Merge pull request #8 from cdslaborg/dev

Resolves #3, resolves #4, resolves #5

.VERSION

@@ -1,4 +1,4 @@
-1.4.2
+1.5.0
 # ParaMonte core library version file.
 # This version number should be incremented
 # only when the version has been released.

.gitignore

@@ -119,20 +119,22 @@ Thumbs.db
 #########################
 
 **/src/kernel/ParaMonte_mod@version@kernel.inc.f90
+**/paramonte-kernel-doc
+**/.ipynb_checkpoints
+**/benchmark
 **/codecov
-**/.ipynb_checkpoints/*
-**/benchmark/*
-**/build/*
-**/trash/*
-**/temp/*
-**/bin/*
-**/R/*
-**/___*___/*
+**/build
+**/trash
+**/temp
+**/bin
+**/R
+**/___*___
 
 #########################
 # ParaMonte temp files
 #########################
 
+*sc.html
 *_log.txt
 *_time.txt
 *_chain.txt
@@ -189,8 +191,8 @@ _deps
 # documentation
 #########################
 
+**/paramonte-kernel-doc/*
 **/devscripts/*
-**/doxygen/*
 **/draft/*
 **/doc/*
 

.travis.yml

@@ -17,9 +17,17 @@ cache:
     - $HOME/Library/Caches/Homebrew
     - /usr/local/Homebrew
 
+after_success:
+ #- bash <(curl -s https://codecov.io/bash)
+ - bash <(curl --connect-timeout 10 --retry 10 --retry-max-time 0 https://codecov.io/bash) || (sleep 30 && bash <(curl --connect-timeout 10 --retry 10 --retry-max-time 0 https://codecov.io/bash))
+
 matrix:
   include:
 
+    ################################################################################################################################
+    ####  linux test latest release
+    ################################################################################################################################
+
     - os: linux
       dist: trusty
       addons:
@@ -50,6 +58,10 @@ matrix:
         - cd libparamonte_cpp_linux_x64_gnu_release_dynamic_heap_mpi && ./build.sh && ./run.sh --nproc 2 && cd ..
         - cd libparamonte_fortran_linux_x64_gnu_release_dynamic_heap_mpi && ./build.sh && ./run.sh --nproc 2 && cd ..
 
+    ################################################################################################################################
+    ####  linux complete build
+    ################################################################################################################################
+
     - os: linux
       dist: trusty
       addons:
@@ -99,6 +111,34 @@ matrix:
         #- cd ${pmRootDir}/bin/libparamonte_cpp_linux_x64_gnu_release_dynamic_heap_mpi && ./build.sh && ./run.sh --nproc 2
         #- cd ${pmRootDir}/bin/libparamonte_fortran_linux_x64_gnu_release_dynamic_heap_mpi && ./build.sh && ./run.sh --nproc 2
 
