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Merge pull request #66 from nlesc-dirac/dev 

merge dev into master
This commit is contained in:
Sarod Yatawatta 2018-10-03 16:12:58 +02:00 committed by GitHub
parent a604fd6d6f 6b7d8815ec
commit 432df53deb
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
31 changed files with 4288 additions and 205 deletions
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47
.codedocs Normal file
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@ -0,0 +1,47 @@
# CodeDocs.xyz Configuration File
# Optional project name, if left empty the GitHub repository name will be used.
PROJECT_NAME = "SageCal"
# One or more directories and files that contain example code to be included.
#EXAMPLE_PATH =
# One or more directories and files to exclude from documentation generation.
# Use relative paths with respect to the repository root directory.
EXCLUDE = pkg build
# One or more wildcard patterns to exclude files and directories from document
# generation.
#EXCLUDE_PATTERNS =
# One or more symbols to exclude from document generation. Symbols can be
# namespaces, classes, or functions.
#EXCLUDE_SYMBOLS =
# Override the default parser (language) used for each file extension.
EXTENSION_MAPPING =
# Set the wildcard patterns used to filter out the source-files.
# If left blank the default is:
# *.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl,
# *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php,
# *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox, *.py,
# *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
FILE_PATTERNS = *.c \
*.cpp \
*.cxx \
*.cu \
*.h \
*.hpp \
*.md
# Hide undocumented class members.
#HIDE_UNDOC_MEMBERS =
# Hide undocumented classes.
#HIDE_UNDOC_CLASSES =
# Specify a markdown page whose contents should be used as the main page
# (index.html). This will override a page marked as \mainpage. For example, a
# README.md file usually serves as a useful main page.
USE_MDFILE_AS_MAINPAGE = README.md

16
.editorconfig Normal file
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@ -0,0 +1,16 @@
# top-most EditorConfig file
root = true
# Unix-style newlines with a newline ending every file
[*]
charset = utf-8
trim_trailing_whitespace = true
end_of_line = lf
insert_final_newline = true
# Tab indentation (no size specified)
[Makefile]
indent_style = tab
[*.{c,h,cpp,hpp}]
indent_size = 2

2
.gitignore vendored
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@ -1,3 +1,5 @@
build
.idea .idea
*/*.png */*.png

21
.travis.yml
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@ -6,18 +6,17 @@ language: cpp
#env: #env:
before_install: before_install:
- docker pull ubuntu:xenial - docker pull fdiblen/ubuntu1604-test:latest
- docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name ubuntu-build ubuntu:xenial - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name ubuntu-build fdiblen/ubuntu1604-test:latest
- docker pull fdiblen/sl7-test:latest
- docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name sl-build fdiblen/sl7-test:latest
# - docker pull base/archlinux
# - docker run -itd -v "${TRAVIS_BUILD_DIR}:/travis/workdir" --name arch-build base/archlinux
script: script:
- export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi) - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
- echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH" - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH, PR=$PR, BRANCH=$BRANCH"
- docker exec ubuntu-build apt-get update -y - docker exec -e BRANCH=$BRANCH -e IMAGE='ubuntu' ubuntu-build /bin/bash -c "/travis/workdir/build-tests/compile_sagecal.sh"
- docker exec ubuntu-build apt-get install software-properties-common -y - docker exec -e BRANCH=$BRANCH -e IMAGE='sl7' sl-build /bin/bash -c "/travis/workdir/build-tests/compile_sagecal.sh"
- docker exec ubuntu-build add-apt-repository -s ppa:kernsuite/kern-3 -y # - docker exec --env BRANCH=$BRANCH arch-build /bin/bash -c "/travis/workdir/build-tests/arch/prepare-arch.sh"
- docker exec ubuntu-build apt-add-repository multiverse # - docker exec --env BRANCH=$BRANCH arch-build /bin/bash -c "/travis/workdir/build-tests/arch/compile-arch.sh"
- docker exec ubuntu-build apt-get update -y
- docker exec ubuntu-build apt-get install -y git cmake g++ pkg-config libcfitsio-bin libcfitsio-dev libopenblas-base libopenblas-dev wcslib-dev wcslib-tools libglib2.0-dev libcasa-casa2 casacore-dev casacore-data casacore-tools
- |
docker exec --env BRANCH=$BRANCH ubuntu-build /bin/bash -c "/travis/workdir/test-builds/test-ubuntu.sh"

