- Paper: https://doi.org/10.1016/j.ascom.2017.11.003
- Wiki: https://github.com/miguelcarcamov/gpuvmem/wiki
If you use GPUVMEM for your research please do not forget to cite Cárcamo et al.
@article{CARCAMO201816,
title = "Multi-GPU maximum entropy image synthesis for radio astronomy",
journal = "Astronomy and Computing",
volume = "22",
pages = "16 - 27",
year = "2018",
issn = "2213-1337",
doi = "https://doi.org/10.1016/j.ascom.2017.11.003",
url = "http://www.sciencedirect.com/science/article/pii/S2213133717300094",
author = "M. Cárcamo and P.E. Román and S. Casassus and V. Moral and F.R. Rannou",
keywords = "Maximum entropy, GPU, ALMA, Inverse problem, Radio interferometry, Image synthesis"
}
-
Install git-lfs
a.
sudo apt-get install git-lfs
-
Install casacore latest stable version v3.2.1
a.
git clone --single-branch --branch v3.2.1 https://github.com/casacore/casacore.git
b.
sudo apt-get install -y build-essential cmake gfortran g++ libncurses5-dev libreadline-dev flex bison libblas-dev liblapacke-dev libcfitsio-dev wcslib-dev libhdf5-serial-dev libfftw3-dev python-numpy libboost-python-dev libpython2.7-dev
b.
cd casacore
c.
mkdir build
d.
cd build
e.
cmake -DUSE_FFTW3=ON -DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_THREADS=ON ..
f.
make -j
g.
sudo make install
-
Install Boost
a.
sudo apt-get -y install libboost-all-dev
-
Install cfitsio
a.
sudo apt-get -y install libcfitsio-dev
-
Download or clone gpuvmem.
-
To compile GPUVMEM you will need:
- cfitsio - Usually the package is called
libcfitsio-dev
. - cmake >= 3.8
- git-lfs -
git-lfs
- casacore >= v3.1.2 (https://github.com/casacore/casacore - branch v3.1.2. please make sure you have installed the github version, Ubuntu package doesn't work well since doesn't have the
put()
function). - CUDA 9, 9.1, 9.2, 10.0 and 11.0. Remember to add binaries and libraries to the PATH and LD_LIBRARY_PATH environment variables, respectively.
- OpenMP
- cfitsio - Usually the package is called
-
To run the cmake tests you need to run
git lfs install
if not installled and thengit-lfs pull
to pull the measurement sets and model input FITS images.
docker pull ghcr.io/miguelcarcamov/gpuvmem:latest
cd gpuvmem
mkdir build
cd build
cmake ..
make -j
Create your FITS model input astrometry data on the header, typically we use the resulting dirty image from CASA's tclean.
Usage: ./bin/gpuvmem [options]
-O --output_image [default: mod_out.fits]
Name of the output visibility file/s (separated by a comma)
-e --eta [default: -1]
Variable that controls the minimum image value in the entropy prior
-T --threshold [default: 0]
Threshold to calculate the spectral index image above a certain number of
sigmas in I_nu_0
-p --path [default: mem/]
Path to save FITS images. With last trail / included. (Example ./../mem/)
-G --gpus [default: 0]
Index of the GPU/s you are going to use separated by a comma
-R --robust_parameter [default: 2]
Robust weighting parameter when gridding. -2.0 for uniform weighting, 2.0
for natural weighting and 0.0 for a tradeoff between these two.
-X --blockSizeX [default: -1]
GPU block X Size for image/Fourier plane (Needs to be pow of 2)
-Y --blockSizeY [default: -1]
GPU block Y Size for image/Fourier plane (Needs to be pow of 2)
-V --blockSizeV [default: -1]
GPU block V Size for visibilities (Needs to be pow of 2)
-t --iterations [default: 500]
Number of iterations for optimization
-g --gridding [default: 0]
Use gridded visibilities. This is done in CPU (Need to select the CPU thre
ads that will grid the input visibilities)
-z --initial_values [default: NULL]
Initial values for image/s
-Z --regularization_factors [default: NULL]
Regularization factors for each regularization (separated by a comma)
Flags:
-v --verbose [default: (unset)]
Shows information through all the execution
-x --nopositivity [default: (unset)]
Runs gpuvmem with no positivity restrictions on the images
-a --apply-noise [default: (unset)]
Applies random gaussian noise to visibilities
-P --print-images [default: (unset)]
Prints images per iteration
-E --print-errors [default: (unset)]
Prints final error maps
-s --save_modelcolumn [default: (unset)]
Saves the model visibilities on the model column of the input MS
-M --use-radius-mask [default: (unset)]
Use a mask based on a radius instead of the noise estimation
Help:
-h --help [default: (unset)]
Shows this help
-w --warranty [default: (unset)]
Shows warranty details
-c --copyright [default: (unset)]
Shows copyright conditions
Mandatory:
-i --input [default: NULL]
Name of the input visibility file/s (separated by a comma)
-o --output [default: NULL]
Name of the output visibility file/s (separated by a comma)
-m --model_input [default: mod_in_0.fits]
FITS file including a complete header for astrometry
Optional:
-n --noise [default: -1]
Noise factor parameter
-N --noise_cut [default: 10]
Noise-cut Parameter
-F --ref_frequency [default: -1]
Reference frequency in Hz (if alpha is not zero). It will be calculated fr
om the measurement set if not set
-r --random_sampling [default: 1]
Percentage of data used when random sampling
-f --output_file [default: NULL]
Output file where final objective function values are saved
-
The normal flow of the program starts by creating a synthesizer, creating an optimizer, creating an objective function, and adding the terms to the objective function. It is also possible to add a convolution kernel for gridding and a weighting scheme.
-
Objects can be created by their respective factory or by their constructors.
-
The configuration of each objective function term is parameterized by the penalty factor (-Z), the index of the image from where data will be calculated and the index of the image where results are going to be applied.
- This will return a restored image: A convolution of the model image with the CLEAN beam + residuals (Jy/beam)
- Residuals (Jy/beam)
- The script file is on the scripts folder and it is named
restore.py
Restoring usage:
python restore.py residual_folder.ms mem_model.fits restored_output 2.0
The last parameter, is the robust parameter that you want to use to clean the residuals.
- Miguel Cárcamo - The University of Manchester - miguel.carcamo@postgrad.manchester.ac.uk
- Nicolás Muñoz - Universidad de Santiago de Chile
- Fernando Rannou - Universidad de Santiago de Chile
- Pablo Román - Universidad de Santiago de Chile
- Simón Casassus - Universidad de Chile
- Axel Osses - Universidad de Chile
- Victor Moral - Universidad de Chile
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