initial empty project

.gitattributes

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

.github/Dockerfile

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

.github/default-mca-params.conf

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

.gitignore

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+*~

.travis.yml

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

CMakeLists.txt

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