86
CMakeLists.txt
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@ -3,6 +3,13 @@ enable_language(CXX)
#--------------------------------------- project #--------------------------------------- project
project (SageCal) project (SageCal)
if (NOT EXISTS ${CMAKE_BINARY_DIR}/CMakeCache.txt)
if (NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release" FORCE)
endif()
endif()
set(PROJECT_VERSION_MAJOR 0) set(PROJECT_VERSION_MAJOR 0)
set(PROJECT_VERSION_MINOR 6) set(PROJECT_VERSION_MINOR 6)
set(PROJECT_VERSION_PATCH 0) set(PROJECT_VERSION_PATCH 0)
@ -10,6 +17,7 @@ set(PROJECT_VERSION_REVISION 1)
set(PROJECT_VERSION set(PROJECT_VERSION
"${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}") "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
message(STATUS "\n############################\n# HOST SYSTEM v${CMAKE_HOST_SYSTEM_NAME}\n############################")
message(STATUS "\n############################\n# Building SageCal v${PROJECT_VERSION}\n############################") message(STATUS "\n############################\n# Building SageCal v${PROJECT_VERSION}\n############################")
include(CheckCXXCompilerFlag) include(CheckCXXCompilerFlag)
@ -27,7 +35,6 @@ SET(LIBRARY_OUTPUT_PATH "${MAINFOLDER}/dist/lib")
set( CMAKE_MODULE_PATH $ENV{CMAKE_MODULE_PATH} ) set( CMAKE_MODULE_PATH $ENV{CMAKE_MODULE_PATH} )
set( CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH} ) set( CMAKE_PREFIX_PATH $ENV{CMAKE_PREFIX_PATH} )
#--------------------------------------- cmake modules #--------------------------------------- cmake modules
list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_SOURCE_DIR}/CMakeModules) list(INSERT CMAKE_MODULE_PATH 0 ${CMAKE_SOURCE_DIR}/CMakeModules)
@ -49,14 +56,15 @@ IF("${isSystemDir}" STREQUAL "-1")
SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
ENDIF("${isSystemDir}" STREQUAL "-1") ENDIF("${isSystemDir}" STREQUAL "-1")
# libsynthesis has mix of C++ and Fortran which is not handled well by
# versions before 2.8.
if(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
if(NOT LIB_EXTRA_SYNTHESIS)
set(LIB_EXTRA_SYNTHESIS gfortran)
endif(NOT LIB_EXTRA_SYNTHESIS)
endif(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
# # libsynthesis has mix of C++ and Fortran which is not handled well by
# # versions before 2.8.
# if(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
# if(NOT LIB_EXTRA_SYNTHESIS)
# set(LIB_EXTRA_SYNTHESIS gfortran)
# endif(NOT LIB_EXTRA_SYNTHESIS)
# endif(${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} LESS 2.8)
#
#--------------------------------------- SageCal dependencies #--------------------------------------- SageCal dependencies
@ -72,7 +80,7 @@ include_directories(${CASACORE_INCLUDE_DIR})
#cfitsio #cfitsio
find_package(CfitsIO REQUIRED) find_package(CfitsIO REQUIRED)
include_directories(${CFITSIO_INCLUDE_DIR}) include_directories(${CFITSIO_INCLUDE})
#lapack #lapack
find_package(LAPACK REQUIRED) find_package(LAPACK REQUIRED)
@ -90,10 +98,21 @@ include_directories(${OpenBLAS_INCLUDE_DIR})
#find_package(BLAS REQUIRED) #find_package(BLAS REQUIRED)
#include_directories(${BLAS_INCLUDE_DIR}) #include_directories(${BLAS_INCLUDE_DIR})
# FIXME: is this really needed? # ##gfortran
##gfortran enable_language(Fortran)
#find_package(GFortranLibs REQUIRED) #find_package(GFortranLibs REQUIRED)
#include_directories(${GFORTRAN_INCLUDE_DIR}) # include_directories(${GFORTRAN_INCLUDE_DIR})
# enable_language(Fortran)
# # get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
# set(FC "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
# set(CMAKE_Fortran_COMPILER "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
#
##hdf5 ##hdf5
#find_package(HDF5 REQUIRED) #find_package(HDF5 REQUIRED)
@ -121,11 +140,9 @@ endif()
#--------------------------------------- build parameters for all targets #--------------------------------------- build parameters for all targets
#set (CMAKE_CXX_FLAGS "-g -O3 -Wall -Wextra -std=c++11 -W -pedantic -ansi -fPIC -fpermissive -fno-omit-frame-pointer -fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -std=c++0x -g -O3")
# set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall -Wextra -W -pedantic -ansi -fPIC -fpermissive") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -pg -Wall -DNDEBUG -Wextra -Wcast-align -Wpointer-arith -Woverloaded-virtual -Wwrite-strings -Wcast-qual -Wctor-dtor-privacy -Wno-long-long-Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Werror -Wno-unused")
set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall")
# FIXME: add debug build option
#set (CMAKE_CXX_FLAGS_DEBUG "-g -pg -pedantic -Wall -DNDEBUG -Wextra -Wcast-align -Wpointer-arith -Woverloaded-virtual -Wwrite-strings -Wcast-qual -Wctor-dtor-privacy -Wno-long-long-Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept -Wold-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel -Wstrict-overflow=5 -Wswitch-default -Wundef -Werror -Wno-unused")
@ -133,6 +150,7 @@ set (CMAKE_CXX_FLAGS "-std=c++0x -g -O3 -Wall")
#--------------------------------------- summary #--------------------------------------- summary
message(STATUS "\n############################\n# Configuration summary\n############################") message(STATUS "\n############################\n# Configuration summary\n############################")
message (STATUS "CMAKE_SYSTEM .......... = ${CMAKE_SYSTEM}") message (STATUS "CMAKE_SYSTEM .......... = ${CMAKE_SYSTEM}")
message (STATUS "CMAKE_INSTALL_PREFIX .. = ${CMAKE_INSTALL_PREFIX}")
message (STATUS "CMAKE_BUILD_TYPE ...... = ${CMAKE_BUILD_TYPE}") message (STATUS "CMAKE_BUILD_TYPE ...... = ${CMAKE_BUILD_TYPE}")
message (STATUS "BUILD_SHARED_LIBS ..... = ${BUILD_SHARED_LIBS}") message (STATUS "BUILD_SHARED_LIBS ..... = ${BUILD_SHARED_LIBS}")
message (STATUS "CMAKE_INSTALL_NAME_DIR = ${CMAKE_INSTALL_NAME_DIR}") message (STATUS "CMAKE_INSTALL_NAME_DIR = ${CMAKE_INSTALL_NAME_DIR}")
@ -143,30 +161,36 @@ message (STATUS "CMAKE_CXX_FLAGS ....... = ${CMAKE_CXX_FLAGS}")
message (STATUS "ENABLE_MPI ............ = ${ENABLE_MPI}") message (STATUS "ENABLE_MPI ............ = ${ENABLE_MPI}")
message (STATUS "ENABLE_CUDA ........... = ${ENABLE_CUDA}") message (STATUS "ENABLE_CUDA ........... = ${ENABLE_CUDA}")
message (STATUS "CASACORE_INCLUDE_DIR........... = ${CASACORE_INCLUDE_DIR}") message (STATUS "CASACORE_INCLUDE_DIR....= ${CASACORE_INCLUDE_DIR}")
message (STATUS "CASACORE_LIBRARIES........... = ${CASACORE_LIBRARIES}") message (STATUS "CASACORE_LIBRARIES......= ${CASACORE_LIBRARIES}")
message (STATUS "OpenBLAS_LIB .......... = ${OpenBLAS_LIB}") message (STATUS "OpenBLAS_LIB .......... = ${OpenBLAS_LIB}")
message (STATUS "GLIB_PKG_INCLUDE_DIRS.............. = ${GLIB_PKG_INCLUDE_DIRS}") message (STATUS "GLIB_PKG_INCLUDE_DIRS...= ${GLIB_PKG_INCLUDE_DIRS}")
message (STATUS "GLIB_PKG_LIBRARIES............. = ${GLIB_PKG_LIBRARIES}") message (STATUS "GLIB_PKG_LIBRARIES......= ${GLIB_PKG_LIBRARIES}")
#message (STATUS "LAPACK-INC ............ = ${LAPACK_INCLUDE_DIR}") #message (STATUS "LAPACK-INC ............ = ${LAPACK_INCLUDE_DIR}")
message (STATUS "LAPACK_LIBRARIES........... = ${LAPACK_LIBRARIES}") message (STATUS "LAPACK_LIBRARIES........= ${LAPACK_LIBRARIES}")
#message (STATUS "GFORTRAN-INC ......... = ${GFORTRAN_INCLUDE_DIR}") # message (STATUS "GFORTRAN-INC ......... = ${GFORTRAN_INCLUDE_DIR}")
#message (STATUS "GFORTRAN-LIBS ......... = ${LIBGFORTRAN_LIBRARIES}") # message (STATUS "GFORTRAN-LIBS ......... = ${LIBGFORTRAN_LIBRARIES}")
message (STATUS "CMAKE_Fortran_COMPILER = ${CMAKE_Fortran_COMPILER}")
message (STATUS "CFITSIO_INCLUDE_DIR.......... = ${CFITSIO_INCLUDE_DIR}") message (STATUS "CFITSIO_ROOT_DIR........= ${CFITSIO_ROOT_DIR}")
message (STATUS "CFITSIO_LIBRARIES.......... = ${CFITSIO_LIBRARIES}") message (STATUS "CFITSIO_INCLUDE.........= ${CFITSIO_INCLUDE}")
message (STATUS "CFITSIO_LIB.............= ${CFITSIO_LIB}")
message (STATUS "WCSLIB_INCLUDE_DIR........... = ${WCSLIB_INCLUDE_DIR}") message (STATUS "WCSLIB_INCLUDE_DIRS.....= ${WCSLIB_INCLUDE_DIRS}")
message (STATUS "WCSLIB_LIBRARIES ........... = ${WCSLIB_LIBRARIES}") message (STATUS "WCSLIB_LIBRARIES .......= ${WCSLIB_LIBRARIES}")
message (STATUS "HDF5_INCLUDE_DIR........... = ${HDF5_INCLUDE_DIRS}") message (STATUS "HDF5_INCLUDE_DIR........= ${HDF5_INCLUDE_DIRS}")
message (STATUS "HDF5_LIBRARIES........... = ${HDF5_LIBRARIES}") message (STATUS "HDF5_LIBRARIES..........= ${HDF5_LIBRARIES}")
message (STATUS "CMAKE_CURRENT_BINARY_DIR..........= ${CMAKE_CURRENT_BINARY_DIR}")
message (STATUS "CMAKE_CURRENT_LIST_DIR..........= ${CMAKE_CURRENT_LIST_DIR}")
message (STATUS "CMAKE_INSTALL_PREFIX..........= ${CMAKE_INSTALL_PREFIX}")
#--------------------------------------- include directories #--------------------------------------- include directories
add_subdirectory(src) add_subdirectory(src)
@ -177,3 +201,5 @@ add_subdirectory(src)
# FIXME: this will be the final step for testing # FIXME: this will be the final step for testing
#file(COPY ${PROJECT_SOURCE_DIR}/test DESTINATION ${MAINFOLDER}/dist/test) #file(COPY ${PROJECT_SOURCE_DIR}/test DESTINATION ${MAINFOLDER}/dist/test)
install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/dist/ DESTINATION ${CMAKE_INSTALL_PREFIX})

