General overhaul of the build and test system

Jenkinsfile

@@ -1,39 +1,56 @@
-def PROJECT_NAME=JOB_NAME.split("\\s|/")[2].toLowerCase()
-
 pipeline {
-    agent { 
-        docker {
-            image "fluidity/baseimages:${PROJECT_NAME}"
-            label 'azure-linux-8core'
-        } 
-    }
+    agent none
     environment {
         MPLBACKEND = 'PS'
         OMPI_MCA_btl = '^openib'
     }
     stages {
-        stage('Configuring') {   
-            steps { 
-                slackSend "Build started - ${env.JOB_NAME} ${env.BUILD_NUMBER} (<${env.BUILD_URL}|Open>)"
-                sh './configure --enable-2d-adaptivity' 
-            }
-        }    
-        stage('Building') {       
-            steps { 
-                sh 'make -j' ;
-                sh 'make -j fltools' ;
-                sh 'make manual'
-            }
-        }
-        stage('Testing') {       
-            steps { 
-                sh 'make unittest' ;
-                sh 'make THREADS=8 test' ;
-                sh 'make THREADS=8 mediumtest'
-                junit 'tests/test_result*xml'
-            }
-        }
-    }
+        stage('Testing') {
+            parallel {
+                // For each combination of parameters required, build and test
+                stage('Build and test xenial autoconf container') {
+                     agent { 
+                        docker {
+                           image "fluidity/baseimages:xenial"
+                           label 'dockerhost'
+                        }
+                     } 
+                     steps {
+                        slackSend "Build started - ${env.JOB_NAME} ${env.BUILD_NUMBER} (<${env.BUILD_URL}|Open>)"
+                        sh './configure --enable-2d-adaptivity' 
+                        sh 'make' ;
+                        sh 'make fltools' ;
+                        sh 'make manual'
+                        sh 'make unittest' ;
+                        sh 'make THREADS=8 shorttest' ;
+                        sh 'make THREADS=8 mediumtest'
+                        junit 'tests/test_result*xml'
+                     }
+                }
+                stage('Build and test xenial cmake container') {
+                     agent { 
+                        docker {
+                           image "fluidity/baseimages:xenial"
+                           label 'dockerhost'
+                        }
+                     } 
+                     environment {
+                        PETSc_DIR = '/usr/lib/petscdir/3.6.3/linux-gnu-c-opt/lib/petsc/conf'
+                     }
+                     steps {
+                        slackSend "Build started - ${env.JOB_NAME} ${env.BUILD_NUMBER} (<${env.BUILD_URL}|Open>)"
+                        sh 'cmake -D USE_LIBMBA=ON -DUSE_EXODUSII=ON .' 
+                        sh 'make' ;
+                        sh 'make fltools' ;
+                        sh 'make unittest' ;
+                        sh 'make THREADS=8 shorttest' ;
+                        sh 'find . -name test_results.xml' ;
+                        junit 'test_results.xml'
+                     }
+                }
+           }
+       }
+    }        
     post {
         aborted {
             slackSend(color: '#DEADED',

Makefile.in

@@ -62,11 +62,8 @@ CXXFLAGS= @CPPFLAGS@ @CXXFLAGS@ -I./include
 
 LINKER  = @LINKER@ @LDFLAGS@ $(CXXFLAGS)
 
-FLLINKER = @FLLINKER@ @LDFLAGS@ $(FCFLAGS)
-
 LIBS    = -L./lib -l$(FLUIDITY) @LIB_FEMDEM@ ./lib/libadaptivity.a \
-           ./lib/libvtkfortran.a @LIBSPATIALINDEX@  @SPUDLIB@ @FLIBJUDY@ \
-           @LIBS@ @BLAS_LIBS@
+           ./lib/libvtkfortran.a @LIBS@ @BLAS_LIBS@
 
