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NIFTy

Planned maintenance on Wednesday, 2021-01-20, 17:00-18:00. Expect some interruptions during that time

Commit bb4b79c0 authored by Martin Reinecke's avatar Martin Reinecke
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switch to pyHealpix and adjust dependencies accordingly

parent a0fe1025
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.gitlab-ci.yml
View file @ bb4b79c0
......@@ -12,8 +12,8 @@ variables:
before_script:
- apt-get update
- >
apt-get install -y build-essential python python-pip python-dev git
gfortran autoconf gsl-bin libgsl-dev wget
apt-get install -y build-essential python python-pip python-dev git
autoconf gsl-bin libgsl-dev wget python-numpy cython
- pip install -r ci/requirements_base.txt
- chmod +x ci/*.sh
......@@ -26,10 +26,8 @@ test_min:
test_mpi:
stage: test
script:
- apt-get install -y openmpi-bin libopenmpi-dev
- pip install astropy healpy mpi4py
- pip install git+https://github.com/mrbell/gfft
- ci/install_libsharp.sh
- apt-get install -y openmpi-bin libopenmpi-dev python-mpi4py
- ci/install_pyHealpix.sh
- python setup.py build_ext --inplace
- nosetests -vv
......@@ -40,11 +38,8 @@ test_mpi_fftw:
- >
apt-get install -y libatlas-base-dev libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3
libfftw3-quad3 libfftw3-single3
- pip install astropy healpy mpi4py
- pip install git+https://github.com/mrbell/gfft
- ci/install_libsharp.sh
- ci/install_pyfftw.sh
libfftw3-quad3 libfftw3-single3 python-mpi4py python-pyfftw
- ci/install_pyHealpix.sh
- python setup.py build_ext --inplace
- nosetests -vv
......@@ -58,12 +53,8 @@ test_mpi_fftw_hdf5:
libfftw3-quad3 libfftw3-single3
- >
apt-get install -y libhdf5-10 libhdf5-dev libhdf5-openmpi-10
libhdf5-openmpi-dev hdf5-tools
- pip install astropy healpy mpi4py
- pip install git+https://github.com/mrbell/gfft
- ci/install_h5py.sh
- ci/install_libsharp.sh
- ci/install_pyfftw.sh
libhdf5-openmpi-dev hdf5-tools python-mpi4py python-pyfftw python-h5py
- ci/install_pyHealpix.sh
- python setup.py build_ext --inplace
- nosetests -vv --with-coverage --cover-package=nifty --cover-branches
- >
......
Dockerfile
View file @ bb4b79c0
......@@ -8,17 +8,15 @@ RUN \
libopenmpi-dev libatlas-base-dev libfftw3-bin libfftw3-dev \
libfftw3-double3 libfftw3-long3 libfftw3-mpi-dev libfftw3-mpi3 \
libfftw3-quad3 libfftw3-single3 libhdf5-10 libhdf5-dev \
libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools python-h5py
libhdf5-openmpi-10 libhdf5-openmpi-dev hdf5-tools python-h5py python-pyfftw
# python dependencies
ADD ci/requirements.txt /tmp/requirements.txt
RUN pip install -r /tmp/requirements.txt
# install libsharp and pyfftw
ADD ci/install_libsharp.sh /tmp/install_libsharp.sh
ADD ci/install_pyfftw.sh /tmp/install_pyfftw.sh
RUN cd /tmp && chmod +x install_libsharp.sh && ./install_libsharp.sh
RUN cd /tmp && chmod +x install_pyfftw.sh && ./install_pyfftw.sh
# install pyHealpix
ADD ci/install_pyHealpix.sh /tmp/install_pyHealpix.sh
RUN cd /tmp && chmod +x install_pyHealpix.sh && ./install_pyHealpix.sh
# copy sources and install nifty
COPY . /tmp/NIFTy
......
README.md
View file @ bb4b79c0
......@@ -38,36 +38,26 @@ certain grids, **fields** that are defined on spaces, and **operators**
that apply to fields.