10
CMakeModules/FindCasaCore.cmake
View File

@ -71,7 +71,15 @@
# directly fed to the linker. # directly fed to the linker.
# #
# Usage: casacore_resolve_dependencies(result components...) # Usage: casacore_resolve_dependencies(result components...)
#
if (NOT "$ENV{CASACORE_ROOT_DIR}" STREQUAL "")
set(CASACORE_ROOT_DIR "$ENV{CASACORE_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
endif()
macro(casacore_resolve_dependencies _result) macro(casacore_resolve_dependencies _result)
set(${_result} ${ARGN}) set(${_result} ${ARGN})
set(_index 0) set(_index 0)

31
CMakeModules/FindCfitsIO.cmake
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@ -3,11 +3,11 @@
# CFITSIO_ROOT_DIR - CFITSIO root directory # CFITSIO_ROOT_DIR - CFITSIO root directory
# Variables defined by this module: # Variables defined by this module:
# CFITSIO_FOUND - system has CFITSIO # CFITSIO_FOUND - system has CFITSIO
# CFITSIO_INCLUDE_DIR - the CFITSIO include directory (cached) # CFITSIO_INCLUDE - the CFITSIO include directory (cached)
# CFITSIO_INCLUDE_DIRS - the CFITSIO include directories # CFITSIO_INCLUDES - the CFITSIO include directories
# (identical to CFITSIO_INCLUDE_DIR) # (identical to CFITSIO_INCLUDE)
# CFITSIO_LIBRARY - the CFITSIO library (cached) # CFITSIO_LIBRARY - the CFITSIO library (cached)
# CFITSIO_LIBRARIES - the CFITSIO libraries # CFITSIO_LIB - the CFITSIO libraries
# (identical to CFITSIO_LIBRARY) # (identical to CFITSIO_LIBRARY)
# CFITSIO_VERSION_STRING the found version of CFITSIO, padded to 3 digits # CFITSIO_VERSION_STRING the found version of CFITSIO, padded to 3 digits
@ -33,12 +33,17 @@
if(NOT CFITSIO_FOUND) if(NOT CFITSIO_FOUND)
find_path(CFITSIO_INCLUDE_DIR fitsio.h if (NOT "$ENV{CFITSIO_ROOT_DIR}" STREQUAL "")
set(CFITSIO_ROOT_DIR "$ENV{CFITSIO_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
endif()
find_path(CFITSIO_INCLUDE fitsio.h
HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES include include/cfitsio HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES include include/cfitsio
include/libcfitsio0) include/libcfitsio0)
if(CFITSIO_INCLUDE_DIR) if(CFITSIO_INCLUDE)
FILE(READ "${CFITSIO_INCLUDE_DIR}/fitsio.h" CFITSIO_H) FILE(READ "${CFITSIO_INCLUDE}/fitsio.h" CFITSIO_H)
set(CFITSIO_VERSION_REGEX ".*#define CFITSIO_VERSION[^0-9]*([0-9]+)\\.([0-9]+).*") set(CFITSIO_VERSION_REGEX ".*#define CFITSIO_VERSION[^0-9]*([0-9]+)\\.([0-9]+).*")
if ("${CFITSIO_H}" MATCHES ${CFITSIO_VERSION_REGEX}) if ("${CFITSIO_H}" MATCHES ${CFITSIO_VERSION_REGEX})
# Pad CFITSIO minor version to three digit because 3.181 is older than 3.35 # Pad CFITSIO minor version to three digit because 3.181 is older than 3.35
@ -51,24 +56,24 @@ if(NOT CFITSIO_FOUND)
else () else ()
set(CFITSIO_VERSION_STRING "Unknown") set(CFITSIO_VERSION_STRING "Unknown")
endif() endif()
endif(CFITSIO_INCLUDE_DIR) endif(CFITSIO_INCLUDE)
find_library(CFITSIO_LIBRARY cfitsio find_library(CFITSIO_LIBRARY cfitsio
HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES lib) HINTS ${CFITSIO_ROOT_DIR} PATH_SUFFIXES lib)
find_library(M_LIBRARY m) find_library(M_LIBRARY m)
mark_as_advanced(CFITSIO_INCLUDE_DIR CFITSIO_LIBRARY M_LIBRARY) mark_as_advanced(CFITSIO_INCLUDE CFITSIO_LIBRARY M_LIBRARY)
if(CMAKE_VERSION VERSION_LESS "2.8.3") if(CMAKE_VERSION VERSION_LESS "2.8.3")
find_package_handle_standard_args(CFITSIO DEFAULT_MSG find_package_handle_standard_args(CFITSIO DEFAULT_MSG
CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE_DIR) CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE)
else () else ()
include(FindPackageHandleStandardArgs) include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(CFITSIO find_package_handle_standard_args(CFITSIO
REQUIRED_VARS CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE_DIR REQUIRED_VARS CFITSIO_LIBRARY M_LIBRARY CFITSIO_INCLUDE
VERSION_VAR CFITSIO_VERSION_STRING) VERSION_VAR CFITSIO_VERSION_STRING)
endif () endif ()
set(CFITSIO_INCLUDE_DIRS ${CFITSIO_INCLUDE_DIR}) set(CFITSIO_INCLUDES ${CFITSIO_INCLUDE})
set(CFITSIO_LIBRARIES ${CFITSIO_LIBRARY} ${M_LIBRARY}) set(CFITSIO_LIB ${CFITSIO_LIBRARY} ${M_LIBRARY})
endif(NOT CFITSIO_FOUND) endif(NOT CFITSIO_FOUND)