 OBJS = $(shell find . -mindepth 2 -maxdepth 2 -name '*.c' -o -name '*.cpp' -o -name '*.[fF]' -o -name '*.F90' | grep -v ^./lib | xargs)
 MAKE = @MAKE@ -s
@@ -111,12 +108,7 @@ endif
 default: bin/$(FLUIDITY)
 
 sub_system: $(LIBMBA2D) $(LIBMBA3D) @LIB_FEMDEM@ \
-	lib/libadaptivity.a lib/libvtkfortran.a @LIBSPATIALINDEX@ \
-	@SPUDLIB@ @FLIBJUDY@ include/version.h
-
-@FLIBJUDY@:
-	@echo '    MKDIR lib'; mkdir -p lib
-	echo '    MAKE libjudy'; $(MAKE) -C libjudy > make.log && $(MAKE) -C libjudy install >> make.log
+	lib/libadaptivity.a lib/libvtkfortran.a include/version.h
 
 lib/libmba2d.a:
 	@echo '    MKDIR lib'; mkdir -p lib
@@ -134,18 +126,6 @@ lib/libvtkfortran.a:
 	@echo '    MKDIR lib'; mkdir -p lib
 	echo '    MAKE libvtkfortran'; $(MAKE) -C libvtkfortran 2>make.log 2>&1 && cp libvtkfortran/libvtkfortran.a lib/ && cp libvtkfortran/*.mod include/
 
-@LIBSPATIALINDEX@:
-	@echo '    MKDIR lib'; mkdir -p lib
-	echo '    MAKE libspatialindex'; $(MAKE) -C @SPATIALINDEXDIR@ && $(MAKE) -C @SPATIALINDEXDIR@ install >> make.log 2>&1
-
-@SPUDLIB@:
-	@echo '    MKDIR lib'; mkdir -p lib
-ifeq (@SPUD_ONLY@,yes)
-	echo '    MAKE libspud'; $(MAKE) -C libspud && $(MAKE) -C libspud install-libspud
-else
-	echo '    MAKE libspud'; $(MAKE) -C libspud &&  $(MAKE) -C libspud install-libspud && cd libspud/python && python setup.py build && cd ../.. && cp libspud/python/build/lib*/libspud.so python/
-endif
-
 libfemtools: sub_system
 	@echo '    MKDIR lib'; mkdir -p lib
 	@echo '    MAKE debug'
@@ -159,9 +139,7 @@ ifeq (@FEMDEM@,yes)
 	@$(MAKE) -C @FLFEMDEM_PATH@
 endif
 
-@SPUDHEADER@: @SPUDLIB@
-
-main.o: include/version.h @SPUDHEADER@
+main.o: include/version.h
 
 include/version.h: version-info
 	@bin/version-info $@
@@ -358,14 +336,6 @@ endif
 clean: clean-light clean-test python_clean clean-debian
 	@echo "    CLEAN libvtkfortran"
 	@cd libvtkfortran; $(MAKE) clean
-	@echo "    CLEAN libjudy"
-	@cd libjudy; $(MAKE) clean >> make.log 2>&1
-ifeq ($(abspath @SPUDLIB@),$(abspath lib/libspud.a))
-	@echo "    CLEAN libspud"
-	@cd libspud; $(MAKE) clean
-endif
-	@echo "    CLEAN libspatialindex"
-	@cd @SPATIALINDEXDIR@; $(MAKE) clean >> make.log
 	@echo "    CLEAN libmba2d"
 	@cd libmba2d; $(MAKE) clean
 	@echo "    CLEAN libmba3d"
@@ -402,10 +372,7 @@ distclean: clean
 	 test/mvrtree/.deps test/rtree/.deps test/tprtree/.deps         \
          make.log > /dev/null
 	@cd libadaptivity ; make distclean > /dev/null
-	@cd libjudy ; make distclean > /dev/null
 	@cd libvtkfortran ; make distclean > /dev/null
-	@cd libspud ; make distclean > /dev/null ; rm -rf		\
-	 libspud.so.0 libtool diamond/build python/build > /dev/null
 	@cd tools ; make distclean > /dev/null
 	@rm -fr `find ./ -name config.status` `find ./ -name		\
 	 config.log` share include/Judy.h include/Wm4Command.h		\
@@ -424,8 +391,6 @@ distclean: clean
 	 include/Wm4Tetrahedron3.h include/Wm4Triangle2.h		\
 	 include/Wm4Triangle3.h include/Wm4Vector2.h			\
 	 include/Wm4Vector3.h include/confdefs.h include/config.h	\
-	 include/spatialindex include/spud include/spud.h		\
-	 include/spud_enums.h include/tinystr.h include/tinyxml.h	\
 	 include/version.h include/vtk.h				\
 	 preprocessor/check_options.F90 \
 	 preprocessor/register_diagnostics.F90 python/setup.py >	\
@@ -434,20 +399,12 @@ distclean: clean
 	@find ./ \( -name make.log \) -exec rm -f {} \; > /dev/null
 	@rm -f Makefile > /dev/null
 
