Merge branch 'dev'

.gitignore

+*.l4n
+*.e*
+*.o*
 *.orig
 *.4n
 *.o

.gitlab-ci.yml

+# CI script for lib4neuro
+# _local: External dependencies are being downloaded directly into lib4neuro folder and compiled automatically
+# _manual: External dependencies' paths are specified via system variables
+# _system: External dependencies are located in system paths
+
+variables:
+    BUILD_LIB: 'yes'
+    BUILD_EXAMPLES: 'yes'
+    BUILD_TESTS: 'yes'
+    WIN_ARMADILLO_ROOT: 'C:\Users\suser\Desktop\lib4neuro_dependencies\armadillo'
+    WIN_BOOST_ROOT: 'C:\Users\suser\Desktop\lib4neuro_dependencies\boost'
+    WIN_EXPRTK_ROOT: 'C:\Users\suser\Desktop\lib4neuro_dependencies\exprtk'
+    WIN_TURTLE_ROOT: 'C:\Users\suser\Desktop\lib4neuro_dependencies\turtle'
+    clean_after: 'yes'
+
 stages:
     - build
 
-# Windows 10 with dependencies
-# downloaded (and compiled) locally
-# compiled by VisualStudio 2017
-win_visual_studio_static_local_deps:
-    tags:
-        - Win
-
-    image: windows:latest
+## Windows 10
+## Compiled by VisualStudio 2017
+#win_visual_studio_static_local:
+#
+#    only:
+#        refs:
+#            - master
+#            - CItest
+#
+#    tags:
+#        - Win
+#
+#    image: windows:latest
+#
+#    stage: build
+#
+#    variables:
+#        WIN_ARMADILLO_ROOT: ''
+#        WIN_BOOST_ROOT: ''
+#        WIN_EXPRTK_ROOT: ''
+#        WIN_TURTLE_ROOT: ''
+#        DEPENDENCIES_LINK_TYPE: 'static'
+#
+#    before_script:
+#        - 'call VsDevCmd.bat'
+#        - '"C:\Program Files (x86)\IntelSWTools\parallel_studio_xe_2019.5.068\bin\psxevars.bat" intel64 vs2017'
+#        - 'rmdir /s /q build external_dependencies\*'
+#
+#    script:
+#        - 'call build_scripts\windows\win_VS_build_x64_release.bat'
+#
+## Windows 10
+## Compiled by VisualStudio 2017
+#win_visual_studio_2017_static_manual:
+#    tags:
+#        - Win
+#
+#    image: windows:latest
+#
+#    stage: build
+#
+#    variables:
+#        DEPENDENCIES_LINK_TYPE: 'static'
+##        FC: 'C:\Program Files (x86)\IntelSWTools\parallel_studio_xe_2019.5.068\compilers_and_libraries_2019\windows\bin\intel64\ifort.exe'
+#
+#    before_script:
+#        - 'rmdir /s /q build external_dependencies\*'
+#        - 'call VsDevCmd.bat &&
+#           call "C:\Program Files (x86)\IntelSWTools\parallel_studio_xe_2019.5.068\bin\psxevars.bat" intel64 vs2017 &&
+#           copy /b NUL prep_success'
+#
+#    artifacts:
+#        paths:
+#            - 'prep_success'
+#        expire_in: 5 mins
+#
+#    script:
+#        - 'if not exist prep_success ( exit 1 )'
+#        - 'where cl'
+#        - 'where ifort'
+#        - 'echo %cd%'
+#        - 'echo %PATH%'
+#        - 'call build_scripts\windows\win_VS_build_x64_release.bat'
+#
+## Windows 10
+## Compiled by VisualStudio 2015
+#win_visual_studio_2015_static_local:
+#    only:
+#        refs:
+#            - master
+#            - CItest
+#
+#    tags:
+#        - Win
+#
+#    image: windows:latest
+#
+#    stage: build
+#
+#    variables:
+#        WIN_ARMADILLO_ROOT: ''
+#        WIN_BOOST_ROOT: ''
+#        WIN_EXPRTK_ROOT: ''
+#        WIN_TURTLE_ROOT: ''
+#        DEPENDENCIES_LINK_TYPE: 'static'
+#
+#    before_script:
+#        - 'call VsDevCmd.bat'
+#        - 'call "C:\Program Files (x86)\IntelSWTools\compilers_and_libraries_2019.5.281\windows\bin\ifortvars.bat" intel64 vs2015'
+#        - 'rmdir /s /q build external_dependencies\*'
+#
+#    script:
+#        - 'call build_scripts\windows\win_VS2015_build_x64_release.bat'
+#
+## Windows 10
+## Compiled by VisualStudio 2015
+#win_visual_studio_2015_static_manual:
+#    tags:
+#        - Win
+#
+#    image: windows:latest
+#
+#    stage: build
+#
+#    variables:
+#        DEPENDENCIES_LINK_TYPE: 'static'
+#
+#    before_script:
+#        - 'rmdir /s /q build external_dependencies\*'
+#        - 'call VsDevCmd.bat &&
+#           call "C:\Program Files (x86)\IntelSWTools\parallel_studio_xe_2019.5.068\bin\psxevars.bat" intel64 vs2015 &&
+#           copy /b NUL prep_success'
+#
+#    artifacts:
+#        paths:
+#            - 'prep_success'
+#        expire_in: 5 mins
+#
+#    script:
+#        - 'if not exist prep_success ( exit 1 )'
+#        - 'where cl'
+#        - 'where ifort'
+#        - 'echo %cd%'
+#        - 'echo %PATH%'
+#        - 'call build_scripts\windows\win_VS2015_build_x64_release.bat'
+
+# Latest Ubuntu
+ubuntu_shared_system:
+    image: martinbeseda/lib4neuro-ubuntu-system-deps:latest
 