240
CMakeModules/FindGFortranLibs.cmake
View File

@ -24,120 +24,128 @@ if(NOT CMAKE_REQUIRED_QUIET)
message(STATUS "Looking for gfortran related libraries...") message(STATUS "Looking for gfortran related libraries...")
endif() endif()
# enable_language(Fortran)
# if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
#
# # Basically, call "gfortran -v" to dump compiler info to the string
# # GFORTRAN_VERBOSE_STR, which will be used to get necessary paths
# message(STATUS "Extracting library and header information by calling 'gfortran -v'...")
# execute_process(COMMAND "${CMAKE_Fortran_COMPILER}" "-v" ERROR_VARIABLE
# GFORTRAN_VERBOSE_STR RESULT_VARIABLE FLAG)
#
# # For debugging
# message(STATUS "'gfortran -v' returned:")
# message(STATUS "${GFORTRAN_VERBOSE_STR}")
#
# # Detect gfortran version
# string(REGEX MATCH "gcc version [^\t\n ]+" GFORTRAN_VER_STR "${GFORTRAN_VERBOSE_STR}")
# string(REGEX REPLACE "gcc version ([^\t\n ]+)" "\\1" GFORTRAN_VERSION_STRING "${GFORTRAN_VER_STR}")
# message(STATUS "Detected gfortran version ${GFORTRAN_VERSION_STRING}")
# unset(GFORTRAN_VER_STR)
#
# set(MATCH_REGEX "[^\t\n ]+[\t\n ]+")
# set(REPLACE_REGEX "([^\t\n ]+)")
#
# # Find architecture for compiler
# string(REGEX MATCH "Target: [^\t\n ]+"
# GFORTRAN_ARCH_STR "${GFORTRAN_VERBOSE_STR}")
# message(STATUS "Architecture string: ${GFORTRAN_ARCH_STR}")
# string(REGEX REPLACE "Target: ([^\t\n ]+)" "\\1"
# GFORTRAN_ARCH "${GFORTRAN_ARCH_STR}")
# message(STATUS "Detected gfortran architecture: ${GFORTRAN_ARCH}")
# unset(GFORTRAN_ARCH_STR)
#
# # Find install prefix, if it exists; if not, use default
# string(REGEX MATCH "--prefix=[^\t\n ]+[\t\n ]+"
# GFORTRAN_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
# if(NOT GFORTRAN_PREFIX_STR)
# message(STATUS "Detected default gfortran prefix")
# set(GFORTRAN_PREFIX_DIR "/usr/local") # default prefix for gcc install
# else()
# string(REGEX REPLACE "--prefix=([^\t\n ]+)" "\\1"
# GFORTRAN_PREFIX_DIR "${GFORTRAN_PREFIX_STR}")
# endif()
# message(STATUS "Detected gfortran prefix: ${GFORTRAN_PREFIX_DIR}")
# unset(GFORTRAN_PREFIX_STR)
#
# # Find install exec-prefix, if it exists; if not, use default
# string(REGEX MATCH "--exec-prefix=[^\t\n ]+[\t\n ]+" "\\1"
# GFORTRAN_EXEC_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
# if(NOT GFORTRAN_EXEC_PREFIX_STR)
# message(STATUS "Detected default gfortran exec-prefix")
# set(GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_PREFIX_DIR}")
# else()
# string(REGEX REPLACE "--exec-prefix=([^\t\n ]+)" "\\1"
# GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_EXEC_PREFIX_STR}")
# endif()
# message(STATUS "Detected gfortran exec-prefix: ${GFORTRAN_EXEC_PREFIX_DIR}")
# UNSET(GFORTRAN_EXEC_PREFIX_STR)
#
# # Find library directory and include directory, if library directory specified
# string(REGEX MATCH "--libdir=[^\t\n ]+"
# GFORTRAN_LIB_DIR_STR "${GFORTRAN_VERBOSE_STR}")
# if(NOT GFORTRAN_LIB_DIR_STR)
# message(STATUS "Found --libdir flag -- not found")
# message(STATUS "Using default gfortran library & include directory paths")
# set(GFORTRAN_LIBRARIES_DIR
# "${GFORTRAN_EXEC_PREFIX_DIR}/lib/gcc/${GFORTRAN_ARCH}/${GFORTRAN_VERSION_STRING}")
# string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/include")
# else()
# message(STATUS "Found --libdir flag -- yes")
# string(REGEX REPLACE "--libdir=([^\t\n ]+)" "\\1"
# GFORTRAN_LIBRARIES_DIR "${GFORTRAN_LIB_DIR_STR}")
# string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/gcc/" "${GFORTRAN_ARCH}" "/" "${GFORTRAN_VERSION_STRING}" "/include")
# endif()
# message(STATUS "gfortran libraries path: ${GFORTRAN_LIBRARIES_DIR}")
# message(STATUS "gfortran include path dir: ${GFORTRAN_INCLUDE_DIR}")
# unset(GFORTRAN_LIB_DIR_STR)
#
# # There are lots of other build options for gcc & gfortran. For now, the
# # options implemented above should cover a lot of common use cases.
#
# # Clean up be deleting the output string from "gfortran -v"
# unset(GFORTRAN_VERBOSE_STR)
#
# # Find paths for libgfortran, libquadmath, libgomp
# # libgomp needed for OpenMP support without Clang
# find_library(LIBGFORTRAN_LIBRARIES NAMES gfortran libgfortran
# HINTS ${GFORTRAN_LIBRARIES_DIR})
# find_library(LIBQUADMATH_LIBRARIES NAMES quadmath libquadmath
# HINTS ${GFORTRAN_LIBRARIES_DIR})
# find_library(LIBGOMP_LIBRARIES NAMES gomp libgomp
# HINTS ${GFORTRAN_LIBRARIES_DIR})
#
# # Find OpenMP headers
# find_path(LIBGOMP_INCLUDE_DIR NAMES omp.h HINTS ${GFORTRAN_INCLUDE_DIR})
#
# else()
# message(STATUS "CMAKE_Fortran_COMPILER_ID does not match 'GNU'!")
# endif()
#
# include(FindPackageHandleStandardArgs)
#
# # Required: libgfortran, libquadmath, path for gfortran libraries
# # Optional: libgomp, path for OpenMP headers, path for gcc/gfortran headers
# find_package_handle_standard_args(GFortranLibs
# REQUIRED_VARS LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES GFORTRAN_LIBRARIES_DIR
# VERSION_VAR GFORTRAN_VERSION_STRING)
#
# if(GFORTRANLIBS_FOUND)
# message(STATUS "Looking for gfortran libraries -- found")
# message(STATUS "gfortran version: ${GFORTRAN_VERSION_STRING}")
# else()
# message(STATUS "Looking for gfortran libraries -- not found")
# endif()
#
# mark_as_advanced(LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES
# LIBGOMP_LIBRARIES LIBGOMP_INCLUDE_DIR
# GFORTRAN_LIBRARIES_DIR GFORTRAN_INCLUDE_DIR)
# # FindGFortranLIBS.cmake ends here
enable_language(Fortran) enable_language(Fortran)
if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") # if (NOT "$ENV{FC}" STREQUAL "")
# set(FC "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
# Basically, call "gfortran -v" to dump compiler info to the string # set(CMAKE_Fortran_COMPILER "$ENV{FC}" CACHE INTERNAL "Got from environment variable")
# GFORTRAN_VERBOSE_STR, which will be used to get necessary paths # set(GFORTRANLIBS_FOUND "1" CACHE INTERNAL "found environment variable")
message(STATUS "Extracting library and header information by calling 'gfortran -v'...") # endif()
execute_process(COMMAND "${CMAKE_Fortran_COMPILER}" "-v" ERROR_VARIABLE
GFORTRAN_VERBOSE_STR RESULT_VARIABLE FLAG)
# For debugging
message(STATUS "'gfortran -v' returned:")
message(STATUS "${GFORTRAN_VERBOSE_STR}")
# Detect gfortran version
string(REGEX MATCH "gcc version [^\t\n ]+" GFORTRAN_VER_STR "${GFORTRAN_VERBOSE_STR}")
string(REGEX REPLACE "gcc version ([^\t\n ]+)" "\\1" GFORTRAN_VERSION_STRING "${GFORTRAN_VER_STR}")
message(STATUS "Detected gfortran version ${GFORTRAN_VERSION_STRING}")
unset(GFORTRAN_VER_STR)
set(MATCH_REGEX "[^\t\n ]+[\t\n ]+")
set(REPLACE_REGEX "([^\t\n ]+)")
# Find architecture for compiler
string(REGEX MATCH "Target: [^\t\n ]+"
GFORTRAN_ARCH_STR "${GFORTRAN_VERBOSE_STR}")
message(STATUS "Architecture string: ${GFORTRAN_ARCH_STR}")
string(REGEX REPLACE "Target: ([^\t\n ]+)" "\\1"
GFORTRAN_ARCH "${GFORTRAN_ARCH_STR}")
message(STATUS "Detected gfortran architecture: ${GFORTRAN_ARCH}")
unset(GFORTRAN_ARCH_STR)
# Find install prefix, if it exists; if not, use default
string(REGEX MATCH "--prefix=[^\t\n ]+[\t\n ]+"
GFORTRAN_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
if(NOT GFORTRAN_PREFIX_STR)
message(STATUS "Detected default gfortran prefix")
set(GFORTRAN_PREFIX_DIR "/usr/local") # default prefix for gcc install
else()
string(REGEX REPLACE "--prefix=([^\t\n ]+)" "\\1"
GFORTRAN_PREFIX_DIR "${GFORTRAN_PREFIX_STR}")
endif()
message(STATUS "Detected gfortran prefix: ${GFORTRAN_PREFIX_DIR}")
unset(GFORTRAN_PREFIX_STR)
# Find install exec-prefix, if it exists; if not, use default
string(REGEX MATCH "--exec-prefix=[^\t\n ]+[\t\n ]+" "\\1"
GFORTRAN_EXEC_PREFIX_STR "${GFORTRAN_VERBOSE_STR}")
if(NOT GFORTRAN_EXEC_PREFIX_STR)
message(STATUS "Detected default gfortran exec-prefix")
set(GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_PREFIX_DIR}")
else()
string(REGEX REPLACE "--exec-prefix=([^\t\n ]+)" "\\1"
GFORTRAN_EXEC_PREFIX_DIR "${GFORTRAN_EXEC_PREFIX_STR}")
endif()
message(STATUS "Detected gfortran exec-prefix: ${GFORTRAN_EXEC_PREFIX_DIR}")
UNSET(GFORTRAN_EXEC_PREFIX_STR)
# Find library directory and include directory, if library directory specified
string(REGEX MATCH "--libdir=[^\t\n ]+"
GFORTRAN_LIB_DIR_STR "${GFORTRAN_VERBOSE_STR}")
if(NOT GFORTRAN_LIB_DIR_STR)
message(STATUS "Found --libdir flag -- not found")
message(STATUS "Using default gfortran library & include directory paths")
set(GFORTRAN_LIBRARIES_DIR
"${GFORTRAN_EXEC_PREFIX_DIR}/lib/gcc/${GFORTRAN_ARCH}/${GFORTRAN_VERSION_STRING}")
string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/include")
else()
message(STATUS "Found --libdir flag -- yes")
string(REGEX REPLACE "--libdir=([^\t\n ]+)" "\\1"
GFORTRAN_LIBRARIES_DIR "${GFORTRAN_LIB_DIR_STR}")
string(CONCAT GFORTRAN_INCLUDE_DIR "${GFORTRAN_LIBRARIES_DIR}" "/gcc/" "${GFORTRAN_ARCH}" "/" "${GFORTRAN_VERSION_STRING}" "/include")
endif()
message(STATUS "gfortran libraries path: ${GFORTRAN_LIBRARIES_DIR}")
message(STATUS "gfortran include path dir: ${GFORTRAN_INCLUDE_DIR}")
unset(GFORTRAN_LIB_DIR_STR)
# There are lots of other build options for gcc & gfortran. For now, the
# options implemented above should cover a lot of common use cases.
# Clean up be deleting the output string from "gfortran -v"
unset(GFORTRAN_VERBOSE_STR)
# Find paths for libgfortran, libquadmath, libgomp
# libgomp needed for OpenMP support without Clang
find_library(LIBGFORTRAN_LIBRARIES NAMES gfortran libgfortran
HINTS ${GFORTRAN_LIBRARIES_DIR})
find_library(LIBQUADMATH_LIBRARIES NAMES quadmath libquadmath
HINTS ${GFORTRAN_LIBRARIES_DIR})
find_library(LIBGOMP_LIBRARIES NAMES gomp libgomp
HINTS ${GFORTRAN_LIBRARIES_DIR})
# Find OpenMP headers
find_path(LIBGOMP_INCLUDE_DIR NAMES omp.h HINTS ${GFORTRAN_INCLUDE_DIR})
else()
message(STATUS "CMAKE_Fortran_COMPILER_ID does not match 'GNU'!")
endif()
include(FindPackageHandleStandardArgs)
# Required: libgfortran, libquadmath, path for gfortran libraries
# Optional: libgomp, path for OpenMP headers, path for gcc/gfortran headers
find_package_handle_standard_args(GFortranLibs
REQUIRED_VARS LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES GFORTRAN_LIBRARIES_DIR
VERSION_VAR GFORTRAN_VERSION_STRING)
if(GFORTRANLIBS_FOUND)
message(STATUS "Looking for gfortran libraries -- found")
message(STATUS "gfortran version: ${GFORTRAN_VERSION_STRING}")
else()
message(STATUS "Looking for gfortran libraries -- not found")
endif()
mark_as_advanced(LIBGFORTRAN_LIBRARIES LIBQUADMATH_LIBRARIES
LIBGOMP_LIBRARIES LIBGOMP_INCLUDE_DIR
GFORTRAN_LIBRARIES_DIR GFORTRAN_INCLUDE_DIR)
# FindGFortranLIBS.cmake ends here