- [Spaces](http://www.mpa-garching.mpg.de/ift/nifty/space.html)
- `point_space` - unstructured list of points
- `rg_space` - *n*-dimensional regular Euclidean grid
- `lm_space` - spherical harmonics
- `gl_space` - Gauss-Legendre grid on the 2-sphere
- `hp_space` - [HEALPix](http://sourceforge.net/projects/healpix/)
grid on the 2-sphere
- `nested_space` - arbitrary product of grids
- [Fields](http://www.mpa-garching.mpg.de/ift/nifty/field.html)
- `field` - generic class for (discretized) fields
<!-- -->
field.cast_domain field.hat field.power field.smooth
field.conjugate field.inverse_hat field.pseudo_dot field.tensor_dot
field.dim field.norm field.set_target field.transform
field.dot field.plot field.set_val field.weight
field.conjugate field.dim field.norm
field.dot field.set_val field.weight
- [Operators](http://www.mpa-garching.mpg.de/ift/nifty/operator.html)
- `diagonal_operator` - purely diagonal matrices in a specified
basis
- `projection_operator` - projections onto subsets of a specified
basis
- `vecvec_operator` - matrices derived from the outer product of a
vector
- `response_operator` - exemplary responses that include a
convolution, masking and projection
- `propagator_operator` - information propagator in Wiener filter
theory
- `explicit_operator` - linear operators with an explicit matrix
representation
- (and more)
- (and more)
......@@ -81,19 +71,7 @@ Installation
- [Python](http://www.python.org/) (v2.7.x)
- [NumPy](http://www.numpy.org/)
- [SciPy](http://www.scipy.org/)
- [Cython](http://cython.org/)
- [matplotlib](http://matplotlib.org/)
- [GFFT](https://github.com/mrbell/gfft) (v0.1.0) - Generalized Fast
Fourier Transformations for Python - **optional**
- [HEALPy](https://github.com/healpy/healpy) (v1.8.1 without openmp) -
A Python wrapper for
[HEALPix](http://sourceforge.net/projects/healpix/) -**optional,
only needed for spherical spaces**
- [libsharp-wrapper](https://github.com/mselig/libsharp-wrapper)
(v0.1.2 without openmp) - A Python wrapper for the
[libsharp](http://sourceforge.net/projects/libsharp/) library
-**optional, only needed for spherical spaces**
### Download
......@@ -112,57 +90,35 @@ Starting with a fresh Ubuntu installation move to a folder like
- Install basic packages like python, python-dev, gsl and others:
sudo apt-get install curl git autoconf
sudo apt-get install python-dev python-pip gsl-bin libgsl0-dev libfreetype6-dev libpng-dev libatlas-base-dev gfortran
sudo apt-get install curl git autoconf
sudo apt-get install python-dev python-pip gsl-bin libgsl0-dev libfreetype6-dev libpng-dev libatlas-base-dev
- Install matplotlib:
- Using pip install numpy etc...:
sudo apt-get install python-matplotlib
sudo pip install numpy cython
- Using pip install numpy, scipy, etc...:
- Install pyHealpix:
sudo pip install numpy scipy cython pyfits healpy
- Now install the 'non-standard' dependencies. First of all gfft:
curl -LOk https://github.com/mrbell/gfft/tarball/master
tar -xzf master
cd mrbell-gfft*
sudo python setup.py install
cd ..
- Libsharp:
git clone http://git.code.sf.net/p/libsharp/code libsharp-code
cd libsharp-code
sudo autoconf
./configure --enable-pic --disable-openmp
sudo make
cd ..
- Libsharpwrapper:
git clone http://github.com/mselig/libsharp-wrapper.git libsharp-wrapper
cd libsharp-wrapper
sudo python setup.py build_ext
sudo python setup.py install
git clone https://gitlab.mpcdf.mpg.de/mtr/pyHealpix.git
cd pyHealpix
autoreconf -i && ./configure && sudo make install
cd ..