+    ################################################################################################################################
+    #### code coverage
+    ################################################################################################################################
+
+    - os: linux
+      dist: trusty
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - lcov
+            - cmake
+            - gcc-9
+            - gfortran-9
+            - libmpich-dev
+            - mpich
+      script:
+        - echo "FCFLAG = ${FCFLAG}"
+        - cmake --version || echo "cmake not found..."
+        - gfortran --version && FCFLAG="-f $(which gfortran)" || echo "gfortran not found..."
+        - gfortran-9 --version && FCFLAG="-f $(which gfortran-9)" || echo "gfortran-9 not found..."
+        - ./install.sh --codecov --par none --yes-to-all ${FCFLAG}
+
+    ################################################################################################################################
+    #### macOS
+    ################################################################################################################################
+
     - &macOS
       os: osx
       osx_image: xcode12
@@ -122,12 +162,22 @@ matrix:
         - ./install.sh --lang "C C++ Fortran" --build release --lib dynamic --mem heap --par "none mpi" #-s gnu
         - pmRootDir=$(pwd)
         - ls ${pmRootDir}/bin/
-        - cd ${pmRootDir}/bin/libparamonte_c_darwin_x64_gnu_release_dynamic_heap && ls && ./build.sh && ./run.sh
-        - cd ${pmRootDir}/bin/libparamonte_cpp_darwin_x64_gnu_release_dynamic_heap && ls && ./build.sh && ./run.sh
-        - cd ${pmRootDir}/bin/libparamonte_fortran_darwin_x64_gnu_release_dynamic_heap && ls && ./build.sh && ./run.sh
-        - cd ${pmRootDir}/bin/libparamonte_c_darwin_x64_gnu_release_dynamic_heap_mpi && ls && ./build.sh && ./run.sh --nproc 2
-        - cd ${pmRootDir}/bin/libparamonte_cpp_darwin_x64_gnu_release_dynamic_heap_mpi && ls && ./build.sh && ./run.sh --nproc 2
-        - cd ${pmRootDir}/bin/libparamonte_fortran_darwin_x64_gnu_release_dynamic_heap_mpi && ls && ./build.sh && ./run.sh --nproc 2
+        - |
+          for buildDir in ${pmRootDir}/bin/*; do
+            echo ""
+            echo "Running example in ${buildDir}"
+            echo ""
+            if [[ "${dir}" =~ .*"_impi".* || "${dir}" =~ .*"_mpich".* || "${dir}" =~ .*"_openmpi".* ]]; then
+                cd ${buildDir} && ls && ./build.sh && ./run.sh --nproc 2
+            else
+                cd ${buildDir} && ls && ./build.sh && ./run.sh
+            fi
+            cd "${pmRootDir}"
+          done
+
+####################################################################################################################################
+#### OTHER
+####################################################################################################################################
 
 #    - &macOS
 #      os: osx

ACKNOWLEDGMENT.md

@@ -1,9 +1,6 @@
 **The ParaMonte library is an honor-ware and its currency is acknowledgment and citations**.  
 
-As per the ParaMonte library license agreement terms, if you use any parts of 
-this library for any purposes, kindly acknowledge the use of ParaMonte in your 
-work (education/research/industry/development/...) by citing the ParaMonte 
-library's main publications as listed here:  
+If you use ParaMonte, please acknowledge it by citing the ParaMonte library's main publications as listed here:  
 
 ### The ParaMonte Python library  
 

CHANGES.md

@@ -5,9 +5,20 @@ To access the latest release of the package, visit [the ParaMonte GitHub reposit
 
 ## **Version 1.x.x**  
 
-### **Version 1.4.2** -- November 27, 2020
+### **Version 1.5** -- Dec 17, 2020
 
-**Enhancements**  
+**Major Enhancements**  
+
++   This version introduces numerous performance and accuracy enhancements to the ParaMonte library.
++   The entire kernel library is now fully documented and verified with over 866 tests that cover close 
+    to 100% of all lines and functions in the kernel.
++   New prebuilt libraries with GNU compilers and Open-MPI on Linux are added.
++   New flags are now added to the build scripts of the library that automate the process of code coverage generation.
++   The `testing` builds are now removed from the ParaMonte release page as this build is mostly useful for development purposes.  
++   The issue of Windows file locking, that led to the occasional crashes of the 
+    ParaDRAM and ParaDISE simulations in `multiChain` parallelism mode, is now resolved.
+
+**Minor Enhancements**  
 
 +   Minor enhancements to the ParaMonte C/C++/Fortran example build scripts `build.sh` and `build.bat`.  
 +   The default build settings are now limited to `heap` memory allocation with `dynamic` library builds
@@ -17,23 +28,26 @@ To access the latest release of the package, visit [the ParaMonte GitHub reposit
     build the library with `stack` memory allocation by specifying the appropriate build flags with
     the `install.sh` on Unix or `install.bat` script on Windows systems. For further information, 
     see the installation guidelines on the ParaMonte documentation website.
-+   The temporary array creations in debug mode are now resolved.
++   All temporary array creations in debug mode are now resolved, 
+    except when Intel compilers are used, in which case, the debug warning messages are silenced.
 