24
CMakeModules/FindWcsLib.cmake
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@ -32,20 +32,28 @@
# WCSLIB_LIBRARIES - the WCSLIB libraries # WCSLIB_LIBRARIES - the WCSLIB libraries
# (identical to WCSLIB_LIBRARY) # (identical to WCSLIB_LIBRARY)
# find paths
if(NOT WCSLIB_FOUND) if(NOT WCSLIB_FOUND)
find_path(WCSLIB_INCLUDE_DIR wcslib/wcs.h if (NOT "$ENV{WCSLIB_ROOT_DIR}" STREQUAL "")
HINTS ${WCSLIB_ROOT_DIR} PATH_SUFFIXES include) set(WCSLIB_ROOT "$ENV{WCSLIB_ROOT_DIR}" CACHE INTERNAL "Got from environment variable")
find_library(WCSLIB_LIBRARY wcs endif()
HINTS ${WCSLIB_ROOT_DIR} PATH_SUFFIXES lib)
find_path(WCSLIB_INCLUDE wcslib/wcs.h
HINTS ${WCSLIB_ROOT} PATH_SUFFIXES include)
find_library(WCSLIB_LIB wcs
HINTS ${WCSLIB_ROOT} PATH_SUFFIXES lib)
find_library(M_LIBRARY m) find_library(M_LIBRARY m)
mark_as_advanced(WCSLIB_INCLUDE_DIR WCSLIB_LIBRARY M_LIBRARY) mark_as_advanced(WCSLIB_INCLUDE WCSLIB_LIB M_LIBRARY)
include(FindPackageHandleStandardArgs) include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(WCSLIB DEFAULT_MSG find_package_handle_standard_args(WCSLIB DEFAULT_MSG
WCSLIB_LIBRARY M_LIBRARY WCSLIB_INCLUDE_DIR) WCSLIB_LIB M_LIBRARY WCSLIB_INCLUDE)
set(WCSLIB_INCLUDE_DIRS ${WCSLIB_INCLUDE_DIR}) set(WCSLIB_INCLUDE_DIRS ${WCSLIB_INCLUDE})
set(WCSLIB_LIBRARIES ${WCSLIB_LIBRARY} ${M_LIBRARY}) set(WCSLIB_LIBRARIES ${WCSLIB_LIB} ${M_LIBRARY})
set(WCSLIB_INCLUDE ${WCSLIB_INCLUDE})
set(WCSLIB_LIB ${WCSLIB_LIB} ${M_LIBRARY})
endif(NOT WCSLIB_FOUND) endif(NOT WCSLIB_FOUND)

92
CONTRIBUTING.md Normal file
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@ -0,0 +1,92 @@
# Contributing
When contributing to this repository, please first discuss the change you wish to make via issue,
email, or any other method with the owners of this repository before making a change.
Please note we have a code of conduct, please follow it in all your interactions with the project.
## Pull Request Process
1. Ensure any install or build dependencies are removed before the end of the layer when doing a
build.
2. Update the README.md with details of changes to the interface, this includes new environment
variables, exposed ports, useful file locations and container parameters.
3. Increase the version numbers in any examples files and the README.md to the new version that this
Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
do not have permission to do that, you may request the second reviewer to merge it for you.
## Code of Conduct
### Our Pledge
In the interest of fostering an open and welcoming environment, we as
contributors and maintainers pledge to making participation in our project and
our community a harassment-free experience for everyone, regardless of age, body
size, disability, ethnicity, gender identity and expression, level of experience,
nationality, personal appearance, race, religion, or sexual identity and
orientation.
### Our Standards
Examples of behavior that contributes to creating a positive environment
include:
* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting
### Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or
reject comments, commits, code, wiki edits, issues, and other contributions
that are not aligned to this Code of Conduct, or to ban temporarily or
permanently any contributor for other behaviors that they deem inappropriate,
threatening, offensive, or harmful.
### Scope
This Code of Conduct applies both within project spaces and in public spaces
when an individual is representing the project or its community. Examples of
representing a project or community include using an official project e-mail
address, posting via an official social media account, or acting as an appointed
representative at an online or offline event. Representation of a project may be
further defined and clarified by project maintainers.
### Enforcement
Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
complaints will be reviewed and investigated and will result in a response that
is deemed necessary and appropriate to the circumstances. The project team is
obligated to maintain confidentiality with regard to the reporter of an incident.
Further details of specific enforcement policies may be posted separately.
Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.
### Attribution
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at [http://contributor-covenant.org/version/1/4][version]
[homepage]: http://contributor-covenant.org
[version]: http://contributor-covenant.org/version/1/4/

