pyGDM2

pyGDM2 is available on pypi and gitlab.

Detailed documentation with many examples is avaiable at the pyGDM2 documentation website. See also the documentation paper on arXiv (1802.04071)

Requirements

Python

python (2.7 or 3.5+, python)

numpy (numpy)

python headers (under ubuntu, install the package python-dev or python-devel)

Fortran

fortran compiler (tested with gfortran. gcc)

openmp (openmp)

f2py (comes with numpy. link)

Optional Python packages

scipy >= v0.17.0, lower versions supported with restrictions (Strongly recommended. Used for standard solver LU decomposition and several tools. scipy)

matplotlib (Strongly recommended. For all 2D visualization tools. matplotlib)

mpi4py (for MPI parallelized calculation of spectra. mpi4py)

mayavi (for all 3D visualization. mayavi)

PIL (image processing. PIL)

pathos (for multi-threaded generalized propagator operations. pathos)

pytables (v3.x recommended. For hdf5 saving/loading of simulations. pytables)

PaGMO / PyGMO (version 2.4+. Required for the EO submodule. pagmo)

(all available via pip)

Installation under linux

Via pip

Install from pypi repository via

$ pip install pygdm2

Via setup script

The easiest possibility to compile (and install) pyGDM is via the setup-script, which uses the extended distutils from numpy.

To install pyGDM, run in the source directory:

$ python setup.py install

To install to a user-defined location, use the prefix option:

$ python setup.py install --prefix=/some/specific/location

To only compile without installation, use

$ python setup.py build

Manual compilation

clone git:

$ git clone https://gitlab.com/wiechapeter/pyGDM2.git

compile fortran parts:
```
$ cd fortranBase
$ make
```
optional, for system-wide usage add to path and pythonpath, e.g. add following lines to file “/home/USER/.profile”, where “path_of_pyGDM_folder” is the pyGDM installation directory:
```
PATH="path_of_pyGDM_folder:$PATH"
export PATH

PYTHONPATH="path_of_pyGDM_folder:$PYTHONPATH"
export PYTHONPATH
```

Installation under Mac OS X

Using the Anaconda distribution

The default compiler on OSX uses a clang which does not support OpenMP. Hence compilation might fail. We therefore suggest using Anaconda and install gcc from the conda repository in a virtualenv (Here the example of python2. python3 was not tested on OSX so far):

$ conda create -n python2 python=2.7 anaconda

“anaconda” at the end will copy the whole anaconda distribution to the virtial env. You can omit this option and create a “blank” virtual environment to install only selected packages.

Next activate the virtualenv and install the required software:

$ source activate python2
$ xcode-select --install
$ conda install pip
$ conda install gcc
$ pip install pygdm2

Also make sure you have the latest versions of numpy and scipy:

$ pip install numpy scipy --upgrade

Without Anaconda

Alternatively, you can download the latest version and compile it manually without OpenMP support, which should work with the default OSX compiler:

$ python setup.py install --no-openmp

Installation under windows

For windows, we also recommend Anaconda in which pyGDM can be installed easily via pip. See also the MacOS X instructions, but you can skip all steps for installing the gcc compilers, since the windows version of pyGDM comes as pre-compiled binary package.

Via pip

There is a binary for 64bit windows on the pypi repository (tested on Win7 and Win10). Install via

$ pip install pygdm2

Compile using the Anaconda distribution (tested with anaconda3)

get the repo (e.g. download from gitlab)

install gcc compiler

$ conda update conda
$ conda install m2w64-toolchain libpython

compile fortran parts:
```
$ python setupy.py build
```
install:
```
$ python setupy.py install
```

Authors

Python code

P. R. Wiecha

Fortran code

C. Girard

A. Arbouet

R. Marty

P. R. Wiecha

Release files for pyGDM2 1.0.6

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pyGDM2 1.0.6
File	Size	Uploaded
pyGDM2-1.0.6.tar.gz	437.6 kB	Oct 31, 2018	Details

Built distributions (wheels)

Table of built distributions (wheels) for pyGDM2 1.0.6
File	Interpreter	ABI	Platform	Reset
pyGDM2-1.0.6-py3.5-linux-x86_64.egg 451.5 kB Oct 31, 2018	Legacy Egg format	-	-	Details
pyGDM2-1.0.6-py2.7-linux-x86_64.egg 444.4 kB Oct 31, 2018	Legacy Egg format	-	-	Details
pyGDM2-1.0.6-cp37-cp37m-win_amd64.whl 356.9 kB Oct 31, 2018	CPython 3.7	CPython 3.7 pymalloc	Windows x86-64	Details
pyGDM2-1.0.6-cp36-cp36m-win_amd64.whl 368.3 kB Oct 31, 2018	CPython 3.6	CPython 3.6 pymalloc	Windows x86-64	Details
pyGDM2-1.0.6-cp35-cp35m-win_amd64.whl 356.3 kB Oct 31, 2018	CPython 3.5	CPython 3.5 pymalloc	Windows x86-64	Details
pyGDM2-1.0.6-cp27-cp27m-win_amd64.whl 365.4 kB Oct 31, 2018	CPython 2.7	CPython 2.7 pymalloc	Windows x86-64	Details

Total release size: 2.8 MB

Release files / pyGDM2-1.0.6.tar.gz

Download URL	pyGDM2-1.0.6.tar.gz
Size	437.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`0cf7450d7e4a3f594a4ec97f9b288f1387236ce52499953921442226439f2b87`
BLAKE2b-256 checksum How to use checksums	`3a0521628940613d9b3bc01b2e4bd4d5f1d1b50390c866bd205751ddb32b2fcc`
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Uploaded via	`twine/1.11.0 pkginfo/1.4.2 requests/2.18.4 setuptools/39.0.1 requests-toolbelt/0.8.0 tqdm/4.23.4 CPython/2.7.12`

Release files / pyGDM2-1.0.6-py3.5-linux-x86_64.egg

Download URL	pyGDM2-1.0.6-py3.5-linux-x86_64.egg
Size	451.5 kB
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Release files / pyGDM2-1.0.6-py2.7-linux-x86_64.egg

Download URL	pyGDM2-1.0.6-py2.7-linux-x86_64.egg
Size	444.4 kB
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Release files / pyGDM2-1.0.6-cp37-cp37m-win_amd64.whl

Download URL	pyGDM2-1.0.6-cp37-cp37m-win_amd64.whl
Size	356.9 kB
Tags	CPython 3.7 CPython 3.7 pymalloc Windows x86-64
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Release files / pyGDM2-1.0.6-cp36-cp36m-win_amd64.whl

Download URL	pyGDM2-1.0.6-cp36-cp36m-win_amd64.whl
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Release files / pyGDM2-1.0.6-cp35-cp35m-win_amd64.whl

Download URL	pyGDM2-1.0.6-cp35-cp35m-win_amd64.whl
Size	356.3 kB
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Release files / pyGDM2-1.0.6-cp27-cp27m-win_amd64.whl

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