Merge branch 'master' of https://github.com/ornladios/ADIOS2.git

Conflicts:
	examples/heatTransfer/IO_adios2.cpp
	include/core/VariableBase.h
	include/engine/adios1/ADIOS1Reader.h
	source/CMakeLists.txt
	source/engine/adios1/ADIOS1Reader.cpp
	source/functions/adiosFunctions.cpp

CMakeLists.txt

@@ -65,7 +65,7 @@ if(ADIOS_ENABLE_PIC)
   set(CMAKE_POSITION_INDEPENDENT_CODE OFF)
 endif()
 
-option(ADIOS_USE_MPI "Enable the MPI version of ADIOS" ON)
+option(ADIOS_USE_MPI "Enable the MPI version of ADIOS" OFF)
 if(ADIOS_USE_MPI)
   # Workaround for OpenMPI forcing the link of C++ bindings
   add_definitions(-DOMPI_SKIP_MPICXX)

Contributing.md

@@ -12,34 +12,38 @@ To setup your local repository for development:
   1. Fork the main repository on GitHub:
      1. Navigate to https://github.com/ornladios/adios2 in your browser.
      1. Click the `[Fork]` button in the upper right-hand side of the page.
-  2. Clone your fork to your local machine:
+  2. Clone the upstream repository to your local machine:
 ```
-[chuck@hal9000 Code]$ mkdir adios
-[chuck@hal9000 Code]$ cd adios
-[chuck@hal9000 adios]$ git clone git@github.com:<your-GitHub-username-here>/adios2.git source
+$ mkdir adios
+$ cd adios
+$ git clone https://github.com/ornladios/adios2.git source
 Cloning into 'source'...
-remote: Counting objects: 4535, done.
-remote: Compressing objects: 100% (223/223), done.
-remote: Total 4535 (delta 64), reused 0 (delta 0), pack-reused 4301
-Receiving objects: 100% (4535/4535), 1.27 MiB | 0 bytes/s, done.
-Resolving deltas: 100% (2607/2607), done.
+remote: Counting objects: 4632, done.
+remote: Compressing objects: 100% (80/80), done.
+remote: Total 4632 (delta 33), reused 0 (delta 0), pack-reused 4549
+Receiving objects: 100% (4632/4632), 1.23 MiB | 224.00 KiB/s, done.
+Resolving deltas: 100% (2738/2738), done.
 Checking connectivity... done.
-[chuck.atkins@hal9000 adios]$
+$
 ```
   3. Run the `scripts/development/setup.sh` script.  The script will configure an `upstream` remote and link your local master branch to the upstream.
 ```
-[chuck.atkins@hal9000 adios]$ cd source/
-$ ./scripts/developer/setup.sh
-Checking GitHub username...
-Using GitHub user <your-GitHub-username-here>
-Adding upstream remote...
+$ cd source/
+$ ./scripts/developer/setup.sh 
+Enter your GitHub username: chuckatkins
+Setup SSH push access? [(y)/n] y
+Re-configuring local master branch to use upstream
 Fetching origin
+remote: Counting objects: 6, done.
+remote: Compressing objects: 100% (6/6), done.
+remote: Total 6 (delta 0), reused 0 (delta 0), pack-reused 0
+Unpacking objects: 100% (6/6), done.
+From https://github.com/chuckatkins/adios2
 Fetching upstream
 From https://github.com/ornladios/adios2
+ * [new branch]      master     -> upstream/master
  * [new branch]      dashboard  -> upstream/dashboard
  * [new branch]      hooks      -> upstream/hooks
- * [new branch]      master     -> upstream/master
-Re-configuring local master branch to use upstream
 Setting up git aliases...
 Setting up git hooks...
 $
@@ -109,4 +113,5 @@ That will apply the formatting rules used by the ADIOS project.