1970
ChangeLog
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36
Docker/build_images.sh Executable file
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@ -0,0 +1,36 @@
#!/usr/bin/env bash
version=$(date +"%d%m%Y")
for folder in \
sl7-test \
ubuntu1604-test
do
name=${folder%%/}
echo
echo "==========================================="
echo "Building: "$name
echo "==========================================="
cmd="docker build -t fdiblen/$name:$version -t fdiblen/$name:latest ./$name"
echo
echo "Running:"
echo $cmd
echo
echo
eval $cmd
if [ $? -eq 0 ]
then
echo
echo "Successfully built the $name image!"
else
echo
echo "Could not build the $name image" >&2
exit $?
fi
#docker push fdiblen/$name:$version
#docker push fdiblen/$name:latest
done

42
Docker/sl7-test/Dockerfile Normal file
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@ -0,0 +1,42 @@
FROM scientificlinux/sl:7
MAINTAINER f.diblen@esciencecenter.nl
# add EPEL repository for openblas
RUN yum -y \
install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
# install dependencies
RUN yum -y install \
wget git pkgconfig make cmake3 cmake3-gui gcc-gfortran gcc-c++ flex bison \
openblas openblas-devel glib2-devel lapack lapack-devel cfitsio cfitsio-devel \
wcslib wcslib-devel ncurses ncurses-devel readline readline-devel \
python-devel boost boost-devel fftw fftw-devel hdf5 hdf5-devel \
numpy boost-python mpich mpich-devel fftw fftw-libs fftw-devel
RUN mkdir /build && cd /build
# compile casacore
RUN git clone --progress --verbose https://github.com/casacore/casacore.git casacore_src && \
cd casacore_src && \
mkdir build && cd build && \
cmake3 .. -DUSE_FFTW3=ON \
-DCMAKE_INSTALL_PREFIX=/opt/casacore \
-DDATA_DIR=/opt/casacore/data -DUSE_OPENMP=ON \
-DUSE_HDF5=ON \
-DBUILD_PYTHON=ON \
-DUSE_THREADS=ON && \
make -j4 && \
make install
## compile sagecal
#RUN cd /build && \
# mkdir build-sl && cd build-sl && \
# cmake3 .. -DCMAKE_INSTALL_PREFIX=/opt/sagecal \
# -DCASACORE_ROOT_DIR=/opt/casacore \
# -DCASACORE_INCLUDE=/opt/casacore/include/casacore
# make -j4 && \
# make install && \
#
#RUN ls -alsrt /opt/sagecal && \
# /opt/sagecal/bin/sagecal

28
Docker/ubuntu1604-test/Dockerfile Normal file
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@ -0,0 +1,28 @@
FROM ubuntu:xenial
MAINTAINER f.diblen@esciencecenter.nl
RUN apt-get update -y && \
apt-get install software-properties-common -y && \
add-apt-repository -s ppa:kernsuite/kern-3 -y && \
apt-add-repository multiverse && \
apt-get update -y
RUN apt-get install -y \
git cmake g++ pkg-config \
libcfitsio-bin libcfitsio-dev \
libopenblas-base libopenblas-dev \
wcslib-dev wcslib-tools \
libglib2.0-dev \
libcasa-casa2 casacore-dev casacore-data casacore-tools \
mpich \
fftw-dev libfftw3-mpi3 libfftw3-bin
## compile sagecal
#RUN mkdir /build && cd /build \
# mkdir build-ubuntu && cd build-ubuntu && \
# cmake .. -DCMAKE_INSTALL_PREFIX=/opt/sagecal && \
# make -j4 && \
# make install && \
# ls -alsrt /opt/sagecal && \
# /opt/sagecal/bin/sagecal

26
INSTALL.md
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@ -1,6 +1,32 @@
di 28 aug 2018 9:37:58 CEST di 28 aug 2018 9:37:58 CEST
# SAGECal Installation # SAGECal Installation
## das5
Load the modules below before compiling SageCal.
```
module load cmake/3.8.2
module load mpich/ge/gcc/64/3.2
module load gcc/4.9.3
module load casacore/2.3.0-gcc-4.9.3
module load wcslib/5.13-gcc-4.9.3
module load wcslib/5.16-gcc-4.9.3
module load cfitsio/3.410-gcc-4.9.3
```
checkout the source code and compile it with the instructions below(in source folder):
```
git clone https://github.com/nlesc-dirac/sagecal.git
cd sagecal && mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH
make
make install
```
$INSTALL_PATH is where you want to install SageCal.
## Cmake Build ## Cmake Build
### Requirements ### Requirements

339
LICENSE.md Normal file
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@ -0,0 +1,339 @@
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Lesser General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
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For example, if you distribute copies of such a program, whether
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you have. You must make sure that they, too, receive or can get the
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We protect your rights with two steps: (1) copyright the software, and
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Also, for each author's protection and ours, we want to make certain
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Finally, any free program is threatened constantly by software
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The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
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Whether that is true depends on what the Program does.
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You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
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These requirements apply to the modified work as a whole. If
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
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Copyright (C) <year> <name of author>
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it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.

8
README.md
View File

@ -4,9 +4,11 @@
| ------------- | ------------- | | ------------- | ------------- |
| [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=master)](https://travis-ci.org/nlesc-dirac/sagecal) | [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=dev)](https://travis-ci.org/nlesc-dirac/sagecal) | | [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=master)](https://travis-ci.org/nlesc-dirac/sagecal) | [![Build Status](https://travis-ci.org/nlesc-dirac/sagecal.svg?branch=dev)](https://travis-ci.org/nlesc-dirac/sagecal) |
[![Documentation](https://codedocs.xyz/nlesc-dirac/sagecal.svg)](https://codedocs.xyz/nlesc-dirac/sagecal/)
# SAGECAL # SAGECAL
## Features ## Features
- Levenberg-Marquardt, LBFGS, Riemannian Trust Region, Nesterov's accelerated gradient descent algorithms - Levenberg-Marquardt, LBFGS, Riemannian Trust Region, Nesterov's accelerated gradient descent algorithms
@ -23,6 +25,9 @@
Read INSTALL for installation. This file gives a brief guide to use SAGECal. Read INSTALL for installation. This file gives a brief guide to use SAGECal.
Warning: this file may be obsolete. use sagecal -h to see up-to-date options. Warning: this file may be obsolete. use sagecal -h to see up-to-date options.
## Code documentation
Code documentation can be found [here](https://codedocs.xyz/nlesc-dirac/sagecal).
## Step by Step Introduction: ## Step by Step Introduction:
@ -182,3 +187,6 @@ So for this cluster, there will be more than 1 column in the solution file, the
### Additional Info ### Additional Info
See [LOFAR Cookbook Chapter](https://support.astron.nl/LOFARImagingCookbook/sagecal.html). See [LOFAR Cookbook Chapter](https://support.astron.nl/LOFARImagingCookbook/sagecal.html).
Please cite this code using the DOI.
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1289316.svg)](https://doi.org/10.5281/zenodo.1289316)