-**Compiler support**  
+**Compiler Compatibility**  
 
 | Compiler Suite                    | Windows (64bit) | Linux | macOS |  
 |----------------------------------:|:---------------:|:-----:|:-----:|  
 | GNU Compiler Collection > 8.4     | ✅              | ✅    | ✅    |  
-| Intel Parallel Studio > 18.0.0    | ✅              | ✅    | ✅    |  
+| Intel Parallel Studio > 19.1.1    | ✅              | ✅    | ✅    |  
 | Microsoft C/C++ Compiler > 16.0.0 | ✅              | ❌    | ❌    |  
 
 **Compiler / MPI library used for this binary release**  
 
-+   **Windows**: Intel Parallel Studio Version 19.0.4.245 Build 20190417 / Intel(R) MPI Library 2019 Update 4 for Windows  
-+   **Linux**: Intel Parallel Studio Version 18.0.2 20180210 / Intel(R) MPI Library for Linux OS, Version 2018 Update 2 Build 20180125  
++   **Windows**: Intel Parallel Studio Version 19.1.1.216 Build 20200306 / Intel(R) MPI Library 2019 Update 7 for Windows  
++   **Linux**: Intel Parallel Studio Version 19.1.1.217 20200306 / Intel(R) MPI Library for Linux OS, Version 2019 Update 7 Build 20200312
++   **Linux**: GNU 10.2.0 / Open-MPI 4.0.3  
 +   **Linux**: GNU 10.1.0 / MPICH 3.2  
 +   **macOS**: Intel Parallel Studio Version 19.1.0.216 20200306  
 +   **macOS**: GNU 10.2.0 / Open-MPI 4.0.5  
++   **macOS**: GNU 10.2.0 / MPICH 3.3.2  
 
 ### **Version 1.4.1** -- November 15, 2020
 

CMakeLists.txt

@@ -114,8 +114,8 @@ endif()
 
 set(pmcolor "${BoldCyan}")
 set(pmattn  " ${pmcolor}ParaMonte -${ColorReset}")
-set(pmnote  "${pmattn} ${BoldMagenta}NOTE:${ColorReset}")
-set(pmwarn  "${pmattn} ${BoldYellow}WARNING:${ColorReset}")
+set(pmnote  "${pmattn} ${BoldYellow}NOTE:${ColorReset}")
+set(pmwarn  "${pmattn} ${BoldMagenta}WARNING:${ColorReset}")
 set(pmfatal "${pmattn} ${BoldRed}FATAL ERROR:${ColorReset}")
 
 #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -139,7 +139,7 @@ if ("${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
             "       $ buildDir=$(uname -s)$(uname -m) # set build folder to OS name + architecture\n"
             "       $ mkdir $\{buildDir\}\n"
             "       $ cd $\{buildDir\}\n"
-            "       $ CC=gcc FC=gfortran cmake -DBUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/install/dir /path/to/ParaMonte/kernel/src/dir\n\n"
+            "       $ CC=gcc CMAKE_Fortran_COMPILER=gfortran cmake -DBUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/install/dir /path/to/ParaMonte/kernel/src/dir\n\n"
             "   substituting the appropriate syntax for your shell (the above line assumes the bash shell)."
             )
 endif()
@@ -254,7 +254,7 @@ else()
 endif()
 string(TOLOWER ${COMPILER_SUITE} COMPILER_SUITE)
 
-message(STATUS "CMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}")
+message(STATUS "${pmattn} CMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}")
 
 #if(DEFINED CMAKE_BUILD_TYPE AND "${CMAKE_BUILD_TYPE}" MATCHES "[Rr][Ee][Ll]") # release mode requested
 #    if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
@@ -447,6 +447,10 @@ set(ParaMonteTest_SRC_DIR
     "${CMAKE_SOURCE_DIR}/src/kernel/tests"
     CACHE PATH "ParaMonte test source files directory" )
 
+set(ParaMonteTest_SRC_INPUT_DIR
+    "${ParaMonteTest_SRC_DIR}/input"
+    CACHE PATH "ParaMonte test source files directory" )
+
 # set the ParaMonte interface source files directory and loop over them to ensure their existence
 
 set(ParaMonteInterface_SRC_DIR
@@ -561,16 +565,17 @@ endif()
 #set(ParaMonteTest_BIN_DIR "${ParaMonteTest_BLD_DIR}")
 set(ParaMonteTest_BIN_DIR "${ParaMonteTest_BLD_DIR}/bin")
 message( STATUS "${pmattn} ParaMonteTest_BIN_DIR: ${ParaMonteTest_BIN_DIR}" )
+file(REMOVE_RECURSE "${ParaMonteTest_BIN_DIR}/")
 if (NOT EXISTS "${ParaMonteTest_BIN_DIR}/")
     file(MAKE_DIRECTORY "${ParaMonteTest_BIN_DIR}")
 endif()
 
