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initial empty project
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‎.gitattributes

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*.nc filter=lfs diff=lfs merge=lfs -text
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*.nc4 filter=lfs diff=lfs merge=lfs -text

‎.github/Dockerfile

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FROM jcsda/docker-gnu-openmpi-dev:latest
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RUN groupadd jcsda -g 9999 \
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&& adduser jcsdauser \
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&& mkdir -p /jcsda \
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&& chown -R jcsdauser:jcsda /jcsda \
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&& chmod 6755 /jcsda
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USER jcsdauser
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COPY default-mca-params.conf /jcsda/mca-params.conf
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RUN mkdir -p ~/.openmpi \
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&& cp /jcsda/mca-params.conf ~/.openmpi/
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CMD ["/bin/bash"]

‎.github/default-mca-params.conf

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btl=tcp,self
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plm_rsh_no_tree_spawn=1
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btl_base_warn_component_unused=0
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pml=ob1
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rmaps_base_oversubscribe = 1

‎.gitignore

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*~

‎.travis.yml

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language: cpp
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services:
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- docker
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branches:
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only:
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- develop
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- master
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- "/.*/travisci_.*$/"
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before_install:
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- |
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# prepare build directory
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mkdir $HOME/build1
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chmod 777 -R $HOME/build1
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chmod 777 -R $TRAVIS_BUILD_DIR
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- |
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# prepare docker image
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cd .github
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docker build -t jcsda/dockerl2 .
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docker images
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docker run -d -t -e CI_USER_TOKEN \
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-v $HOME/build1:/jcsda/build \
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-v $TRAVIS_BUILD_DIR:/jcsda/src \
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--name jcsda_container jcsda/dockerl2
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docker ps -a
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docker exec jcsda_container bash \
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-c 'git config --global url.https://${CI_USER_TOKEN}@github.com/.insteadOf https://github.com/'
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script:
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- |
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# build/test code
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docker exec jcsda_container bash \
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-c 'cd /jcsda/build && ecbuild /jcsda/src/bundle && cd oisst && make -j 4'
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docker exec jcsda_container bash \
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-c 'cd /jcsda/build/oisst && ctest'
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after_success:

‎CMakeLists.txt

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# (C) Copyright 2019-2019 UCAR.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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################################################################################
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# OISST
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################################################################################
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cmake_minimum_required( VERSION 3.8 FATAL_ERROR )
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project( oisst C CXX Fortran)
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set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH})
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set( ENABLE_OS_TESTS OFF CACHE BOOL "Disable OS tests" FORCE )
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set( ENABLE_LARGE_FILE_SUPPORT OFF CACHE BOOL "Disable testing of large file support" FORCE )
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set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
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include( ecbuild_system NO_POLICY_SCOPE )
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ecbuild_requires_macro_version( 2.5 )
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################################################################################
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# Project
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################################################################################
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ecbuild_declare_project()
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ecbuild_enable_fortran( REQUIRED )
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ecbuild_add_cxx11_flags()
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set( OISST_LINKER_LANGUAGE CXX )
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################################################################################
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# Dependencies
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################################################################################
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# Boost Headers
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set( Boost_MINIMUM_VERSION "1.47" )
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include_directories( ${Boost_INCLUDE_DIR} )
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# NetCDF
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find_package( NetCDF REQUIRED COMPONENTS Fortran )
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include_directories( ${NETCDF_INCLUDE_DIRS} )
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# eckit
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ecbuild_use_package( PROJECT eckit VERSION 1.1.0 REQUIRED )
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include_directories( ${ECKIT_INCLUDE_DIRS} )
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link_libraries( ${ECKIT_LIBRARIES} )
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# fckit
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ecbuild_use_package( PROJECT fckit VERSION 0.4.1 REQUIRED )
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include_directories( ${FCKIT_INCLUDE_DIRS} )
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# atlas
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ecbuild_use_package( PROJECT atlas VERSION 0.18.1 REQUIRED )
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include_directories( ${ATLAS_INCLUDE_DIRS} )
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# oops
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ecbuild_use_package( PROJECT oops VERSION 0.1.0 REQUIRED )
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include_directories( ${OOPS_INCLUDE_DIRS} )
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add_definitions(-DATLASIFIED=1)
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# saber
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ecbuild_use_package( PROJECT saber VERSION 0.0.1 REQUIRED )
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include_directories( ${SABER_INCLUDE_DIRS} )
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# ioda
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ecbuild_use_package( PROJECT ioda VERSION 0.1.0 REQUIRED )
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include_directories( ${IODA_INCLUDE_DIRS} )
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# ufo
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ecbuild_use_package( PROJECT ufo VERSION 0.1.0 REQUIRED )
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include_directories( ${UFO_INCLUDE_DIRS} )
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# MPI
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ecbuild_find_mpi( COMPONENTS CXX Fortran REQUIRED )
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ecbuild_include_mpi()
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link_libraries(${MPI_CXX_LIBRARIES} ${MPI_Fortran_LIBRARIES})
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################################################################################
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# Export package info
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################################################################################
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list( APPEND OISST_TPLS atlas atlas_f LAPACK MPI NetCDF )
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set( OISST_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src
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${CMAKE_CURRENT_BINARY_DIR}/src
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${CMAKE_Fortran_MODULE_DIRECTORY} )
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set( OISST_LIBRARIES oisst )
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get_directory_property( OISST_DEFINITIONS COMPILE_DEFINITIONS )
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foreach( _tpl ${OISST_TPLS} )
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string( TOUPPER ${_tpl} TPL )
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list( APPEND OISST_EXTRA_DEFINITIONS ${${TPL}_DEFINITIONS} ${${TPL}_TPL_DEFINITIONS} )
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list( APPEND OISST_EXTRA_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS} ${${TPL}_TPL_INCLUDE_DIRS} )
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list( APPEND OISST_EXTRA_LIBRARIES ${${TPL}_LIBRARIES} ${${TPL}_TPL_LIBRARIES} )
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endforeach()
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################################################################################
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# Sources
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################################################################################
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include( oisst_compiler_flags )
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include_directories( ${OISST_INCLUDE_DIRS} ${OISST_EXTRA_INCLUDE_DIRS} )
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add_subdirectory( src )
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add_subdirectory( test )
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if(ECBUILD_INSTALL_FORTRAN_MODULES)
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install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR} DESTINATION ${INSTALL_INCLUDE_DIR} )
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endif()
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################################################################################
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# Finalise configuration
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################################################################################
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# prepares a tar.gz of the sources and/or binaries
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ecbuild_install_project( NAME oisst )
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# print the summary of the configuration
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ecbuild_print_summary()

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