-test: serialtest
-
-serialtest: fltools bin/$(FLUIDITY)
+shorttest: fltools bin/$(FLUIDITY)
 	@cd tests; ../bin/testharness -x test_results.xml -l short $(EXCLUDE_TAGS) -n $(THREADS)
 
-mediumtest: fltools bin/$(FLUIDITY) manual spudtools
+mediumtest: fltools bin/$(FLUIDITY) manual
 	@cd tests; ../bin/testharness -x test_results_medium.xml -l medium $(EXCLUDE_TAGS) -n $(THREADS)
 
-.PHONY: spudtools
-
-spudtools:
-	@cd libspud ; $(MAKE) install-spudtools
-	@echo "    INSTALL spudtools"
-
 setuputs: 
 	@echo "SETUP tests"
 	@echo "    RMDIR bin/tests"
@@ -457,10 +414,6 @@ setuputs:
 	@ln -sf ../../tests/data bin/tests/data
 
 build_unittest: fluidity_library libfemtools setuputs
-ifeq (@SPUDLIB@,./lib/libspud.a)
-	@echo "    UNITTEST libspud"
-	@cd libspud/src/tests; $(MAKE) test-binaries; find bin/* -maxdepth 1 -type f -exec ln -sf ../../libspud/src/tests/{} ../../../bin/tests \;
-endif
 	@echo "    UNITTEST error_measures"
 	@cd error_measures/tests; $(MAKE) unittest
 	@echo "    UNITTEST horizontal_adaptivity"
@@ -479,13 +432,9 @@ unittest: build_unittest
 	@echo "RUN bin/tests"
 	@bin/unittestharness bin/tests
 
-bin/spud-preprocess:
-	@echo "Installing spudtools"
-	@$(MAKE) -C libspud install-spudtools
-
-schema: bin/spud-preprocess
+schema:
 	@echo "Rebuilding schema fluidity_options.rng"
-	@./bin/spud-preprocess schemas/fluidity_options.rnc
+	@spud-preprocess schemas/fluidity_options.rnc
 
 .PHONY: makefiles
 
@@ -540,7 +489,7 @@ endif
 install: default fltools 
 	@mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(docdir)/fluidity
 	find bin/ -maxdepth 1 -type f -exec cp '{}' $(DESTDIR)$(bindir) \;
-	rm -f $(DESTDIR)$(bindir)/spud-* $(DESTDIR)$(bindir)/diamond $(DESTDIR)$(bindir)/silenteval $(DESTDIR)$(bindir)/runut
+	rm -rf $(DESTDIR)$(bindir)/silenteval $(DESTDIR)$(bindir)/runut
 	[ -f manual/fluidity_manual.pdf ] && cp manual/fluidity_manual.pdf $(DESTDIR)$(docdir)/fluidity || true
 	mkdir -p $(DESTDIR)$(datadir)/fluidity
 	cp -R schemas $(DESTDIR)$(datadir)/fluidity/
@@ -552,16 +501,6 @@ install: default fltools
 	find $(DESTDIR)$(docdir)/fluidity/examples -type f -exec $(SED) -i "s/\.\.\/\.\.\/bin\///" '{}' \;
 	cd $(DESTDIR)$(docdir)/fluidity ; tar -czvf $(DESTDIR)$(docdir)/fluidity/examples.tar.gz examples/
 	rm -rf $(DESTDIR)$(docdir)/fluidity/examples/
-
-install-diamond: 
-	cd libspud; ./configure --prefix=@prefix@; cd ../..
-	cd libspud; $(MAKE) clean; cd ../..
-	cd libspud; $(MAKE) install-diamond; cd ../..
-	cd libspud; $(MAKE) install-dxdiff; cd ../..
-	cd libspud; $(MAKE) install-spudtools; cd ../..
-	cd libspud; ./configure --prefix=$(PWD); cd ../..
-
-install-user-schemata:
 	mkdir -p $(HOME)/.diamond/schemata/
 	echo "Fluidity Markup Language" > $(HOME)/.diamond/schemata/flml
 	echo "$(PWD)/schemas/fluidity_options.rng" >> $(HOME)/.diamond/schemata/flml