56
build-tests/compile_sagecal.sh Executable file
View File

@ -0,0 +1,56 @@
#!/usr/bin/env bash
echo 'script: ' $0
echo "Building SageCal" && \
echo "Branch --> $BRANCH" && \
echo "Image --> $IMAGE"
BUILD_DIR=$IMAGE'-build'
cd /travis/workdir && \
mkdir $BUILD_DIR && cd $BUILD_DIR
CMAKE_EXE=''
OPTS=''
case $IMAGE in
ubuntu)
echo 'Building for Ubuntu'
CMAKE_EXE=$(which cmake)
OPTS=''
;;
sl7)
echo 'Building for Scientific Linux'
CMAKE_EXE=$(which cmake3)
OPTS='-DCASACORE_ROOT_DIR=/opt/casacore'
;;
arch)
OPTS=''
;;
*)
echo 'Unknown image $IMAGE!'
exit 1
;;
esac
echo 'CMAKE_EXE: ' $CMAKE_EXE
echo 'CMake options: ' $OPTS
echo 'pwd: ' $PWD
echo 'ls -asl: '
ls -asl
echo 'ls -asl /travis/workdir: '
ls -asl /travis/workdir
echo 'ls -asl /travis/workdir/$BUILD_DIR: '
ls -asl /travis/workdir/$BUILD_DIR
$CMAKE_EXE /travis/workdir -DCMAKE_INSTALL_PREFIX=/opt/sagecal $OPTS
make -j4 && \
make install && \
ls -alsrt /opt/sagecal && \
/opt/sagecal/bin/sagecal

3
src/MPI/CMakeLists.txt
View File

@ -18,7 +18,7 @@ add_executable(sagecal-mpi ${SRCFILES})
target_link_libraries(sagecal-mpi target_link_libraries(sagecal-mpi
${CASACORE_LIBRARIES} ${CASACORE_LIBRARIES}
${CFITSIO_LIBRARIES} ${CFITSIO_LIB}
${OpenBLAS_LIB} ${OpenBLAS_LIB}
${LAPACK_LIBRARIES} ${LAPACK_LIBRARIES}
${WCSLIB_LIBRARIES} ${WCSLIB_LIBRARIES}
@ -29,7 +29,6 @@ target_link_libraries(sagecal-mpi
-lopenblas -lopenblas
-lgfortran -lgfortran
-lpthread -lpthread
-lcfitsio
-lm -lm
-ldirac -ldirac
-lradio -lradio

1
src/MPI/data.cpp
View File

@ -1 +0,0 @@
../MS/data.cpp

1166
src/MPI/data.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

1
src/MPI/data.h
View File

@ -1 +0,0 @@
../MS/data.h

174
src/MPI/data.h Normal file
View File

@ -0,0 +1,174 @@
/*
*
Copyright (C) 2006-2008 Sarod Yatawatta <sarod@users.sf.net>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
$Id$
*/
#ifndef __DATA_H__
#define __DATA_H__
#include <unistd.h>
#include <stdio.h>
#include <iostream>
#include <casacore/ms/MeasurementSets/MSIter.h>
#include <casacore/tables/Tables/Table.h>
#include <casacore/tables/Tables/TableVector.h>
#include <casacore/tables/Tables/TableRecord.h>
#include <casacore/tables/Tables/TableColumn.h>
#include <casacore/tables/Tables/TableIter.h>
#include <casacore/tables/Tables/ScalarColumn.h>
#include <casacore/tables/Tables/ArrayColumn.h>
#include <casacore/casa/Arrays/Array.h>
#include <casacore/casa/Arrays/Cube.h>
#include <fstream>
#include <math.h>
#include <complex>
using namespace casacore;
namespace Data
{
struct IOData {
int N; /* no of stations */
int Nbase; /* baselines, exclude autocorrelations */
int tilesz;
int Nchan; /* total no of channels */
int Nms; /* no. of MS */
int *NchanMS; /* total channels per MS : Nms x 1 vector */
double deltat; /* integration time (s) */
int totalt; /* total no of time slots */
double ra0; /* phase center */
double dec0; /* phase center */
double *u; /* uvw coords, size Nbase*tilesz x 1 */
double *v;
double *w;
double *x; /* averaged data, size Nbase*8*tilez x 1
ordered by XX(re,im),XY(re,im),YX(re,im),YY(re,im), baseline, timeslots */
double *xo; /* unaveraged data, size Nbase*8*tilesz*Nchan x 1
ordered by XX(re,im),XY(re,im),YX(re,im),YY(re,im), baseline, timeslots, channel */
double *freqs; /* channel freqs, size Nchan x 1 */
double freq0; /* averaged freq */
double *flag; /* double for conforming with old routines size Nbase*tilesz x 1 */
double deltaf; /* total bandwidth for freq. smearing */
double fratio; /* flagged data ratio = flagged/total, not counting data excluded from uv cut */
/* if 1, all usable data are flagged */
};
/* Station beam info */
struct LBeam {
double *time_utc; /* time coord UTC (s), size tileszx1,
convert from MJD (s) to JD (days) */
int *Nelem; /* no of elements in each station, size Nx1 */
/* position (ITRF) of stations (m)
later changed to logitude,latitude,height (rad,rad,m) */
double *sx; /* x: size Nx1 */
double *sy; /* y: ... */
double *sz; /* z: ... */
/* x,y,z coords of elements, projected, converted to ITRF (m) */
double **xx; /* x coord pointer, size Nx1, each *x: x coord of station, size Nelem[]x1 */
double **yy; /* y ... */
double **zz; /* z ... */
/* pointing center of beams (only one) (could be different from phase center) */
double p_ra0;
double p_dec0;
};
/* read Auxilliary info and setup memory */
void readAuxData(const char *fname, IOData *data);
void readAuxData(const char *fname, IOData *data, LBeam *binfo);
void readAuxDataList(vector<string> msnames, IOData *data);
void readMSlist(char *fname, vector<string> *msnames);
/* load data using MS Iterator */
void loadData(Table t, IOData iodata, double *fratio);
void loadData(Table t, IOData iodata, LBeam binfo, double *fratio);
void loadDataList(vector<MSIter*> msitr, Data::IOData iodata, double *fratio);
/* write back data using MS Iterator */
void writeData(Table t, IOData iodata);
void writeDataList(vector<MSIter*> msitr, IOData iodata);
void freeData(IOData data);
void freeData(IOData data, LBeam binfo);
extern int numChannels;
extern unsigned long int numRows;
struct float2 {
float x,y;
};
extern char *TableName; /* MS name */
extern char *MSlist; /* text file with MS names */
extern char *MSpattern; /* pattern to match all MS names used in calibration */
extern float min_uvcut;
extern float max_uvcut;
extern float max_uvtaper;
extern casacore::String DataField; /* input column DATA/CORRECTED_DATA */
extern casacore::String OutField; /* output column DATA/CORRECTED_DATA */
extern int TileSize; //Tile size
extern int Nt; /* no of worker threads */
extern char *SkyModel; /* sky model file */
extern char *Clusters; /* cluster file */
extern int format; /* sky model format 0: LSM, 1: LSM with 3 order spec idx*/
/* sagecal paramters */
extern int max_emiter;
extern int max_iter;
extern int max_lbfgs;
extern int lbfgs_m;
extern int gpu_threads;
extern int linsolv;
extern int solver_mode;
extern int ccid;
extern double rho;
extern char *solfile;
extern char *initsolfile;
extern char *ignorefile;
extern double nulow,nuhigh;
extern int randomize;
extern int whiten;
extern int DoSim; /* if 1, simulation mode */
extern int doChan; /* if 1, solve for each channel in multi channel data */
extern int doBeam; /* if 1, predict (LOFAR) beam array factor */
extern int DoDiag; /* if >0, enables diagnostics (Leverage) 1: write leverage as output (no residual), 2: only calculate fractions of leverage/noise */
extern int phaseOnly; /* if >0, and if any correction is done, extract phase and do phase only correction */
/* distributed sagecal parameters */
extern int Nadmm; /* ADMM iterations >=1 */
extern int Npoly; /* polynomial order >=1 */
extern int PolyType; /* what kind on polynomials to use 0,1,2,3 */
extern double admm_rho; /* regularization */
extern char *admm_rho_file; /* text file for regularization of each cluster */
extern int aadmm; /* if >0, enable adaptive update of rho */
/* for debugging, upper limit on time slots */
extern int Nmaxtime;
/* skipping initial timeslots */
extern int Nskip;
extern int verbose; /* if >0, enable verbose output */
extern int mdl; /* if given, calculate AIC/MDL for different poly configs and find minimum */
extern int GPUpredict; /* if given, use GPU for model calculation */
extern int heapsize; /* heap size in GPU (MB), for using malloc() */
/* for client server mode */
extern int servermode; /* 0: client, 1: server, else default operation */
extern char *servername; /* server host name or ip address */
extern char *portnumber; /* which port number to use for communication */
}
#endif //__DATA_H__