- Finally, NIFTy:
git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
cd nifty
sudo python setup.py install
cd ..
sudo python setup.py install
cd ..
### Installation on a linux cluster
### Installation on a Linux cluster
This is for you if you want to install NIFTy on a HPC machine or cluster
that is hosted by your university or institute. Most of the dependencies
will most likely already be there, but you won't have superuser
priviledges. In this case, instead:
privileges. In this case, instead of:
sudo python setup.py install
sudo python setup.py install
use:
......@@ -175,82 +131,40 @@ or:
in the instruction above. This will install the python packages into
your local user directory.
For pyHealpix, use:
git clone https://gitlab.mpcdf.mpg.de/mtr/pyHealpix.git
cd pyHealpix
autoreconf -i && ./configure --prefix=$HOME/.local && make install
cd ..
### Installation on OS X 10.11
We advice to install the following packages in the order as they appear
We advise to install the following packages in the order as they appear
below. We strongly recommend to install all needed packages via
MacPorts. Please be aware that not all packages are available on
MacPorts, missing ones need to be installed manually. It may also be
mentioned that one should only use one package manager, as multiple ones
may cause trouble.
- Install basic packages python, scipy, matplotlib and cython:
- Install basic packages numpy and cython:
sudo port install py27-numpy
sudo port install py27-scipy
sudo port install py27-matplotlib
sudo port install py27-cython
- Install gfft. **Depending where you installed GSL you may need to
change the path in setup.py!**:
sudo port install gsl
git clone https://github.com/mrbell/gfft.git}{https://github.com/mrbell/gfft.git
sudo python setup.py install
- Install healpy:
- Install pyHealpix:
sudo port install py27-pyfits
git clone https://github.com/healpy/healpy.git
cd healpy
sudo python setup.py install
cd ..
- Install libsharp and therefore autoconf, automake and libtool.
Installations instructions for libsharp may be found here:
<https://sourceforge.net/p/libsharp/code/ci/master/tree/>:
curl -OL http://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz
tar -xzf autoconf-2.69.tar.gz
cd autoconf-2.69
./configure && make && sudo make install
cd ..
curl -OL http://ftpmirror.gnu.org/automake/automake-1.14.tar.gz
tar -xzf automake-1.14.tar.gz
cd automake-1.14
./configure && make && sudo make install
cd ..
curl -OL http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz
tar -xzf libtool-2.4.2.tar.gz
cd libtool-2.4.2
./configure && make && sudo make install
cd ..
git clone http://git.code.sf.net/p/libsharp/code libsharp-code
cd libsharp-code
sudo autoconf
./configure --enable-pic --disable-openmp
sudo make
cd ..
- Install libsharp-wrapper. **Adopt the path of the libsharp
installation in setup.py** :
sudo port install gcc
sudo port select gcc mp-gcc5
git clone https://github.com/mselig/libsharp-wrapper.git
cd libsharp-wrapper
sudo python setup.py install
git clone https://gitlab.mpcdf.mpg.de/mtr/pyHealpix.git
cd pyHealpix
autoreconf -i && ./configure && sudo make install
cd ..
- Install NIFTy:
git clone https://gitlab.mpcdf.mpg.de/ift/NIFTy.git
cd nifty
sudo python setup.py install
cd ..
sudo python setup.py install
cd ..
### Installation using pypi
......@@ -269,10 +183,10 @@ In oder to run the tests one needs two additional packages:
pip install nose
pip install parameterized
Afterwards the tests (including a coverage report) are run using the following
Afterwards the tests (including a coverage report) are run using the following
command in the repository root:
nosetests --exe --cover-html
......@@ -282,7 +196,7 @@ For a quickstart, you can browse through the [informal
introduction](http://www.mpa-garching.mpg.de/ift/nifty/start.html) or
dive into NIFTY by running one of the demonstrations, e.g.:
>>> run -m nifty.demos.demo_wf1
python demos/wiener_filter.py
Acknowledgement
---------------
......