 1. Lines no longer than 80 characters.
 1. Always use braces { and }, even for 1 line if blocks.
 1. Use 4 spaces for indentation.
+
 There are more formatting rules but these three should at least get you close and prevent any drastic re-writes from the re-formatting tools.  More details can be found by looking at the .clang-format config file n the root of the repository and by looking at the clang-format documentation http://releases.llvm.org/3.8.0/tools/clang/docs/ClangFormatStyleOptions.html.  While the formatting rules are a bit more involved, the main points are:

cmake/FindADIOS1.cmake

+# - Find ADIOS 1.x library, routines for scientific, parallel IO
+#   https://www.olcf.ornl.gov/center-projects/adios/
+#
+# Use this module by invoking find_package with the form:
+#   find_package(ADIOS1
+#     [version] [EXACT]     # Minimum or EXACT version, e.g. 1.6.0
+#     [REQUIRED]            # Fail with an error if ADIOS or a required
+#                           #   component is not found
+#     [QUIET]               # ...
+#     [COMPONENTS <...>]    # Compiled in components: fortran, readonly, 
+                            # sequential (all are case insentative) 
+#   )
+#
+# Module that finds the includes and libraries for a working ADIOS 1.x install.
+# This module invokes the `adios_config` script that should be installed with
+# the other ADIOS tools.
+#
+# To provide a hint to the module where to find the ADIOS installation,
+# set the ADIOS1_ROOT or ADIOS1_DIR environment variable.
+#
+# If this variable is not set, make sure that at least the according `bin/`
+# directory of ADIOS 1.x is in your PATH environment variable.
+#
+# Set the following CMake variables BEFORE calling find_packages to
+# influence this module:
+#   ADIOS1_USE_STATIC_LIBS - Set to ON to force the use of static
+#                           libraries.  Default: OFF
+#
+# This module will define the following variables:
+#   ADIOS1_INCLUDE_DIRS    - Include directories for the ADIOS 1.x headers.
+#   ADIOS1_LIBRARY_PATH    - Full path of the libadios library (.a or .so file)
+#   ADIOS1_DEPENDENCY_LIBRARIES       - ADIOS 1.x dependency libraries.
+#   ADIOS1_FOUND           - TRUE if FindADIOS1 found a working install
+#   ADIOS1_VERSION         - Version in format Major.Minor.Patch
+#
+# Not used for now:
+#   ADIOS1_DEFINITIONS     - Compiler definitions you should add with
+#                           add_definitions(${ADIOS1_DEFINITIONS})
+#
+# Example to find ADIOS 1.x (default)
+# find_package(ADIOS1)
+# if(ADIOS1_FOUND)
+#   include_directories(${ADIOS1_INCLUDE_DIRS})
+#   add_executable(foo foo.c)
+#   target_link_libraries(foo ${ADIOS1_LIBRARY_PATH} ADIOS1_DEPENDENCY_LIBRARIES)
+# endif()
+
+# Example to find ADIOS 1.x using component
+# find_package(ADIOS1 COMPONENTS fortran)
+# if(ADIOS1_FOUND)
+#   include_directories(${ADIOS1_INCLUDE_DIRS})
+#   add_executable(foo foo.c)
+#   target_link_libraries(foo ${ADIOS1_LIBRARY_PATH} ${ADIOS1_DEPENDENCY_LIBRARIES})
+# endif()
+###############################################################################
+#Copyright (c) 2014, Axel Huebl and Felix Schmitt from http://picongpu.hzdr.de
+#All rights reserved.
+
+#Redistribution and use in source and binary forms, with or without
+#modification, are permitted provided that the following conditions are met:
+
+#1. Redistributions of source code must retain the above copyright notice, this
+#list of conditions and the following disclaimer.
+
+#2. Redistributions in binary form must reproduce the above copyright notice,
+#this list of conditions and the following disclaimer in the documentation
+#and/or other materials provided with the distribution.
+
+#3. Neither the name of the copyright holder nor the names of its contributors
+#may be used to endorse or promote products derived from this software without
+#specific prior written permission.
