Merge pull request #54 from kjetil-lye/master

New default for writing, defaulting for C++14

.travis.yml

@@ -8,8 +8,6 @@ matrix:
       addons:
         apt:
           sources:
-
-
           packages:
             - clang
       env:
@@ -52,12 +50,8 @@ matrix:
            COMPILER="CC=gcc-5 && CXX=g++-5" ALSVINN_BUILD_TYPE=Release BOOST_MAJOR_VERSION=1 BOOST_MINOR_VERSION=67 BOOST_RELEASE_VERSION=0 PNETCDF_VERSION=1.11.1 GTEST_VERSION=1.8.0
 
 
-
-
 before_install:
-  - eval ${COMPILER}
-  # cmake
-  - travis_retry sudo add-apt-repository -y ppa:andrew-fuller/cmake
+
 install:
   # https://stackoverflow.com/a/32127147 on how to set the compiler!
   - DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
@@ -66,7 +60,7 @@ install:
   - mkdir ${INSTALL_PREFIX}
   - travis_retry sudo apt-get update -qq
 
-  - sudo apt-get install -y make cmake git build-essential wget doxygen libomp-dev libopenmpi-dev m4 unzip  libcurl4-openssl-dev zlib1g-dev libhdf5-dev curl libnetcdf-dev libgtest-dev
+  - sudo apt-get install -y make git build-essential wget doxygen libomp-dev libopenmpi-dev m4 unzip  libcurl4-openssl-dev zlib1g-dev libhdf5-dev curl libnetcdf-dev libgtest-dev
 
   # Python 3.7
   - sudo add-apt-repository -y ppa:deadsnakes/ppa
@@ -75,6 +69,7 @@ install:
   - curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
   - sudo python3.7 get-pip.py
   - sudo pip3.7 install numpy gitpython dicttoxml scipy netcdf4 matplotlib
+  - sudo pip3.7 install --upgrade cmake
     #
     # Boost
   - cd $DEPS_DIR

CMakeLists.txt

@@ -19,13 +19,13 @@ ELSE()
 	ENDMACRO()
 ENDIF()
 
-project (alsvinn VERSION 0.5.0 LANGUAGES C CXX )
+project (alsvinn VERSION 0.5.1 LANGUAGES C CXX )
 SET(ALSVINN_USE_FLOAT OFF CACHE BOOL "Do all computations with 32 bits
 floating point numbers, instead of 64 bit double precision")
 SET(ALSVINN_USE_CUDA ON CACHE BOOL "Build with CUDA")
 
-set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CUDA_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CUDA_STANDARD 14)
 
 set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
 set(CMAKE_CUDA_STANDARD_REQUIRED TRUE)
@@ -106,6 +106,9 @@ endif()
 # the only way of specify initial data
 find_package(Python ${ALSVINN_PYTHON_VERSION} REQUIRED COMPONENTS Development)
 
+# We want to specify python versions, which the cmake filees from boost do not allow us to
+set(Boost_NO_BOOST_CMAKE ON)
+
 if(ALSVINN_USE_HUNTER_FOR_BOOST AND ALSVINN_USE_HUNTER)
    hunter_add_package(Boost COMPONENTS regex thread system filesystem chrono date_time program_options log python)
    find_package(Boost CONFIG REQUIRED filesystem thread system chrono date_time program_options log log_setup ${ALSVINN_BOOST_PYTHON} ${ALSVINN_BOOST_NUMPY})

alsfvm/src/config/SimulatorSetup.cpp

@@ -355,7 +355,7 @@ alsfvm::shared_ptr<io::Writer> SimulatorSetup::createWriter(
             real endTime = readEndTime(configuration);
             real timeInterval = endTime / numberOfSaves;
 
-            bool writeInitialTimestep = true;
+            bool writeInitialTimestep = false;
 
             if (writerNode.find("writeInitialTimestep") != writerNode.not_found()) {
                 writeInitialTimestep = writerNode.get<bool>("writeInitialTimestep");
@@ -477,8 +477,7 @@ void SimulatorSetup::readEquationParameters(const SimulatorSetup::ptree&
     }
 }
 
-alsfvm::shared_ptr<diffusion::DiffusionOperator>
-SimulatorSetup::createDiffusion(
+alsfvm::shared_ptr<diffusion::DiffusionOperator> SimulatorSetup::createDiffusion(
     const SimulatorSetup::ptree& configuration,
     const grid::Grid& grid,
     const simulator::SimulatorParameters& simulatorParameters,

alsuq/src/config/Setup.cpp

@@ -263,7 +263,7 @@ std::vector<std::shared_ptr<stats::Statistics> > Setup::createStatistics(
         if (statisticsNode.second.find("numberOfSaves") !=
             statisticsNode.second.not_found()) {
 