     stage: build
 
-    before_script:
-        - rmdir /s /q build external_dependencies/*
-        - call VsDevCmd.bat
-        - set DEPENDENCIES_LINK_TYPE=static
-        - set clean_after=yes
-        - set BUILD_LIB=yes
-        - set BUILD_EXAMPLES=yes
-        - set BUILD_TESTS=yes
-
-    script:
-        - call build_scripts\windows\win_VS_build_x64_release.bat
-
-# Windows 10 with dependencies
-# downloaded (and compiled) locally
-# compiled by VisualStudio 2015
-win_visual_studio_2015_static_local_deps:
-    tags:
-        - Win
-
-    image: windows:latest
-
-    stage: build
+    variables:
+        WIN_ARMADILLO_ROOT: ''
+        WIN_BOOST_ROOT: ''
+        WIN_EXPRTK_ROOT: ''
+        WIN_TURTLE_ROOT: ''
+        DEPENDENCIES_LINK_TYPE: 'shared'
 
     before_script:
-        - rmdir /s /q build external_dependencies/*
-        - set DEPENDENCIES_LINK_TYPE=static
-        - set clean_after=yes
-        - set BUILD_LIB=yes
-        - set BUILD_EXAMPLES=yes
-        - set BUILD_TESTS=yes
+        - 'rm -rf build external_dependencies/*'
 
     script:
-        - call build_scripts\windows\win_VS2015_build_x64_release.bat
+        - 'build_scripts/linux/linux_gcc_build_x64_release_system.sh'
 
-# Latest Ubuntu with dependencies
-# in system directories, Boost
-# installed from the official repository
-ubuntu_boost_system:
-    image: martinbeseda/lib4neuro-ubuntu-system-deps:latest
-
-    stage: build
-
-    before_script:
-        - rm -rf build external_dependencies/*
-        - export TERM=xterm
-        - export DEPENDENCIES_LINK_TYPE=shared
-        - export CLEAN_AFTER=yes
-        - export BUILD_LIB=yes
-        - export BUILD_EXAMPLES=yes
-        - export BUILD_TESTS=yes
+# Latest Ubuntu
+ubuntu_static_local:
+    only:
+        refs:
+            - master
+            - CItest
 