3
src/MS/CMakeLists.txt
View File

@ -23,7 +23,7 @@ add_executable(sagecal ${SRCFILES})
target_link_libraries(sagecal target_link_libraries(sagecal
${CASACORE_LIBRARIES} ${CASACORE_LIBRARIES}
${CFITSIO_LIBRARIES} ${CFITSIO_LIB}
${OpenBLAS_LIB} ${OpenBLAS_LIB}
${LAPACK_LIBRARIES} ${LAPACK_LIBRARIES}
${WCSLIB_LIBRARIES} ${WCSLIB_LIBRARIES}
@ -32,7 +32,6 @@ target_link_libraries(sagecal
-lopenblas -lopenblas
-lgfortran -lgfortran
-lpthread -lpthread
-lcfitsio
-lm -lm
-ldirac -ldirac
-lradio -lradio

6
src/buildsky/CMakeLists.txt
View File

@ -1,5 +1,6 @@
find_package(WcsLib REQUIRED) find_package(WcsLib REQUIRED)
include_directories(${WCSLIB_INCLUDE_DIR}/wcslib) include_directories(${WCSLIB_INCLUDE_DIRS}/wcslib)
include_directories(${WCSLIB_INCLUDE_DIRS})
include_directories(./) include_directories(./)
link_directories(${LIBRARY_OUTPUT_PATH}) link_directories(${LIBRARY_OUTPUT_PATH})
@ -8,7 +9,7 @@ FILE(GLOB SRCFILES *.c)
add_executable(buildsky ${SRCFILES}) add_executable(buildsky ${SRCFILES})
target_link_libraries(buildsky target_link_libraries(buildsky
${CFITSIO_LIBRARIES} ${CFITSIO_LIB}
${OpenBLAS_LIB} ${OpenBLAS_LIB}
${LAPACK_LIBRARIES} ${LAPACK_LIBRARIES}
${WCSLIB_LIBRARIES} ${WCSLIB_LIBRARIES}
@ -17,7 +18,6 @@ target_link_libraries(buildsky
-lopenblas -lopenblas
-lgfortran -lgfortran
-lpthread -lpthread
-lcfitsio
-lm -lm
) )

3
src/lib/Dirac/lbfgs.c
View File

@ -423,7 +423,8 @@ cubic_interp(
} }
} }
return 0; /* fallback value */
return (a+b)*0.5;
} }

4
src/lib/Dirac/lbfgs_nocuda.c
View File

@ -187,8 +187,8 @@ cubic_interp(
return b; return b;
} }
} }
/* fallback value */
return 0; return (a+b)*0.5;
} }

6
src/restore/CMakeLists.txt
View File

@ -1,6 +1,7 @@
find_package(WcsLib REQUIRED) find_package(WcsLib REQUIRED)
find_package(FFTW REQUIRED) find_package(FFTW REQUIRED)
include_directories(${WCSLIB_INCLUDE_DIR}/wcslib) include_directories(${WCSLIB_INCLUDE_DIRS}/wcslib)
include_directories(${WCSLIB_INCLUDE_DIRS})
include_directories(./) include_directories(./)
link_directories(${LIBRARY_OUTPUT_PATH}) link_directories(${LIBRARY_OUTPUT_PATH})
@ -9,7 +10,7 @@ FILE(GLOB SRCFILES *.c)
add_executable(restore ${SRCFILES}) add_executable(restore ${SRCFILES})
target_link_libraries(restore target_link_libraries(restore
${CFITSIO_LIBRARIES} ${CFITSIO_LIB}
${OpenBLAS_LIB} ${OpenBLAS_LIB}
${LAPACK_LIBRARIES} ${LAPACK_LIBRARIES}
${WCSLIB_LIBRARIES} ${WCSLIB_LIBRARIES}
@ -20,7 +21,6 @@ target_link_libraries(restore
-lopenblas -lopenblas
-lgfortran -lgfortran
-lpthread -lpthread
-lcfitsio
-lm -lm
) )

11
test-builds/test-ubuntu.sh
View File

@ -1,11 +0,0 @@
#!/bin/bash
echo "Building SageCal" && \
echo "Branch --> $BRANCH" && \
cd /travis/workdir && \
mkdir build && cd build && \
cmake .. -DENABLE_CUDA=OFF && \
make -j4 && \
ls -alsrt ./dist/bin && \
./dist/bin/sagecal

29
test/Change_freq.py Executable file
View File

@ -0,0 +1,29 @@
#!/usr/bin/env python
from pyrap.tables import *
# You can use this script to create different MS data files by copying a single MS
# into MS with different names and changing their frequencies to unique values
# change freq
def read_corr(msname,freq):
import os
import math
tf=table(msname+'/SPECTRAL_WINDOW',readonly=False)
ch0=tf.getcol('CHAN_FREQ')
ch0[0,0]=freq
reffreq=tf.getcol('REF_FREQUENCY')
reffreq[0]=ch0[0,0]
tf.putcol('CHAN_FREQ',ch0)
tf.putcol('REF_FREQUENCY',reffreq)
tf.close()
if __name__ == '__main__':
# args MS
import sys
argc=len(sys.argv)
if argc==3:
read_corr(sys.argv[1],float(sys.argv[2]))
else:
print("thisscript MS frequency")
exit()

5
test/dosage-mpi.sh Executable file
View File

@ -0,0 +1,5 @@
# Before running this, make sure you have at least 2 data files with names matching the pattern '*.ms'
# This command assumes sagecal-mpi binary is at ../src/MPI/sagecal-mpi
# 'regularization_factors.txt' should exactly match the cluster info given by '3c196.sky.txt.cluster'
mpirun -np 3 ../src/MPI/sagecal-mpi -f '*.ms' -A 10 -P 2 -Q 2 -G regularization_factors.txt -s 3c196.sky.txt -c 3c196.sky.txt.cluster -p zsol -n 2 -t 10 -e 4 -g 2 -l 10 -m 7 -x 30 -F 1 -j 5 -B 1 -k 1 -K 3 -W 0 -V > sagecal-mpi.ms.output

1
test/dosage.sh
View File

@ -1,2 +1,3 @@
# Before running this, untar sm.ms.tar and build sagecal # Before running this, untar sm.ms.tar and build sagecal
# this command assumes sagecal binary is at ../src/MS/sagecal
../src/MS/sagecal -d sm.ms -s extended_source_list.txt -c extended_source_list.txt.cluster -n 4 -t 10 -p sm.ms.solutions -e 4 -g 2 -l 10 -m 7 -x 30 -F 1 -j 2 -k -1 -B 1 -W 0 > sm.ms.output ../src/MS/sagecal -d sm.ms -s extended_source_list.txt -c extended_source_list.txt.cluster -n 4 -t 10 -p sm.ms.solutions -e 4 -g 2 -l 10 -m 7 -x 30 -F 1 -j 2 -k -1 -B 1 -W 0 > sm.ms.output

6
test/regularization_factors.txt Normal file
View File

@ -0,0 +1,6 @@
# format
# cluster_id hybrid admm_rho
-1 2 4
2 1 2
# end