 # set up test bin directory
 
-set(ParaMonteTest_INPUT_DIR "${ParaMonteTest_BIN_DIR}/input")
-message( STATUS "${pmattn} ParaMonteTest_INPUT_DIR: ${ParaMonteTest_INPUT_DIR}" )
-if (NOT EXISTS "${ParaMonteTest_INPUT_DIR}/")
-    file(MAKE_DIRECTORY "${ParaMonteTest_INPUT_DIR}")
+set(ParaMonteTest_BIN_INPUT_DIR "${ParaMonteTest_BIN_DIR}/input")
+message( STATUS "${pmattn} ParaMonteTest_BIN_INPUT_DIR: ${ParaMonteTest_BIN_INPUT_DIR}" )
+if (NOT EXISTS "${ParaMonteTest_BIN_INPUT_DIR}/")
+    file(MAKE_DIRECTORY "${ParaMonteTest_BIN_INPUT_DIR}")
 endif()
 
 #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -585,7 +590,26 @@ endif()
 set(ParaMonteTest_EXE_NAME testParaMonte)
 
 # Define the library name
-if (NOT DEFINED PMLIB)
+if (NOT DEFINED PMLIB_NAME)
+
+    # \todo
+    # This library name definition requires further enhancement to match the name defined by the bash installer, whenever cmake is used directly.
+
+    message ( WARNING 
+            " \n"
+            " ${pmwarn} The ParaMonte Library name is not predefined.\n"
+            " ${pmwarn} This is highly unusual and should not happen.\n"
+            " ${pmwarn} Normally, the library name is defined by the ParaMonte installer \n"
+            " ${pmwarn} or passed to cmake for abuild via cmake. The most likely cause of this\n"
+            " ${pmwarn} warning message is that you are either building the library directly via\n"
+            " ${pmwarn} cmake and forgot to predefine the library name or, the Bash installation that you\n"
+            " ${pmwarn} are using is corrupted. If the latter is the case, please report the issue at:\n"
+            " ${pmwarn} \n"
+            " ${pmwarn} https://github.com/cdslaborg/paramonte/issues,\n"
+            " ${pmwarn} \n"
+            " ${pmwarn} to resolve it. Note that even if the library might be properly built, the naming \n"
+            " ${pmwarn} used might not follow the conventional naming rules of the ParaMonte library.\n"
+            )
 
     if (HEAP_ARRAY_ENABLED)
         set(MEMORY_ALLOCATION heap)
@@ -606,22 +630,22 @@ if (NOT DEFINED PMLIB)
     else()
         set(LANG_ABBR ${INTERFACE_LANGUAGE})
     endif()
-    set(PMLIB paramonte_${LANG_ABBR}_${PLATFORM}_${ARCHITECTURE}_${PMCS}_${BTYPE}_${LTYPE}_${MEMORY_ALLOCATION} )
+    set(PMLIB_NAME paramonte_${LANG_ABBR}_${PLATFORM}_${ARCHITECTURE}_${PMCS}_${BTYPE}_${LTYPE}_${MEMORY_ALLOCATION} )
 
     if (CAF_ENABLED)
-        set(PMLIB ${PMLIB}_caf${CAFTYPE})
+        set(PMLIB_NAME ${PMLIB_NAME}_caf${CAFTYPE})
     endif()
 
     if (MPI_ENABLED)
-        set(PMLIB ${PMLIB}_mpi)
+        set(PMLIB_NAME ${PMLIB_NAME}_mpi)
     endif()
 
     if (OMP_ENABLED)
-        set(PMLIB ${PMLIB}_omp)
+        set(PMLIB_NAME ${PMLIB_NAME}_omp)
     endif()
 
     #if (MT_ENABLED)
-    #    set(PMLIB ${PMLIB}_mt)
+    #    set(PMLIB_NAME ${PMLIB_NAME}_mt)
     #endif()
 
 endif()

README.md

@@ -87,7 +87,7 @@ Currently, the following compiler suites are supported for builds from source:
 | Compiler Suite                    | Linux | macOS | Windows (64bit) |  
 |----------------------------------:|:-----:|:-----:|:---------------:|  
 | GNU Compiler Collection > 8.4     |✓|✓| ✗         |  
-| Intel Parallel Studio > 18.0.0    |✓|✓| ✓         |  
+| Intel Parallel Studio > 19.0.4    |✓|✓| ✓         |  
 
 For more information and quick-start in the programming language of your choice, visit the [ParaMonte library homepage](https://www.cdslab.org/paramonte).  
 