+
+#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+#AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+
+###############################################################################
+# Required cmake version
+###############################################################################
+
+cmake_minimum_required(VERSION 2.8.5)
+
+
+###############################################################################
+# ADIOS
+###############################################################################
+# get flags for adios_config, -l is the default
+#-f for fortran, -r for readonly, -s for sequential (nompi)
+set(OPTLIST "-l")
+if(ADIOS1_FIND_COMPONENTS)
+    foreach(COMP ${ADIOS1_FIND_COMPONENTS})
+        string(TOLOWER ${COMP} comp)
+        if(comp STREQUAL "fortran")
+            set(OPTLIST "${OPTLIST}f")
+        elseif(comp STREQUAL "readonly")
+            set(OPTLIST "${OPTLIST}r")
+        elseif(comp STREQUAL "sequential")
+            set(OPTLIST "${OPTLIST}s")
+        else()
+            message("ADIOS 1.x component ${COMP} is not supported. Please use fortran, readonly, or sequential")
+        endif()
+    endforeach()
+endif()
+
+# we start by assuming we found ADIOS and falsify it if some
+# dependencies are missing (or if we did not find ADIOS at all)
+set(ADIOS1_FOUND TRUE)
+
+
+# find `adios_config` program #################################################
+#   check the ADIOS1_ROOT and ADIOS1_DIR hint and the normal PATH
+find_file(ADIOS1_CONFIG
+    NAME adios_config
+    PATHS $ENV{ADIOS1_ROOT}/bin $ENV{ADIOS1_DIR}/bin $ENV{INSTALL_PREFIX}/bin $ENV{PATH})
+
+if(ADIOS1_CONFIG)
+    message(STATUS "Found 'adios_config': ${ADIOS1_CONFIG}")
+else(ADIOS1_CONFIG)
+    set(ADIOS1_FOUND FALSE)
+    message(STATUS "Can NOT find 'adios_config' - set ADIOS1_ROOT, ADIOS1_DIR or INSTALL_PREFIX, or check your PATH")
+endif(ADIOS1_CONFIG)
+
+# check `adios_config` program ################################################
+if(ADIOS1_FOUND)
+    execute_process(COMMAND ${ADIOS1_CONFIG} ${OPTLIST}
+                    OUTPUT_VARIABLE ADIOS1_LINKFLAGS
+                    RESULT_VARIABLE ADIOS1_CONFIG_RETURN
+                    OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT ADIOS1_CONFIG_RETURN EQUAL 0)
+        set(ADIOS1_FOUND FALSE)
+        message(STATUS "Can NOT execute 'adios_config' - check file permissions")
+    endif()
+
+    # find ADIOS1_ROOT_DIR
+    execute_process(COMMAND ${ADIOS1_CONFIG} -d
+                    OUTPUT_VARIABLE ADIOS1_ROOT_DIR
+                    OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT IS_DIRECTORY "${ADIOS1_ROOT_DIR}")
+        set(ADIOS1_FOUND FALSE)
+        message(STATUS "The directory provided by 'adios_config -d' does not exist: ${ADIOS1_ROOT_DIR}")
+    endif()
+endif(ADIOS1_FOUND)
+
+# option: use only static libs ################################################
+if(ADIOS1_USE_STATIC_LIBS)
+    # carfully: we have to restore the original path in the end
+    set(_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})
+    set(CMAKE_FIND_LIBRARY_SUFFIXES .a)
+endif()
+
+
+# we found something in ADIOS1_ROOT_DIR and adios_config works #################