-    script:
-        - build_scripts/linux/linux_gcc_build_x64_debug_system.sh
-
-# Latest Ubuntu with dependencies
-# downloaded (and compiled) locally
-ubuntu_boost_local_static_deps:
     image: martinbeseda/ubuntu-ci:latest
 
     stage: build
 
+    variables:
+        WIN_ARMADILLO_ROOT: ''
+        WIN_BOOST_ROOT: ''
+        WIN_EXPRTK_ROOT: ''
+        WIN_TURTLE_ROOT: ''
+        DEPENDENCIES_LINK_TYPE: 'static'
+
     before_script:
-        - rm -rf build external_dependencies/*
-        - export TERM=xterm
-        - export DEPENDENCIES_LINK_TYPE=static
-        - export CLEAN_AFTER=yes
-        - export BUILD_LIB=yes
-        - export BUILD_EXAMPLES=yes
-        - export BUILD_TESTS=yes
+        - 'rm -rf build external_dependencies/*'
 
     script:
-        - build_scripts/linux/linux_gcc_build_x64_debug_local.sh
+        - 'build_scripts/linux/linux_gcc_build_x64_release_local.sh'
+
+# Latest CentOS
+centos_static_local:
+    only:
+        refs:
+            - master
+            - CItest
 
-# Latest CentOS with dependencies
-# downloaded (and compiled) locally
-centos_local_deps:
     image: martinbeseda/centos-ci:latest
 
     stage: build
 
+    variables:
+        WIN_ARMADILLO_ROOT: ''
+        WIN_BOOST_ROOT: ''
+        WIN_EXPRTK_ROOT: ''
+        WIN_TURTLE_ROOT: ''
+        DEPENDENCIES_LINK_TYPE: 'static'
+
     before_script:
-        - rm -rf build external_dependencies/*
-        - export TERM=xterm
-        - export DEPENDENCIES_LINK_TYPE=static
-        - export CLEAN_AFTER=yes
-        - export BUILD_LIB=yes
-        - export BUILD_EXAMPLES=yes
-        - export BUILD_TESTS=yes
+        - 'rm -rf build external_dependencies/*'
 
     script:
-        - scl enable devtoolset-8 -- build_scripts/linux/linux_gcc_build_x64_debug_local.sh
+        - 'build_scripts/linux/linux_gcc_build_x64_release_local.sh'

build.sh

@@ -5,5 +5,5 @@ export CLEAN_AFTER=no
 rm -f build/CMakeCache.txt
 
 export DEPENDENCIES_LINK_TYPE=static
-build_scripts/linux/linux_gcc_build_x64_debug_local.sh
+build_scripts/linux/linux_gcc_build_x64_release_local.sh
 cd ../..

build_docs.sh

@@ -2,7 +2,7 @@
 
 echo "Generating documentation into folder 'docs'...";
 doxygen 2>&1;
-cd docs/latex;
+cd docs/latex || exit 1;
 echo "Building LaTeX documentation../";
 make >/dev/null && echo "Documentation was built." || exit -1;
 cd ../..;

build_scripts/compile_salomon.sh

+#!/usr/bin/bash
+
+current_dir=$(pwd)
+script_dir=$(dirname $0)
+
+if [ $script_dir = '.' ]
+then
+    script_dir="$current_dir"
+fi
+
+source ${script_dir}/load_salomon_modules.inc
+
+#./clean.sh
+
+$(pwd)/build.sh