@@ -133,9 +133,8 @@ Citing ParaMonte
 
 The ParaMonte library is an honor-ware and its currency is acknowledgment and citations.  
 
-As per the ParaMonte library license agreement terms, if you use any parts of this library for any purposes, 
-kindly acknowledge the use of the ParaMonte library in your work (education/research/industry/development/...) 
-by citing the ParaMonte library's main publications as listed in [ACKNOWLEDGMENT.md](https://github.com/cdslaborg/paramonte/blob/master/ACKNOWLEDGMENT.md).  
+If you use ParaMonte, please acknowledge it by citing the ParaMonte library's main publications 
+as listed in [ACKNOWLEDGMENT.md](https://github.com/cdslaborg/paramonte/blob/master/ACKNOWLEDGMENT.md).  
 
 Visit [the ParaMonte library homepage](https://www.cdslab.org/paramonte/notes/overview/preface/#how-to-acknowledge-the-use-of-the-paramonte-library-in-your-work) 
 to access the PDF version of these files free of charge.  

auxil/genReadme.py

@@ -211,7 +211,7 @@ def getLogFunc(point): return -0.5 * np.sum( point**2 )
 | Compiler Suite                    | Linux | macOS | Windows (64bit) |  
 |----------------------------------:|:-----:|:-----:|:---------------:|  
 | GNU Compiler Collection > 8.4     |✓|✓| ✗         |  
-| Intel Parallel Studio > 18.0.0    |✓|✓| ✓         |  
+| Intel Parallel Studio > 19.0.4    |✓|✓| ✓         |  
 
 For more information and quick-start in the programming language of your choice, visit the [ParaMonte library homepage](https://www.cdslab.org/paramonte).  
 """
@@ -318,9 +318,8 @@ def getLogFunc(point): return -0.5 * np.sum( point**2 )
 readme["citation"]["main"] = readme["citation"]["title"] + """
 The ParaMonte library is an honor-ware and its currency is acknowledgment and citations.  
   
-As per the ParaMonte library license agreement terms, if you use any parts of this library for any purposes, 
-kindly acknowledge the use of the ParaMonte library in your work (education/research/industry/development/...) 
-by citing the ParaMonte library's main publications as listed in [ACKNOWLEDGMENT.md](https://github.com/cdslaborg/paramonte/blob/master/ACKNOWLEDGMENT.md).  
+If you use ParaMonte, please acknowledge it by citing the ParaMonte library's main publications 
+as listed in [ACKNOWLEDGMENT.md](https://github.com/cdslaborg/paramonte/blob/master/ACKNOWLEDGMENT.md).  
 
 Visit [the ParaMonte library homepage](https://www.cdslab.org/paramonte/notes/overview/preface/#how-to-acknowledge-the-use-of-the-paramonte-library-in-your-work) 
 to access the PDF version of these files free of charge.  

auxil/testMPI.f90

@@ -47,12 +47,16 @@ program testMPI
 
     integer(IK) :: ierrMPI, imageID, imageCount
     logical     :: isInitialized
-
-
+    logical     :: isFinalized
 
     call mpi_initialized( isInitialized, ierrMPI )
     if (.not. isInitialized) call mpi_init(ierrMPI)
     call mpi_comm_rank(mpi_comm_world, imageID, ierrMPI)
     call mpi_comm_size(mpi_comm_world, imageCount, ierrMPI)
+    call mpi_finalized( isFinalized, ierrMPI )
+    if (.not. isFinalized) then
+        call mpi_barrier(mpi_comm_world,ierrMPI)
+        call mpi_finalize(ierrMPI)
+    end if
 
 end program testMPI