Release 0.1.0

.gitignore

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+*.fits

.gitmodules

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+[submodule "cmake_modules/ecrc"]
+	path = cmake_modules/ecrc
+	url = https://github.com/ecrc/ecrc_cmake.git

ATM_PARAM.md

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+Atmospheric parameters {#ATM_PARAM}
+===================================
+
+The parameter file is named "prof%d-atmos-night%d.txt", where the %d are integers representing:
+* the index of the observation
+* the index of the night
+
+These files must contain the following parameters in this strict order.
+
+Each parameter must be preceded by a blank line (used for comments).
+
+* The number of layers
+* r0 at wfs lambda
+* profile strength (units as in  E-SPE-ESO-276-0206_atmosphericparameters)
+* altitude of layers (meters)
+* outer scale (meters)
+
+See an example below:
+~~~{.txt}
+Nlayer
+10
+r0 @ wfs lambda
+0.128916
+cn2 ESO units
+16.1481 3.93694 3.15623 2.16198 1.04095 0.800734 0.867462 1.72825 0.411711 0.144132  
+h in meters
+30 200 390 1880 4500 7500 10500 13500 16500 19500  
+l0 in meters
+25 25 25 25 25 25 25 25 25 25 
+~~~

CMakeLists.txt

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+    cmake_minimum_required(VERSION 3.2.3)
+
+
+    #set common absolute path
+    get_filename_component(COMMON "${CMAKE_SOURCE_DIR}/common" ABSOLUTE)
+
+    include(${CMAKE_SOURCE_DIR}/${project}/CMake_project)
+    message(STATUS "project ${PROJECT_NAME} with ${languages}")
+    PROJECT(${PROJECT_NAME} ${languages})
+
+    # directly make an error if in-source build
+    if("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
+        message(FATAL_ERROR "In-source builds are not allowed.\n"
+                            "Please create a build directory first and execute cmake configuration from "
+                            "this directory. Example: mkdir build && cd build && cmake ..")
+    endif()
+
+    #########################
+    ### VARIABLES ###########
+    #########################
+    option(MOAO_TESTING "Generates testing binaries" OFF)
+    option(GPU "Enable GPU support" OFF)
+    option(USE_INTERSAMPLE "Go through the intersample process and generates PSFs" OFF)
+
+    # Version
+    # Number 0.1.1 is temptative, may differ from actual release.
+    SET( MOAO_VERSION_MAJOR 0 )
+    SET( MOAO_VERSION_MINOR 1 )
+    SET( MOAO_VERSION_PATCH 1 )
+    set( MOAO_VERSION "${MOAO_VERSION_MAJOR}.${MOAO_VERSION_MINOR}.${MOAO_VERSION_PATCH}" )
+
+    # Set the RPATH config
+    # --------------------
+    # use, i.e. don't skip the full RPATH for the build tree
+    set(CMAKE_SKIP_BUILD_RPATH  FALSE)
+    # when building, use the install RPATH already
+    # (automated test will need this)
+    set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+    # the RPATH to be used when installing
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+    # Packaging (make package)
+    SET(CPACK_PACKAGE_VERSION ${MOAO_VERSION})
+    SET(CPACK_GENERATOR "TGZ")
+    INCLUDE(CPack)
+
+    # Define the common include directory of the project