build_scripts/linux/linux_gcc_build_x64_debug_gprof_system.sh

+#!/bin/sh
+
+clear
+
+export BOOST_ROOT=${PWD}../../external_dependencies/boost
+export LIB4NEURO_INCLUDE_DIR=${PWD}/../../include
+
+
+# Should we build the examples? (yes/no)
+BUILD_EXAMPLES=yes
+
+# Should we build the unit-tests? (yes/no)
+BUILD_TESTS=yes
+
+# Should we build the lib4neuro library? (yes)
+BUILD_LIB=yes
+
+# C++ compiler
+CXX_COMPILER="g++"
+C_COMPILER="gcc"
+
+#**********************DO NOT CHANGE BEYOND THIS LINE****************************************
+if [ -z ${DEPENDENCIES_LINK_TYPE} ]; then DEPENDENCIES_LINK_TYPE=static; fi
+if [ -z ${CLEAN_AFTER} ]; then CLEAN_AFTER=yes; fi
+
+LINK_TYPE=static
+if [ ${DEPENDENCIES_LINK_TYPE} = "shared" ]
+then
+    LINK_TYPE=shared
+fi
+
+CLEAN_AF=yes
+if [ ${CLEAN_AFTER} = "no" ]
+then
+    CLEAN_AF=no
+fi
+
+BUILD_ERROR_OCCURED=0
+
+RED='\033[0;31m'
+CYAN='\033[0;36m'
+YELLOW='\033[1;33m'
+GREEN='\033[0;32m'
+WHITE='\033[1;37m'
+NC='\033[0m' # No Color
+echo -e "Building the '${CYAN}lib4neuro${NC}' project for ${WHITE}Debug${NC}"
+
+
+BUILD_SOMETHING=no
+BUILD_SOMETHING_LIB=no
+
+if [ ${BUILD_LIB} = "yes" ]
+then
+    echo "${CYAN}lib4neuro${NC} build type: ${WHITE}Debug${NC}"
+    echo "${CYAN}lib4neuro${NC} build architecture: ${WHITE}x64${NC}"
+    echo "${CYAN}lib4neuro${NC} will be built in '${YELLOW}build/lib/${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+if [ ${BUILD_TESTS} = "yes" ]
+then
+    echo -e "${CYAN}lib4neuro${NC} unit tests will be built in '${YELLOW}build/unit-tests${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+if [ ${BUILD_EXAMPLES} = "yes" ]
+then
+    echo -e "${CYAN}lib4neuro${NC} examples will be built in '${YELLOW}build/examples${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+rm -rf ../../external_dependencies/boost/*
+rm -rf ../../external_dependencies/exprtk/*
+
+# Should we build the lib4neuro library? (yes)
+if [ ${BUILD_SOMETHING_LIB} = "yes" -a ${BUILD_ERROR_OCCURED} = "0" ]
+then
+
+    if [ ${BUILD_LIB} = "yes" ]
+    then
+        ./linux_clean_lib.sh
+    fi
+
+    if [ ${BUILD_EXAMPLES} = "yes" ]
+    then
+        ./linux_clean_examples.sh
+    fi
+
+    if [ ${BUILD_TESTS} = "yes" ]
+    then
+        ./linux_clean_tests.sh
+    fi	
+
+    echo -e "Building the '${CYAN}lib4neuro${NC}' project for ${WHITE}Debug${NC} (preparing makefiles)"
+	
+    cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER=${CXX_COMPILER} -DCMAKE_C_COMPILER=${C_COMPILER} -DBOOST_LIBRARYDIR=${BOOST_LIBRARYDIR} -DBOOST_INCLUDEDIR=${BOOST_INCLUDEDIR} -DBUILD_TESTS=${BUILD_TESTS} -DBUILD_EXAMPLES=${BUILD_EXAMPLES} -DBUILD_LIB=${BUILD_LIB} -DDEPENDENCIES_LINK_TYPE=${LINK_TYPE} -S . -B build || { echo -e "${RED}Makefile preparation finished with errors${NC}!"; BUILD_ERROR_OCCURED=1; }
+
+	if [ ${BUILD_ERROR_OCCURED} -eq 0 ]
+	then
+        echo -e "Building the '${CYAN}lib4neuro${NC}' project for ${WHITE}Debug${NC} (building)"
+        cmake --build build --config Debug -- -j ${N_CORES} && echo -e "${GREEN}Build complete${NC}." || { echo -e "${RED}Build finished with errors${NC}!"; BUILD_ERROR_OCCURED=1; }
+	fi
+
+fi
+
+if [ ${BUILD_ERROR_OCCURED} -eq 1 ]
+then
+    echo -e "${RED}Build encountered some errors!${NC}"
+    exit 1
+fi

build_scripts/linux/linux_gcc_build_x64_debug_local.sh

@@ -5,12 +5,14 @@ clear
 export BOOST_ROOT=${PWD}../../external_dependencies/boost
 export LIB4NEURO_INCLUDE_DIR=${PWD}/../../include
 