ci/install_h5py.sh deleted 100644 → 0
View file @ a0fe1025
#!/bin/bash
wget https://api.github.com/repos/h5py/h5py/tags -O - | grep tarball_url | grep -v rc | head -n 1 | cut -d '"' -f 4 | wget -i - -O h5py.tar.gz
tar xzf h5py.tar.gz
cd h5py-h5py*
export CC=mpicc
export HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
python setup.py configure --mpi
python setup.py build
python setup.py install
cd ..
rm -r h5py-h5py*
rm h5py.tar.gz
ci/install_libsharp.sh deleted 100644 → 0
View file @ a0fe1025
#!/bin/bash
git clone http://git.code.sf.net/p/libsharp/code libsharp-code
cd libsharp-code
autoconf && ./configure --enable-pic --disable-openmp && make
cd ..
git clone https://github.com/mselig/libsharp-wrapper libsharp-wrapper
cd libsharp-wrapper
python setup.py build_ext install
cd ..
rm -r libsharp-code
rm -r libsharp-wrapper
ci/install_pyfftw.sh deleted 100644 → 0
View file @ a0fe1025
#!/bin/bash
git clone -b mpi https://github.com/fredRos/pyFFTW.git
cd pyFFTW/
CC=mpicc python setup.py build_ext install
cd ..
rm -r pyFFTW
ci/requirements.txt
View file @ bb4b79c0
numpy
scipy
cython
astropy
healpy
mpi4py
ipython==5.3.0
nose
nose-parameterized
parameterized
coverage
git+https://gitlab.mpcdf.mpg.de/ift/mpi_dummy.git
git+https://gitlab.mpcdf.mpg.de/ift/keepers.git
git+https://gitlab.mpcdf.mpg.de/ift/D2O.git
ci/requirements_base.txt
View file @ bb4b79c0
numpy
scipy
cython
nose
nose-parameterized
parameterized
coverage
git+https://gitlab.mpcdf.mpg.de/ift/mpi_dummy.git
git+https://gitlab.mpcdf.mpg.de/ift/keepers.git
......
nifty/config/nifty_config.py
View file @ bb4b79c0
......@@ -25,12 +25,10 @@ import keepers
# Setup the dependency injector
dependency_injector = keepers.DependencyInjector(
[('mpi4py.MPI', 'MPI'),
'healpy',
'libsharp_wrapper_gl'])
'pyHealpix'])
dependency_injector.register('pyfftw', lambda z: hasattr(z, 'FFTW_MPI'))
# Initialize the variables
variable_fft_module = keepers.Variable(
'fft_module',
......@@ -38,35 +36,23 @@ variable_fft_module = keepers.Variable(
lambda z: (('pyfftw' in dependency_injector)
if z == 'fftw' else True))
def _healpy_validator(use_healpy):
if not isinstance(use_healpy, bool):
def _pyHealpix_validator(use_pyHealpix):
if not isinstance(use_pyHealpix, bool):
return False
if not use_healpy:
if not use_pyHealpix:
return True
if 'healpy' not in dependency_injector:
return False
healpy = dependency_injector['healpy']
if lv(healpy.__version__) < lv('1.8.1'):
if 'pyHealpix' not in dependency_injector:
return False
pyHealpix = dependency_injector['pyHealpix']
return True
variable_use_healpy = keepers.Variable(
'use_healpy',
variable_use_pyHealpix = keepers.Variable(
'use_pyHealpix',
[True, False],
_healpy_validator,
_pyHealpix_validator,
genus='boolean')
variable_use_libsharp = keepers.Variable(
'use_libsharp',
[True, False],
lambda z: (('libsharp_wrapper_gl' in
dependency_injector)
if z else True) and isinstance(z, bool),
genus='boolean')
def _dtype_validator(dtype):
try:
np.dtype(dtype)
......@@ -91,8 +77,7 @@ variable_default_distribution_strategy = keepers.Variable(
nifty_configuration = keepers.get_Configuration(
name='NIFTy',
variables=[variable_fft_module,
variable_use_healpy,
variable_use_libsharp,
variable_use_pyHealpix,
variable_default_field_dtype,
variable_default_distribution_strategy],
file_name='NIFTy.conf',
......
