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Python Module for Adios

Project Description
ADIOS Python/Numpy wrapper

This directory contains the codes for the ADIOS Python/Numpy wrapper
to call the native ADIOS library. This module is built by Cython.

This module requires ADIOS built with the GNU C compiler with
relocatable codes. Add -fPIC flag to CFLAGS before configuring ADIOS.

== Quick install with pip ==

ADIOS Python wrapper can be installed with pip. Check if pip is
installed already. Otherwise, install pip first:

$ wget
$ sudo python
$ python --user
to install in a local directory, $HOME/.local

Before installing ADIOS Python wrappers, make sure Numpy and MPI4Py
installed. Otherwise, install them as follows:

$ pip install numpy
$ pip install mpi4py

Then, install Adios and Adios-MPI wrapper as follows:

$ pip install adios
$ pip install adios_mpi

If you want to install in a custom directory, use the following:
$ pip install --install-option="--prefix=$PREFIX" adios
$ pip install --install-option="--prefix=$PREFIX" adios_mpi

== Build and install with make ==

A Makefile is included for building. The following commands will
display instructions on how to build and install python wrappers for

$ make
$ make install

Have 'adios_config' and 'python' in the path and run

$ make python

If you need a MPI-enabled ADIOS wrapper, which requires MPI4Py, type
the following:

$ make MPI=y python

After successful building, you can install in a python path. There are
three options

$ python install

which will install python's default installation location. This may
require an admin privilege.

You may want to use a custom directory to install. Type

$ python install --prefix=/dir/to/install

and append the directory to the PYTHONPATH environment variable

You can also install in your local directory, run

$ python install --user

== Test cases and examples ==

Test cases and example files are located in tests and example

== Compile with Cython (only for developers) ==

The C++ code (adios.cpp and adios_mpi.cpp) has been already generated
by with Cython (version 0.20.1) and included here. Just in case to
reproduce the C++ code, try the following command. Otherwise, one can
skip this part.

$ make CYTHON=y python

for the serial version of Adios wrapper. If you need to generated C++
for MPI-enabled version, try the following

$ make CYTHON=y MPI=y python

== Upload to PyPI ==

Create $HOME/.pypirc as follows:
index-servers =

username: {{your_username}}
password: {{your_password}}

Then, do the followings:
$ python register
$ python sdist upload

== Build Document ==

Need sphinx. Install as follows:
$ pip install Sphinx

== Trouble Shooting ==

-. Custom MPICC and MPICXX

If one needs to use a custom MPICC and MPICXX command (e.g., Titan),
then use the following command:

$ python build_ext --mpicc=cc --mpicxx=CC

Or, to do with pip, try:

$ pip --global-option=build_ext \
--global-option=--mpicc=cc --global-option=--mpicxx=CC adios

-. Import error due to undefined "clock_gettime" symbol

When getting the following error:

$ python Traceback (most recent call last):
File "", line 8, in <module>
import adios as ad
ImportError: /path/to/ undefined symbol: clock_gettime

Try to use the following command to install:

$ pip install --global-option build_ext --global-option -lrt adios
$ pip install --global-option build_ext --global-option -lrt adios_mpi

-. "Could not find any downloads that satisfy the requirement" with pip

If the error is caused by a certificate error, then, try

$ wget
$ pip --cert cacert.pem search adios
$ pip --cert cacert.pem install adios
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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
adios-1.11.1.post1.tar.gz (228.0 kB) Copy SHA256 Checksum SHA256 Source Feb 10, 2017

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