assemble/CMakeLists.txt

@@ -0,0 +1,6 @@
+file(GLOB lib_srcs RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.F90)
+add_library_sources(${lib_srcs})
+add_subdirectory(tests EXCLUDE_FROM_ALL)
+
+set(unittests ${assemble_unittests};${unittests} PARENT_SCOPE)
+set(unittest_meshes_3d ${assemble_unittest_meshes_3d};${unittest_meshes_3d} PARENT_SCOPE)

assemble/tests/CMakeLists.txt

@@ -0,0 +1,17 @@
+cmake_minimum_required(VERSION 2.6)
+enable_language (Fortran CXX)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/tests)
+
+file(GLOB tests RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.F90)
+list(REMOVE_ITEM tests test_mba_supermesh.F90 test_legacy_cv_faces.F90 test_lagrangian_remap.F90 test_adapt_mesh_mba3d.F90 test_pressure_solve.F90 test_matrix_free.F90 test_dg_interpolation_quads.F90 test_dg_diffusion.F90)
+foreach(unittest IN LISTS tests)
+   get_filename_component(test_name ${unittest} NAME_WE)
+   add_library(${test_name}_main OBJECT test_main.cpp)
+   set_target_properties(${test_name}_main PROPERTIES COMPILE_FLAGS -DTESTNAME=${test_name}_)
+   add_executable(${test_name} ${unittest} $<TARGET_OBJECTS:${test_name}_main>)
+   target_link_libraries(${test_name} fluidity ${FLUIDITY_PACKAGE_LIBS})
+   list(APPEND unittests ${test_name})
+endforeach()
+
+set(assemble_unittests ${unittests} PARENT_SCOPE)
+set(assemble_unittest_meshes_3d "cube_prismatic;cube_unstructured;" PARENT_SCOPE)

assemble/tests/Makefile.in

@@ -41,7 +41,7 @@ CXXFLAGS= @CPPFLAGS@ @CXXFLAGS@ -I../include -I../../include
 
 LDFLAGS  = @LDFLAGS@
 
-LIBS = ./lib/libadaptivity.a ./lib/libvtkfortran.a @LIBSPATIALINDEX@ @SPUDLIB@ @FLIBJUDY@ @LIBS@
+LIBS = ./lib/libadaptivity.a ./lib/libvtkfortran.a @LIBS@
 FLIBS = @FLIBS@
 LIBFLUIDITY=../../lib/lib$(FLUIDITY).a
 

bathymetry/CMakeLists.txt

@@ -0,0 +1 @@
+add_library_sources(NetCDF_reader.cpp SampleNetCDF2.cpp import_bath_data.cpp read_netcdf_interface.cpp)

bathymetry/Makefile.in

@@ -51,7 +51,7 @@ CXXFLAGS = -I../include @CXXFLAGS@ @CPPFLAGS@
 
 LDFLAGS   = @LDFLAGS@
 LIBS    = -L../lib -l$(FLUIDITY) @LIBS@ @BLAS_LIBS@ \
-		  ../lib/libvtkfortran.a @LIBSPATIALINDEX@ @SPUDLIB@ @FLIBJUDY@
+		  ../lib/libvtkfortran.a
 
 OBJS = NetCDF_reader.o SampleNetCDF2.o import_bath_data.o read_netcdf_interface.o
 

climatology/CMakeLists.txt

@@ -0,0 +1,2 @@
+add_executable(create_climatology_atlas EXCLUDE_FROM_ALL create_climatology_atlas.cpp)
+target_link_libraries(create_climatology_atlas fluidity vtkfortran ${spatialindex} adaptivity ${VTK_LIBRARIES} ${MPI_LIBRARIES} ${PETSC_PACKAGE_LIBS} ${PETSC_LIB} ${ZOLTAN_LIB} ${SPUD_LIB} ${JUDY_LIB} ${UDUNITS_LIB} ${MBA2D_LIBS} ${PYTHON_LIBRARIES})