-            bool writeInitialTimestep = true;
+            bool writeInitialTimestep = false;
 
             if (statisticsNode.second.find("writeInitialTimestep") !=
                 statisticsNode.second.not_found()) {

documentation/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "Alsvinn"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.5.0
+PROJECT_NUMBER         = 0.5.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

library_examples/alsuq/generate_parameters/CMakeLists.txt

@@ -17,7 +17,7 @@ ELSE()
 	ENDMACRO()
 ENDIF()
 project (generate_parameters LANGUAGES C CXX)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 find_package(Alsvinn REQUIRED)
 add_executable(generate_parameters src/main.cpp)
 

library_examples/alsuq/only_statistics/CMakeLists.txt

@@ -17,7 +17,7 @@ ELSE()
 	ENDMACRO()
 ENDIF()
 project (structure_functions LANGUAGES C CXX)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 find_package(Alsvinn REQUIRED)
 add_executable(structure_functions src/main.cpp)
 

library_examples/alsuq/structure_standalone/CMakeLists.txt

@@ -17,7 +17,7 @@ ELSE()
 	ENDMACRO()
 ENDIF()
 project (structure_functions LANGUAGES C CXX)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 
 if (EXISTS "${CMAKE_SOURCE_DIR}/../../../cmake/git_find/GetGitRevisionDescription.cmake")
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/../../../cmake/git_find")

library_examples/dlls/writer/CMakeLists.txt

@@ -2,7 +2,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 3.10)
 PROJECT(dll_writer_example C CXX)
 include(GenerateExportHeader)
 find_package(MPI REQUIRED)
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 
 add_library(dll_writer_example SHARED src/dll_writer_example.cpp)
 target_compile_definitions(dll_writer_example PUBLIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX)

python/alsvinn/alsvinn.py

@@ -65,11 +65,13 @@ def remove_fvm_writer(self):
     def set_equation_parameters(self, parameters):
         self.fvmSettings["equationParameters"] = parameters
 
-    def set_fvm_writer(self, type, basename, number_of_saves):
+    def set_fvm_writer(self, type, basename, number_of_saves, write_initial_timestep):
         self.fvmSettings["writer"] = {}
         self.fvmSettings["writer"]["type"] = type
         self.fvmSettings["writer"]["basename"] = basename
         self.fvmSettings["writer"]["numberOfSaves"] = number_of_saves
+        self.fvmSettings["writer"]["writeInitialTimestep"] = int(write_initial_timestep)
+
 
     def set_cartesian_grid(self, lower_corner, upper_corner, dimensions):
         self.fvmSettings["grid"] = {"lowerCorner" : lower_corner,
@@ -362,13 +364,14 @@ def __readValues(self, output, document):
     def set_uq_value(self, key, value):
         self.uqSettings[key] = value
 
-    def add_statistics(self, statisticsName, writer, basename, numberOfSaves):
+    def add_statistics(self, statisticsName, writer, basename, numberOfSaves, writeInitialTimestep):
         if 'stats' not in self.uqSettings.keys():
             self.uqSettings['stats']  = []
         elif type(self.uqSettings['stats']) is not list:
             self.uqSettings['stats'] = [self.uqSettings['statistics']['stat']]
         self.uqSettings['stats'].append({'name' : statisticsName,
                                                 'numberOfSaves' : numberOfSaves,
+                                                "writeInitialTimestep" : int(writeInitialTimestep),
                                                 'writer':{
                                                     'type' : writer,
                                                     'basename' : basename
@@ -420,7 +423,8 @@ def run(name=None, equation=None,
         generator=None,
         diffusion_operator=None,
         diffusion_reconstruction=None,
-	functionals=None
+        functionals=None,
+        write_initial_timestep=True
         ):
 
     initial_data_file_is_temporary = False
@@ -516,7 +520,7 @@ def run(name=None, equation=None,
     if integrator is not None:
         alsvinn_object.set_fvm_value("integrator", integrator)
     if number_of_saves is not None:
-        alsvinn_object.set_fvm_writer("netcdf", name, number_of_saves)
+        alsvinn_object.set_fvm_writer("netcdf", name, number_of_saves, write_initial_timestep)
 
     if dimension is not None and upper_corner is not None and lower_corner is not None:
         alsvinn_object.set_cartesian_grid(lower_corner, upper_corner, dimension)
@@ -544,7 +548,7 @@ def run(name=None, equation=None,
             number_of_saves = 1
         alsvinn_object.set_uq_value('stats',[])
         for stat in statistics:
-            alsvinn_object.add_statistics(stat, 'netcdf', name, number_of_saves)
+            alsvinn_object.add_statistics(stat, 'netcdf', name, number_of_saves, write_initial_timestep)
     if functionals is not None:
         if number_of_saves is None:
             number_of_saves = 1

python/test/test_number_of_saves.py

@@ -11,8 +11,8 @@
     PLACES = 15
 
 def make_xml_content(pythonname, output_basename, number_of_saves, samples=1, without_initial=False, endTime=1.3):
-    if without_initial:
-        without_initial_string = '<writeInitialTimestep>false</writeInitialTimestep>'
+    if not without_initial:
+        without_initial_string = '<writeInitialTimestep>true</writeInitialTimestep>'
     else:
         without_initial_string = ''
     return f"""

python/test/test_text_cache.py

@@ -129,7 +129,7 @@ def test_cache(self):
             xmlname],
                        check=True)
 
-        for timestep in range(2):
+        for timestep in range(1):
             with netCDF4.Dataset(f"{output_basename}_{timestep}.nc") as f:
                 python_from_dataset = f.getncattr(python_key)
                 self.assertEqual(python_content, python_from_dataset)