+if(ADIOS1_FOUND)
+    # ADIOS headers
+    list(APPEND ADIOS1_INCLUDE_DIRS ${ADIOS1_ROOT_DIR}/include)
+
+    # check for compiled in dependencies, recomve ";" in ADIOS1_LINKFLAGS (from cmake build)
+    string(REGEX REPLACE ";" " " ADIOS1_LINKFLAGS "${ADIOS1_LINKFLAGS}")
+    message(STATUS "  ADIOS1 linker flags (unparsed): ${ADIOS1_LINKFLAGS}")
+
+    # find all library paths -L
+    #   note: this can cause trouble if some libs are specified twice from
+    #         different sources (quite unlikely)
+    #         http://www.cmake.org/pipermail/cmake/2008-November/025128.html
+    set(ADIOS1_LIBRARY_DIRS "")
+    string(REGEX MATCHALL " -L([A-Za-z_0-9/\\.-]+)" _ADIOS1_LIBDIRS " ${ADIOS1_LINKFLAGS}")
+    foreach(_LIBDIR ${_ADIOS1_LIBDIRS})
+        string(REPLACE " -L" "" _LIBDIR ${_LIBDIR})
+        list(APPEND ADIOS1_LIBRARY_DIRS ${_LIBDIR})
+    endforeach()
+    # we could append ${CMAKE_PREFIX_PATH} now but that is not really necessary
+
+    #message(STATUS "ADIOS1 DIRS to look for libs: ${ADIOS1_LIBRARY_DIRS}")
+
+    # parse all -lname libraries and find an absolute path for them
+    string(REGEX MATCHALL " -l([A-Za-z_0-9\\.-]+)" _ADIOS1_LIBS " ${ADIOS1_LINKFLAGS}")
+    foreach(_LIB ${_ADIOS1_LIBS})
+        string(REPLACE " -l" "" _LIB ${_LIB})
+
+        # find static lib: absolute path in -L then default
+        find_library(_LIB_DIR NAMES ${_LIB} PATHS ${ADIOS1_LIBRARY_DIRS} CMAKE_FIND_ROOT_PATH_BOTH)
+
+        # found?
+        if(_LIB_DIR)
+            if(_LIB STREQUAL "adios")
+                message(STATUS "  Found the main adios library in ${_LIB_DIR}")
+                set(ADIOS1_LIBRARY_PATH "${_LIB_DIR}")
+                #message(STATUS "    ADIOS1_LIBRARY_PATH set to ${ADIOS1_LIBRARY_PATH}")
+            else()
+                message(STATUS "  Found ${_LIB} in ${_LIB_DIR}")
+                list(APPEND ADIOS1_DEPENDENCY_LIBRARIES "${_LIB_DIR}")
+            endif()
+        else(_LIB_DIR)
+            set(ADIOS1_FOUND FALSE)
+            message(STATUS "ADIOS1: Could NOT find library '${_LIB}'")
+        endif(_LIB_DIR)
+
+        # clean cached var
+        unset(_LIB_DIR CACHE)
+        unset(_LIB_DIR)
+    endforeach()
+
+    #add libraries which are already using cmake format
+    string(REGEX MATCHALL "/([A-Za-z_0-9/\\.-]+)\\.([a|so]+)" _ADIOS1_LIBS_SUB "${ADIOS1_LINKFLAGS}")
+    list(APPEND ADIOS1_DEPENDENCY_LIBRARIES "${_ADIOS1_LIBS_SUB}")
+
+    # add the version string
+    execute_process(COMMAND ${ADIOS1_CONFIG} -v
+                    OUTPUT_VARIABLE ADIOS1_VERSION
+                    OUTPUT_STRIP_TRAILING_WHITESPACE)
+    
+endif(ADIOS1_FOUND)
+
+# unset checked variables if not found
+if(NOT ADIOS1_FOUND)
+    unset(ADIOS1_INCLUDE_DIRS)
+    unset(ADIOS1_DEPENDENCY_LIBRARIES)
+    unset(ADIOS1_LIBRARY_PATH)
+endif(NOT ADIOS1_FOUND)
+
+
+# restore CMAKE_FIND_LIBRARY_SUFFIXES if manipulated by this module ###########
+if(ADIOS1_USE_STATIC_LIBS)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES ${_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+endif()
+
+
+###############################################################################
+# FindPackage Options