+    include_directories( ${CMAKE_SOURCE_DIR}/include )
+
+    ## CMAKE MODULES :: ECRC
+    ## REQUIRED FOR TESTS TO LINK LIBRARIES
+    include(${PROJECT_SOURCE_DIR}/cmake_modules/CMake_initEcrc)
+
+
+    list(APPEND link_lib "")
+    ################################ 
+    # load fits library (compulsory)
+    set(CFITSIO_ROOT $ENV{CFITSIO_ROOT} CACHE PATH "Path to the root of cfitsio")
+    if("${CFITSIO_ROOT}" STREQUAL "")
+        message( FATAL_ERROR "Environment variable CFITSIO_ROOT is not set. Specify it with -DCFITSIO_ROOT=path/to/cfitsio")
+    endif()
+        message( WARNING "Environment variable CFITSIO_ROOT ${CFITSIO_ROOT}")
+    include_directories(${CFITSIO_ROOT}/include)
+    link_directories(${CFITSIO_ROOT})
+    list(INSERT link_lib 0 "cfitsio" )
+
+
+    ################################ 
+    # load fftw3 library
+    # no need to set this up if fftw is in /usr/lib
+    set(FFTW_ROOT $ENV{FFTW_ROOT} CACHE PATH "Path to the root of fftw3")
+    if("${FFTW_ROOT}" STREQUAL "")
+        message( FATAL_ERROR "Environment variable FFTW_ROOT is not set. Specify it with -DFFTW_ROOT=path/to/fftw3")
+    endif()
+    include_directories(${FFTW_ROOT}/include)
+    link_directories( ${FFTW_ROOT} )
+    list(INSERT link_lib 0 "fftw3" )
+
+
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ")
+    set(extra_flags "")
+
+    if(${USE_LAPACK})
+        include (${CMAKE_SOURCE_DIR}/cmake_modules/CMake_loadLapack)
+    	set(extra_flags "${extra_flags} -DUSE_LAPACK")     
+	if(USE_OPENMP)
+            find_package(OpenMP)
+            set(extra_flags "${extra_flags} -DUSE_OPENMP")
+        endif()
+    endif()
+
+    if(${USE_CHAMELEON})
+        include (${CMAKE_SOURCE_DIR}/cmake_modules/CMake_loadChameleon)
+    	set(extra_flags "${extra_flags} -DUSE_CHAMELEON")     
+    endif()
+
+    if(${USE_INTERSAMPLE})
+        set(extra_flags "${extra_flags} -DUSE_INTERSAMPLE")
+    endif()
+
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${extra_flags}")
+
+    if(${GPU})
+        set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} ${extra_flags} --shared --compiler-options '-fPIC' -gencode arch=compute_30,code=sm_30 --compiler-options -Wall")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_GPU ")
+    endif()
+
+
+
+    # MOAO code
+    include(${CMAKE_SOURCE_DIR}/${project}/CMakeLists.txt)
+
+    #building library
+    #if(${GPU})
+    #    CUDA_ADD_LIBRARY(moao_chameleon SHARED ${SRC} )
+    #    set_target_properties(moao_chameleon PROPERTIES LINKER_LANGUAGE C )
+    #else()
+    #    ADD_LIBRARY(moao_chameleon SHARED ${SRC} )
+    #endif()
+    #target_link_libraries(moao_chameleon "${link_lib}" )
+
+    #buiding executable
+    #set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_CHAMELEON -DUSE_MATCOV_TILED -DUSE_INTERSAMPLE -DCHECK_CHAMELEON")     
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_MATCOV_TILED ")     
+    if(${GPU})
+        CUDA_ADD_EXECUTABLE(${MAIN} ${SRC})
+        set_target_properties(${MAIN} PROPERTIES LINKER_LANGUAGE C )
+    else()
+        ADD_EXECUTABLE(${MAIN} ${SRC})
+    endif()
+    target_link_libraries(${MAIN} "${link_lib}")
+    #add_dependencies()
+
+