nifty/operators/fft_operator/transformations/gllmtransformation.py
View file @ bb4b79c0
......@@ -23,7 +23,7 @@ from nifty import GLSpace, LMSpace
from slicing_transformation import SlicingTransformation
import lm_transformation_factory as ltf
libsharp = gdi.get('libsharp_wrapper_gl')
pyHealpix = gdi.get('pyHealpix')
class GLLMTransformation(SlicingTransformation):
......@@ -31,9 +31,9 @@ class GLLMTransformation(SlicingTransformation):
# ---Overwritten properties and methods---
def __init__(self, domain, codomain=None, module=None):
if 'libsharp_wrapper_gl' not in gdi:
if 'pyHealpix' not in gdi:
raise ImportError(
"The module libsharp is needed but not available.")
"The module pyHealpix is needed but not available.")
super(GLLMTransformation, self).__init__(domain, codomain,
module=module)
......@@ -108,14 +108,12 @@ class GLLMTransformation(SlicingTransformation):
lmax = self.codomain.lmax
mmax = self.codomain.mmax
sjob=pyHealpix.sharpjob_d()
sjob.set_Gauss_geometry(nlat,nlot)
sjob.set_triangular_alm_info(lmax,mmax)
if issubclass(inp.dtype.type, np.complexfloating):
[resultReal, resultImag] = [self.libsharpMap2Alm(x,
nlat=nlat,
nlon=nlon,
lmax=lmax,
mmax=mmax,
**kwargs)
[resultReal, resultImag] = [sjob.map2alm(x)
for x in (inp.real, inp.imag)]
[resultReal, resultImag] = [ltf.buildIdx(x, lmax=lmax)
......@@ -123,22 +121,7 @@ class GLLMTransformation(SlicingTransformation):
result = self._combine_complex_result(resultReal, resultImag)
else:
result = self.libsharpMap2Alm(inp, nlat=nlat, nlon=nlon, lmax=lmax,
mmax=mmax)
result = sjob.map2alm(inp)
result = ltf.buildIdx(result, lmax=lmax)
return result
# ---Added properties and methods---
def libsharpMap2Alm(self, inp, **kwargs):
if inp.dtype == np.dtype('float32'):
return libsharp.map2alm_f(inp, **kwargs)
elif inp.dtype == np.dtype('float64'):
return libsharp.map2alm(inp, **kwargs)
else:
self.logger.debug("performing dtype conversion for libsharp "
"compatibility.")
casted_inp = inp.astype(np.dtype('float64'), copy=False)
result = libsharp.map2alm(casted_inp, **kwargs)
return result
nifty/operators/fft_operator/transformations/hplmtransformation.py
View file @ bb4b79c0
......@@ -24,7 +24,7 @@ from slicing_transformation import SlicingTransformation
import lm_transformation_factory as ltf
hp = gdi.get('healpy')
pyHealpix = gdi.get('pyHealpix')
class HPLMTransformation(SlicingTransformation):
......@@ -32,9 +32,9 @@ class HPLMTransformation(SlicingTransformation):
# ---Overwritten properties and methods---
def __init__(self, domain, codomain=None, module=None):
if 'healpy' not in gdi:
if 'pyHealpix' not in gdi:
raise ImportError(
"The module healpy is needed but not available")
"The module pyHealpix is needed but not available")
super(HPLMTransformation, self).__init__(domain, codomain,
module=module)
......@@ -62,7 +62,7 @@ class HPLMTransformation(SlicingTransformation):
raise TypeError(
"domain needs to be a HPSpace")
lmax = 3 * domain.nside - 1
lmax = 2 * domain.nside
result = LMSpace(lmax=lmax, dtype=np.dtype('float64'))
cls.check_codomain(domain, result)
......@@ -81,24 +81,17 @@ class HPLMTransformation(SlicingTransformation):
nside = domain.nside
lmax = codomain.lmax
if 3 * nside - 1 != lmax:
raise ValueError(
'ERROR: codomain has 3*nside-1 != lmax.')