+###############################################################################
+
+# handles the REQUIRED, QUIET and version-related arguments for find_package
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ADIOS1
+    REQUIRED_VARS ADIOS1_LIBRARY_PATH ADIOS1_DEPENDENCY_LIBRARIES ADIOS1_INCLUDE_DIRS
+    VERSION_VAR ADIOS1_VERSION
+)
+
+##########################################################################
+# Add target and dependencies to ADIOS2
+##########################################################################
+#message(STATUS "ADIOS1 Find ended with ${ADIOS1_FOUND}")
+    if(ADIOS1_FOUND AND NOT TARGET adios1::adios)
+      message(STATUS "Add library ADIOS1 to the build")
+      add_library(adios1::adios UNKNOWN IMPORTED)
+      set_target_properties(adios1::adios PROPERTIES
+        IMPORTED_LOCATION "${ADIOS1_LIBRARY_PATH}"
+        INTERFACE_LINK_LIBRARIES "${ADIOS1_DEPENDENCY_LIBRARIES}"
+        INTERFACE_INCLUDE_DIRECTORIES "${ADIOS1_INCLUDE_DIRS}"
+      )
+    endif()

examples/CMakeLists.txt

@@ -4,3 +4,4 @@
 #------------------------------------------------------------------------------#
 
 add_subdirectory(hello)
+add_subdirectory(heatTransfer)

examples/heatTransfer/CMakeLists.txt

+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+add_subdirectory(write)
+add_subdirectory(read)

examples/heatTransfer/IO_adios2.cpp

@@ -60,6 +60,8 @@ IO::IO(const Settings &s, MPI_Comm comm)
 
     bpWriter = ad->Open(m_outputfilename, "w", comm, bpWriterSettings);
 
+    // ad->Open(m_outputfilename, "w", comm, bpWriterSettings);
+
     if (bpWriter == nullptr)
         throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
 }

examples/heatTransfer/read/CMakeLists.txt

+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+if(ADIOS_USE_MPI)
+  if(ADIOS_USE_ADIOS1)
+    find_package(ADIOS1 REQUIRED)
+    find_package(MPI COMPONENTS C REQUIRED)
+
+    add_executable(headTransfer_read_adios1 heatRead_adios1.cpp PrintData.cpp)
+    target_include_directories(headTransfer_read_adios1
+      PRIVATE ${MPI_C_INCLUDE_PATH}
+    )
+    target_link_libraries(headTransfer_read_adios1
+      adios1::adios ${MPI_C_LIBRARIES}
+    )
+
+    if(ADIOS_BUILD_TESTING)
+      add_test(
+        NAME Example::heatTransfer::read::adios1
+        COMMAND heatRead_adios1
+      )
+    endif()
+  endif()
+endif()
+

examples/heatTransfer/read/PrintData.cpp

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * PrintData.cpp
+ *
+ *  Created on: Apr 2017
+ *      Author: Norbert Podhorszki
+ */
+
+#include "PrintData.h"
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <string>
+
+void printData(double *xy, uint64_t *size, uint64_t *offset, int rank,
+               int steps)
+{
+    std::ofstream myfile;
+    std::string filename = "data." + std::to_string(rank);
+    myfile.open(filename);
+    double *data = xy;
+    uint64_t nelems = size[0] * size[1];
+    for (int step = 0; step < steps; step++)
+    {
+        myfile << "rank=" << rank << " size=" << size[0] << "x" << size[1]
+               << " offsets=" << offset[0] << ":" << offset[1]
+               << " step=" << step << std::endl;
+
+        myfile << " time   row   columns " << offset[1] << "..."