+# Add path to MPICH binaries on CentOS
+export PATH=${PATH}:/usr/lib64/mpich/bin
 
 # Should we build the examples? (yes/no)
 BUILD_EXAMPLES=yes
 
 # Should we build the unit-tests? (yes/no)
-BUILD_TESTS=yes
+BUILD_TESTS=no
 
 # Should we rebuild BOOST? (yes/no)
 #REBUILD_BOOST=yes
@@ -18,8 +20,10 @@ BUILD_TESTS=yes
 BUILD_LIB=yes
 
 # C++ compiler
-CXX_COMPILER="g++"
-C_COMPILER="gcc"
+#CXX_COMPILER="g++"
+#C_COMPILER="gcc"
+CXX_COMPILER="mpicxx"
+C_COMPILER="mpicc"
 
 #**********************DO NOT CHANGE BEYOND THIS LINE****************************************
 if [ -z ${DEPENDENCIES_LINK_TYPE} ]; then DEPENDENCIES_LINK_TYPE=static; fi

build_scripts/linux/linux_gcc_build_x64_debug_system.sh

@@ -5,6 +5,8 @@ clear
 export BOOST_ROOT=${PWD}../../external_dependencies/boost
 export LIB4NEURO_INCLUDE_DIR=${PWD}/../../include
 
+# Add path to MPICH binaries on CentOS
+export PATH=${PATH}:/usr/lib64/mpich/bin
 
 # Should we build the examples? (yes/no)
 BUILD_EXAMPLES=yes
@@ -18,6 +20,8 @@ BUILD_LIB=yes
 # C++ compiler
 CXX_COMPILER="g++"
 C_COMPILER="gcc"
+CXX_COMPILER="mpicxx"
+C_COMPILER="mpicc"
 
 #**********************DO NOT CHANGE BEYOND THIS LINE****************************************
 if [ -z ${DEPENDENCIES_LINK_TYPE} ]; then DEPENDENCIES_LINK_TYPE=static; fi