return None
def _transformation_of_slice(self, inp, **kwargs):
lmax = self.codomain.lmax
mmax = lmax
sjob=pyHealpix.sharpjob_d()
sjob.set_Healpix_geometry(nside)
sjob.set_triangular_alm_info(lmax,mmax)
if issubclass(inp.dtype.type, np.complexfloating):
[resultReal, resultImag] = [hp.map2alm(x.astype(np.float64,
copy=False),
lmax=lmax,
mmax=mmax,
pol=True,
use_weights=False,
**kwargs)
[resultReal, resultImag] = [sjob.map2alm(x)
for x in (inp.real, inp.imag)]
[resultReal, resultImag] = [ltf.buildIdx(x, lmax=lmax)
......@@ -107,9 +100,7 @@ class HPLMTransformation(SlicingTransformation):
result = self._combine_complex_result(resultReal, resultImag)
else:
result = hp.map2alm(inp.astype(np.float64, copy=False),
lmax=lmax, mmax=mmax, pol=True,
use_weights=False)
result = sjob.map2alm(inp)
result = ltf.buildIdx(result, lmax=lmax)
return result
nifty/operators/fft_operator/transformations/lmgltransformation.py
View file @ bb4b79c0
......@@ -23,7 +23,7 @@ from nifty import GLSpace, LMSpace
from slicing_transformation import SlicingTransformation
import lm_transformation_factory as ltf
libsharp = gdi.get('libsharp_wrapper_gl')
pyHealpix = gdi.get('pyHealpix')
class LMGLTransformation(SlicingTransformation):
......@@ -31,9 +31,9 @@ class LMGLTransformation(SlicingTransformation):
# ---Overwritten properties and methods---
def __init__(self, domain, codomain=None, module=None):
if 'libsharp_wrapper_gl' not in gdi:
if 'pyHealpix' not in gdi:
raise ImportError(
"The module libsharp is needed but not available.")
"The module pyHealpix is needed but not available.")
super(LMGLTransformation, self).__init__(domain, codomain,
module=module)
......@@ -114,38 +114,20 @@ class LMGLTransformation(SlicingTransformation):
lmax = self.domain.lmax
mmax = self.domain.mmax
sjob=pyHealpix.sharpjob_d()
sjob.set_Gauss_geometry(nlat,nlot)
sjob.set_triangular_alm_info(lmax,mmax)
if issubclass(inp.dtype.type, np.complexfloating):
[resultReal, resultImag] = [ltf.buildLm(x, lmax=lmax)
for x in (inp.real, inp.imag)]
[resultReal, resultImag] = [self.libsharpAlm2Map(x,
nlat=nlat,
nlon=nlon,
lmax=lmax,
mmax=mmax,
cl=False,
**kwargs)
[resultReal, resultImag] = [sjob.alm2map(x)
for x in [resultReal, resultImag]]
result = self._combine_complex_result(resultReal, resultImag)
else:
result = ltf.buildLm(inp, lmax=lmax)
result = self.libsharpAlm2Map(result, nlat=nlat, nlon=nlon,
lmax=lmax, mmax=mmax, cl=False)
result = sjob.alm2map(result)
return result
# ---Added properties and methods---
def libsharpAlm2Map(self, inp, **kwargs):
if inp.dtype == np.dtype('complex64'):
return libsharp.alm2map_f(inp, **kwargs)
elif inp.dtype == np.dtype('complex128'):
return libsharp.alm2map(inp, **kwargs)
else:
self.logger.debug("Performing dtype conversion for libsharp "
"compatibility.")
casted_inp = inp.astype(np.dtype('complex128'), copy=False)
result = libsharp.alm2map(casted_inp, **kwargs)
return result