+               << offset[1] + size[1] - 1 << std::endl;
+        myfile << "        ";
+        for (int j = 0; j < size[1]; j++)
+        {
+            myfile << std::setw(9) << offset[1] + j;
+        }
+        myfile << std::endl;
+        myfile << "------------------------------------------------------------"
+                  "--\n";
+        for (int i = 0; i < size[0]; i++)
+        {
+            myfile << std::setw(5) << step << std::setw(5) << offset[0] + i;
+            for (int j = 0; j < size[1]; j++)
+            {
+                myfile << std::setw(9) << std::setprecision(2)
+                       << data[i * size[1] + j];
+            }
+            myfile << std::endl;
+        }
+        data += nelems;
+    }
+    myfile.close();
+}

examples/heatTransfer/read/PrintData.h

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * PrintData.h
+ *
+ *  Created on: Apr 2017
+ *      Author: Norbert Podhorszki
+ */
+
+#ifndef PRINTDATA_H_
+#define PRINTDATA_H_
+
+#include <cstdint>
+
+void printData(double *xy, uint64_t *size, uint64_t *offset, int rank,
+               int steps);
+
+#endif /* PRINTDATA_H_ */

examples/heatTransfer/read/heatRead_adios1.cpp

+
+#include <mpi.h>
+
+#include "adios_read.h"
+#include <cstdint>
+#include <iomanip>
+#include <iostream>
+#include <math.h>
+#include <memory>
+#include <stdexcept>
+#include <string>
+
+#include "PrintData.h"
+
+int main(int argc, char *argv[])
+{
+    MPI_Init(&argc, &argv);
+
+    if (argc < 2)
+    {
+        std::cout << "Not enough arguments: need an input file\n";
+        return 1;
+    }
+    const char *inputfile = argv[1];
+
+    /* World comm spans all applications started with the same aprun command
+     on a Cray XK6. So we have to split and create the local
+     'world' communicator for the reader only.
+     In normal start-up, the communicator will just equal the MPI_COMM_WORLD.
+     */
+
+    int wrank, wnproc;
+    MPI_Comm_rank(MPI_COMM_WORLD, &wrank);
+    MPI_Comm_size(MPI_COMM_WORLD, &wnproc);
+    MPI_Barrier(MPI_COMM_WORLD);
+
+    const unsigned int color = 2;
+    MPI_Comm mpiReaderComm;
+    MPI_Comm_split(MPI_COMM_WORLD, color, wrank, &mpiReaderComm);
+
+    int rank, nproc;
+    MPI_Comm_rank(mpiReaderComm, &rank);
+    MPI_Comm_size(mpiReaderComm, &nproc);
+
+    adios_read_init_method(ADIOS_READ_METHOD_BP, mpiReaderComm, "verbose=3");
+
+    ADIOS_FILE *f;
+    f = adios_read_open_file(inputfile, ADIOS_READ_METHOD_BP, mpiReaderComm);
+    if (f == NULL)
+    {
+        std::cout << adios_errmsg() << std::endl;
+        return -1;
+    }
+
+    ADIOS_VARINFO *vgndx = adios_inq_var(f, "gndx");
+    ADIOS_VARINFO *vgndy = adios_inq_var(f, "gndy");
+
+    unsigned int gndx = *(unsigned int *)vgndx->value;
+    unsigned int gndy = *(unsigned int *)vgndy->value;
+
+    if (rank == 0)
+    {
+        std::cout << "gndx = " << gndx << std::endl;
+        std::cout << "gndy = " << gndy << std::endl;
+    }
+    adios_free_varinfo(vgndx);
+    adios_free_varinfo(vgndy);
+
+    // 1D decomposition of the columns, which is inefficient for reading!