LICENSE

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+Copyright (c) 2017, King Abdullah University of Science and Technology,
+Observatoire de Paris Meudon
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+MOAO
+========
+The MOAO project is an experimental framework for the simulation 
+of Multi-Object Adaptive Optics systems.
+Using a pseudo-analytical approach leveraged by the computational power of 
+manycore architectures (x86 and GPUs), the MOAO framework calculates 
+the Tomographic Reconstructor matrix and generates Point Spread Function (PSF)
+for arbitrary MOAO systems and atmospheric conditions.
+
+
+Installation
+-------------
+First download the sources:
+~~~
+git clone https://github.com/ecrc/moao MOAO-git
+~~~
+
+Then, initialize the submodules:
+~~~
+cd MOAO-git
+git submodule init
+git submodule update
+~~~
+
+Create a build directory and run CMake:
+~~~
+mkdir build
+cd build
+cmake .. -Dproject=chameleon
+~~~
+
+The following options can be added:
+* -DUSE_INTERSAMPLE=ON to generate PSFs
+* -DGPU=ON to enable GPU computation
+
+Finally, compile the project:
+~~~
+make
+~~~
+
+
+Execution
+----------
+In order to run the MOAO simulation, some values must be defined:
+* the number of core : n_cores
+* the number of GPUs (if cuda is enabled): n_gpus
+* the tile size : tile
+* the number of short exposure performed with a single tomographic reconstructor : maxobs
+* the number of tomographic reconstructor used a long exposure : maxrefine
+* the path to the system parameters : sys_path
+* the path to the atmospheric parameters : atm_path
+
+Run the following command with the actual values:
+~~~
+./moao --n_cores= --n_gpus= --tile= --maxrefine= --maxobs= --sys_path= --atm_path=
+~~~
+
+Inputs
+------
+The execution of the MOAO framework requires:
+* A text file describing the [System parameters](@ref SYS_PARAM)
+* A command matrix ( Dx.fits)
+* A text file describing the [Atmospheric parameters](@ref ATM_PARAM) 
+
+In order to compute the PSFs, some additional input data are required:
+* The influence function of the actuators (abs2fi.fits)
+* The list of valid subapertures (idx.fits)
+* The optical transfer function of the telescope (otftel.fits)
+
+All those files can be generated by a provided [python script](@ref PY_README) relying on cython.
+
+Input samples can be downloaded as follow :
+~~~
+wget --quiet --no-check-certificate  "https://drive.google.com/uc?export=download&id=0Bw6iRA3hQZNCVEtVRjA1Q2xwM00" -O moao_inputs.tar.gz
+~~~
+These samples contain the corresponding PSF output for a single iteration (maxrefine=1, maxobs=1)
+
+Dependencies
+------------
+This project has several dependencies listed below.
+
+### Simulation ###
+
+* chameleon     (https://project.inria.fr/chameleon/)
+* starpu        (http://starpu.gforge.inria.fr/)
+* cfitsio       (https://heasarc.gsfc.nasa.gov/fitsio/)
+* fftw3         (http://www.fftw.org/)
+
+And, optionally: 
+* cuda
+
+### Parameter generation ###
+In addition to the dependencies mentioned above,
+the parameter generation, detailed in [cython/pipeline/README.md](@ref PY_README) depends on:
+
+* python2
+
+with the packages
+
+* astropy
+* cython 
+
+Note that installing anaconda2 (https://conda.io/docs/user-guide/install/download.html) 
+provide all these dependencies.
+
+
+References
+==========
+1. H. Ltaief, D. Gratadour, A. Charara, and E. Gendron, Adaptive Optics Simulation for the
+World's Biggest Eye on Multicore Architectures with Multiple GPUs, *ACM Platform for
+Advanced Scientific Computing*, 2016.
+2. E. Gendron, A. Charara, A. Abdelfattah, D. Gratadour, D. Keyes, H. Ltaief, C. Morel, F.
+Vidal, A. Sevin, and G. Rousset, A Novel Fast and Accurate Pseudo-Analytical Simulation Approach
+for MOAO", *in Adaptive Optics Systems IV, Proceedings of the SPIE 9148*, 2014.
+3. A. Charara, H. Ltaief, D. Gratadour, D. Keyes, A. Sevin, A. Abdelfattah, E. Gendron and C.
+Morel, and F. Vidal, Pipelining Computational Stages of the Tomographic Reconstructor for
+Multi-object Adaptive Optics on a Multi-GPU System, *Proceedings of the ACM International
+Conference for High Performance Computing, Networking, Storage and Analysis*, pp. 262-273, 2014.
+4. A. Abdelfattah, E. Gendron, D. Gratadour, D. Keyes, H. Ltaief, A. Sevin, and F. Vidal, High
+Performance Pseudo-analytical Simulation of Multi-Object Adaptive Optics over Multi-GPU
+Systems, *Proceedings of the 20th International Euro-Par Conference*, vol. 8632, pp .704–715, 2014.
+
+
+Questions?
+==========
+Please feel free to create an issue on Github for any questions and inquiries.
+
+
+Handout
+========
+![Handout](docs/MOAO-handout-final.png)