build_scripts/linux/linux_gcc_build_x64_release_local.sh

+#!/bin/sh
+
+clear
+
+export BOOST_ROOT=${PWD}../../external_dependencies/boost
+export LIB4NEURO_INCLUDE_DIR=${PWD}/../../include
+
+# Add path to MPICH binaries on CentOS
+export PATH=${PATH}:/usr/lib64/mpich/bin 
+
+# Should we build the examples? (yes/no)
+BUILD_EXAMPLES=yes
+
+# Should we build the unit-tests? (yes/no)
+BUILD_TESTS=no
+
+# Should we rebuild BOOST? (yes/no)
+#REBUILD_BOOST=yes
+# Should we build the lib4neuro library? (yes)
+BUILD_LIB=yes
+
+# C++ compiler
+#CXX_COMPILER="g++"
+#C_COMPILER="gcc"
+CXX_COMPILER="mpicxx"
+C_COMPILER="mpicc"
+FORTRAN_COMPILER="mpif90"
+
+#**********************DO NOT CHANGE BEYOND THIS LINE****************************************
+if [ -z ${DEPENDENCIES_LINK_TYPE} ]; then DEPENDENCIES_LINK_TYPE=static; fi
+if [ -z ${CLEAN_AFTER} ]; then CLEAN_AFTER=yes; fi
+
+export LINK_TYPE=static
+if [ ${DEPENDENCIES_LINK_TYPE} = "shared" ]
+then
+    export LINK_TYPE=shared
+fi
+
+CLEAN_AF=yes
+if [ ${CLEAN_AFTER} = "no" ]
+then
+    CLEAN_AF=no
+fi
+
+
+BUILD_ERROR_OCCURED=0
+
+RED='\033[0;31m'
+CYAN='\033[0;36m'
+YELLOW='\033[1;33m'
+GREEN='\033[0;32m'
+WHITE='\033[1;37m'
+NC='\033[m' # No Color
+echo -e "Building the ${CYAN}lib4neuro${NC} project for ${WHITE}Release${NC}"
+
+
+BUILD_SOMETHING=no
+BUILD_SOMETHING_LIB=no
+
+if [ ${BUILD_LIB} = "yes" ]
+then
+    echo -e "${CYAN}lib4neuro${NC} build type: ${WHITE}Release${NC}"
+    echo -e "${CYAN}lib4neuro${NC} build architecture: ${WHITE}x64${NC}"
+    echo -e "${CYAN}lib4neuro${NC} will be built in '${YELLOW}build/lib/${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+if [ $BUILD_TESTS = "yes" ]
+then
+    echo -e "${CYAN}lib4neuro${NC} unit tests will be built in '${YELLOW}build/unit-tests${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+if [ ${BUILD_EXAMPLES} = "yes" ]
+then
+    echo -e "${CYAN}lib4neuro${NC} examples will be built in '${YELLOW}build/examples${NC}'"
+    BUILD_SOMETHING=yes
+    BUILD_SOMETHING_LIB=yes
+fi
+
+#if [ ${REBUILD_BOOST} = "yes" ]
+#then
+#    echo -e "The required '${CYAN}BOOST${NC}' library will be recompiled in the directory '${YELLOW}external_dependencies/boost${NC}'"
+#    rm -rf ../../external_dependencies/boost/stage
+#    rm -rf ../../external_dependencies/boost/bin.v2
+#    BUILD_SOMETHING=yes
+#fi
+
+# Boost rebuild
+#if [ ${REBUILD_BOOST} = "yes" ]
+#then
+#    ./build_boost_gcc.sh || BUILD_ERROR_OCCURED=1
+#fi
+
+# Should we build the lib4neuro library? (yes)
+if [ ${BUILD_SOMETHING_LIB} = "yes" -a $BUILD_ERROR_OCCURED = "0" ]
+then
+
+    if [ ${BUILD_LIB} = "yes" ]
+    then
+        ./linux_clean_lib.sh
+    fi
+
+    if [ ${BUILD_EXAMPLES} = "yes" ]
+    then
+        ./linux_clean_examples.sh
+    fi
+
+    if [ ${BUILD_TESTS} = "yes" ]
+    then
+        ./linux_clean_tests.sh
+    fi
+
+    echo -e "Building the '${CYAN}lib4neuro${NC}' project for ${WHITE}Release${NC} (preparing makefiles)"
+
+    cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_Fortran_COMPILER=${FORTRAN_COMPILER} -DCMAKE_CXX_COMPILER=${CXX_COMPILER} -DCMAKE_C_COMPILER=${C_COMPILER} -DBOOST_LIBRARYDIR=${BOOST_LIBRARYDIR} -DBOOST_INCLUDEDIR=${BOOST_INCLUDEDIR} -DBUILD_TESTS=${BUILD_TESTS} -DBUILD_EXAMPLES=${BUILD_EXAMPLES} -DBUILD_LIB=${BUILD_LIB} -DDEPENDENCIES_LINK_TYPE=${LINK_TYPE} -S . -B build || { echo -e "${RED}Makefile preparation finished with errors${NC}!"; BUILD_ERROR_OCCURED=1; }
+	if [ ${BUILD_ERROR_OCCURED} = "0" ]
+	then
+        echo -e "Building the '${CYAN}lib4neuro${NC}' project for ${WHITE}Release${NC} (building)"
+
+        . $(pwd)/set_env_n_cores