+    uint64_t readsize[2] = {gndx, gndy / nproc};
+    uint64_t offset[2] = {0LL, rank * readsize[1]};
+    if (rank == nproc - 1)
+    {
+        // last process should read all the rest of columns
+        readsize[1] = gndy - readsize[1] * (nproc - 1);
+    }
+
+    std::cout << "rank " << rank << " reads " << readsize[1]
+              << " columns from offset " << offset[1] << std::endl;
+
+    ADIOS_VARINFO *vT = adios_inq_var(f, "T");
+
+    double *T = new double[vT->nsteps * readsize[0] * readsize[1]];
+
+    // Create a 2D selection for the subset
+    ADIOS_SELECTION *sel = adios_selection_boundingbox(2, offset, readsize);
+
+    // Arrays are read by scheduling one or more of them
+    // and performing the reads at once
+    adios_schedule_read(f, sel, "T", 0, vT->nsteps, T);
+    adios_perform_reads(f, 1);
+
+    printData(T, readsize, offset, rank, vT->nsteps);
+    adios_read_close(f);
+    adios_free_varinfo(vT);
+    delete[] T;
+    // Terminate
+    adios_selection_delete(sel);
+    adios_read_finalize_method(ADIOS_READ_METHOD_BP);
+    MPI_Finalize();
+    return 0;
+}

examples/heatTransfer/write/CMakeLists.txt

+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+if(ADIOS_USE_MPI)
+  find_package(MPI COMPONENTS C REQUIRED)
+
+  add_executable(heatTransfer_write_adios2
+    main.cpp
+    HeatTransfer.cpp
+    Settings.cpp
+    IO_adios2.cpp
+  )
+  target_include_directories(heatTransfer_write_adios2
+    PRIVATE ${MPI_C_INCLUDE_PATH}
+  )
+  target_link_libraries(heatTransfer_write_adios2 adios2 ${MPI_C_LIBRARIES})
+
+  if(ADIOS_BUILD_TESTING)
+    add_test(
+      NAME Example::heatTransfer::write::adios2
+      COMMAND heatTransfer_write_adios2
+    )
+  endif()
+
+  if(ADIOS_USE_ADIOS1)
+    find_package(ADIOS1 REQUIRED)
+    find_package(MPI COMPONENTS C REQUIRED)
+
+    add_executable(heatTransfer_write_adios1
+      main.cpp
+      HeatTransfer.cpp
+      Settings.cpp
+      IO_adios1.cpp
+    )
+    target_include_directories(heatTransfer_write_adios1
+      PRIVATE ${MPI_C_INCLUDE_PATH}
+    )
+    target_link_libraries(heatTransfer_write_adios1
+      adios1::adios ${MPI_C_LIBRARIES}
+    )
+
+    if(ADIOS_BUILD_TESTING)
+      add_test(
+        NAME Example::heatTransfer::write::adios1
+        COMMAND heatTransfer_write_adios1
+      )
+    endif()
+  endif()
+endif()

examples/heatTransfer/HeatTransfer.cpp → examples/heatTransfer/write/HeatTransfer.cpp

@@ -10,7 +10,6 @@
  *     Author: Norbert Podhorszki
  *
  */
-#include <mpi.h>
 
 #include <iomanip>
 #include <iostream>

examples/heatTransfer/HeatTransfer.h → examples/heatTransfer/write/HeatTransfer.h

@@ -12,6 +12,7 @@
 #define HEATTRANSFER_H_
 
 #include <mpi.h>
+
 #include <vector>
 
 #include "Settings.h"

examples/heatTransfer/IO.h → examples/heatTransfer/write/IO.h

@@ -13,11 +13,11 @@
 
 #include "HeatTransfer.h"
 #include "Settings.h"
+
 #include <mpi.h>
 
 class IO
 {
-
 public:
     IO(const Settings &s, MPI_Comm comm);
     ~IO();

examples/heatTransfer/write/IO_adios2.cpp

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * IO_ADIOS2.cpp
+ *
+ *  Created on: Feb 2017
+ *      Author: Norbert Podhorszki
+ */
+
+#include "IO.h"
+#include "ADIOS_CPP.h"
+
+#include <string>
+
+static int rank_saved;
+adios::ADIOS *ad = nullptr;
+std::shared_ptr<adios::Engine> bpWriter;
+adios::Variable<double> *varT = nullptr;
+
+IO::IO(const Settings &s, MPI_Comm comm)
+{
+    rank_saved = s.rank;
+    m_outputfilename = s.outputfile + ".bp";
+    ad = new adios::ADIOS("adios2.xml", comm, adios::Verbose::INFO);
+
+    // Define method for engine creation
+    // 1. Get method def from config file or define new one
+
+    adios::Method &bpWriterSettings = ad->DeclareMethod("output");
