and it will install all the
pyasdf (assuming you installed the
Anaconda Python distribution
as recommended above).
$ conda install -c conda-forge pyasdf
pyasdf with parallel I/O¶
You only have to make sure to have a parallel version of
h5py installed. A
simple way is to just use one on conda, e.g.:
$ conda install -c spectraldns h5py-parallel
Additionally you need
mpi4py. The one on
conda might work, if not,
For all of the following steps make sure that the MPI package of your local
supercomputer/cluster is loaded. The
mpi4py potentially shipping with
Anaconda might not work on your cluster - if that is the case uninstall it
and reinstall with
pip at which point it should link against your
cluster’s MPI implementation.
$ conda uninstall mpi4py $ pip install mpi4py
After everything is installed, you can run the following command to print information about the current system.
$ python -c "import pyasdf; pyasdf.print_sys_info()"
which will print something along the following lines:
pyasdf version 0.1.4 =============================================================================== CPython 2.7.9, compiler: GCC 4.2.1 (Apple Inc. build 5577) Darwin 14.3.0 64bit Machine: x86_64, Processor: i386 with 8 cores =============================================================================== HDF5 version 1.8.17, h5py version: 2.5.0 MPI: Open MPI, version: 1.10.1, mpi4py version: 2.0.0 Parallel I/O support: True Problematic multiprocessing: False =============================================================================== Other_modules: dill: 0.2.5 lxml: 3.7.2 numpy: 1.11.3 obspy: 1.0.3 prov: 1.4.0 scipy: 0.18.1
To assert that your installation is working properly, execute
$ python -m pyasdf.tests
and make sure all tests pass. Otherwise please contact the developers.
Building the Documentation¶
The documentation requires
sphinx and the Bootstrap theme. Install both
$ pip install sphinx sphinx-bootstrap-theme
Build the doc with
$ cd doc $ make html
Finally open the
doc/_build/html/index.html file with the browser of your