+    if (!bpWriterSettings.isUserDefined())
+    {
+        // if not defined by user, we can change the default settings
+        bpWriterSettings.SetEngine("BPFileWriter"); // BP is the default engine
+        bpWriterSettings.AllowThreads(
+            1); // allow 1 extra thread for data processing
+        bpWriterSettings.AddTransport(
+            "File", "lucky=yes"); // ISO-POSIX file is the default transport
+                                  // Passing parameters to the transport
+        bpWriterSettings.SetParameters(
+            "have_metadata_file",
+            "yes"); // Passing parameters to the engine
+        bpWriterSettings.SetParameters(
+            "Aggregation",
+            std::to_string((s.nproc + 1) / 2)); // number of aggregators
+    }
+
+    // define T as 2D global array
+    varT = &ad->DefineVariable<double>(
+        "T",
+        // Global dimensions
+        {s.gndx, s.gndy},
+        // local size, could be defined later using SetSelection()
+        {s.ndx, s.ndy},
+        // offset of the local array in the global space
+        {s.offsx, s.offsy});
+
+    // add transform to variable
+    // adios::Transform tr = adios::transform::BZIP2( );
+    // varT.AddTransform( tr, "" );
+    // varT.AddTransform( tr,"accuracy=0.001" );  // for ZFP
+
+    bpWriter = ad->Open(m_outputfilename, "w", comm, bpWriterSettings,
+                        adios::IOMode::COLLECTIVE);
+
+    if (bpWriter == nullptr)
+        throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
+}
+
+IO::~IO()
+{
+    bpWriter->Close();
+    delete ad;
+}
+
+void IO::write(int step, const HeatTransfer &ht, const Settings &s,
+               MPI_Comm comm)
+{
+#if 1
+
+    /* This selection is redundant and not required, since we defined
+     * the selection already in DefineVariable(). It is here just as an example.
+     */
+    // Make a selection to describe the local dimensions of the variable we
+    // write and its offsets in the global spaces. This could have been done in
+    // adios.DefineVariable()
+    adios::SelectionBoundingBox sel({s.offsx, s.offsy}, {s.ndx, s.ndy});
+    varT->SetSelection(sel);
+
+    /* Select the area that we want to write from the data pointer we pass to
+       the
+       writer.
+       Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
+       Engine will copy this bounding box from the data pointer into the output
+       buffer.
+       Size of the bounding box should match the "space" selection which was
+       given
+       above.
+       Default memspace is always the full selection.
+    */
+    adios::SelectionBoundingBox memspace =
+        adios::SelectionBoundingBox({s.ndx, s.ndy}, {1, 1});
+    varT->SetMemorySelection(memspace);
+
+    bpWriter->Write<double>(*varT, ht.data());
+    bpWriter->Advance();
+
+#else
+
+    bpWriter->Write<double>(*varT, ht.data_noghost().data());
+    bpWriter->Advance();
+
+#endif
+}

examples/heatTransfer/Settings.cpp → examples/heatTransfer/write/Settings.cpp

@@ -11,6 +11,8 @@
 #include <cstdlib>
 #include <errno.h>
 
+#include <stdexcept>
+
 #include "Settings.h"
 
 static unsigned int convertToUint(std::string varName, char *arg)
@@ -80,5 +82,3 @@ Settings::Settings(int argc, char *argv[], int rank, int nproc) : rank{rank}
     else
         rank_down = rank + npx;
 }
-
-Settings::~Settings() {}

examples/heatTransfer/Settings.h → examples/heatTransfer/write/Settings.h

@@ -11,7 +11,7 @@
 #ifndef SETTINGS_H_
 #define SETTINGS_H_
 
-#include <memory>
+#include <string>
 
 class Settings
 {
@@ -48,7 +48,6 @@ public:
     int rank_down;
 
     Settings(int argc, char *argv[], int rank, int nproc);
-    ~Settings();
 };
 
 #endif /* SETTINGS_H_ */