diff --git a/CMakeLists.txt b/CMakeLists.txt
index 240c0554fa3d27d6e03b4e638a2fc353171b9092..5d3f59d51f93ab3df10fec779ab7360547354ddd 100644
--- a/CMakeLists.txt
+++ b/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)
diff --git a/Contributing.md b/Contributing.md
index d3824aa0d9a89c0968f7b0d4bfe29fcd21e701f4..0348aa104ab0aedfc0070c6da3859fcd7c54351e 100644
--- a/Contributing.md
+++ b/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:
diff --git a/cmake/FindADIOS1.cmake b/cmake/FindADIOS1.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..da0fdd08dbf1ae6c6f0f3257c719a9a8734d01d1
--- /dev/null
+++ b/cmake/FindADIOS1.cmake
@@ -0,0 +1,260 @@
+# - 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()
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index ffe6d00e4d8057f0e861d7e2209d16b7f2b26fe6..59d0aaef3e1741211ad8274c17dc9f2b361b879b 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -4,3 +4,4 @@
#------------------------------------------------------------------------------#
add_subdirectory(hello)
+add_subdirectory(heatTransfer)
diff --git a/examples/heatTransfer/CMakeLists.txt b/examples/heatTransfer/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e4cd30c850a0af1b3cd322cd386cb61a766109
--- /dev/null
+++ b/examples/heatTransfer/CMakeLists.txt
@@ -0,0 +1,7 @@
+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+add_subdirectory(write)
+add_subdirectory(read)
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index 26d83c1bf674acbe96ff59f8c27e81b02b0de547..aea0493ca7dfbbea62f9568f63c4a289bbaa1bba 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/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");
}
diff --git a/examples/heatTransfer/read/CMakeLists.txt b/examples/heatTransfer/read/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c82cf01a868db9bfbd2b445abef274c5cb866ece
--- /dev/null
+++ b/examples/heatTransfer/read/CMakeLists.txt
@@ -0,0 +1,27 @@
+#------------------------------------------------------------------------------#
+# 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()
+
diff --git a/examples/heatTransfer/read/PrintData.cpp b/examples/heatTransfer/read/PrintData.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..030fa561f1cc1a6e3dc62b24d8cf45f98583bfcd
--- /dev/null
+++ b/examples/heatTransfer/read/PrintData.cpp
@@ -0,0 +1,54 @@
+/*
+ * 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();
+}
diff --git a/examples/heatTransfer/read/PrintData.h b/examples/heatTransfer/read/PrintData.h
new file mode 100644
index 0000000000000000000000000000000000000000..308ace34007f88c15498464b1555b5cca3ed1f6b
--- /dev/null
+++ b/examples/heatTransfer/read/PrintData.h
@@ -0,0 +1,19 @@
+/*
+ * 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_ */
diff --git a/examples/heatTransfer/read/heatRead_adios1.cpp b/examples/heatTransfer/read/heatRead_adios1.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..bcedac6d5a84b700b9e7045eee1b222146b29341
--- /dev/null
+++ b/examples/heatTransfer/read/heatRead_adios1.cpp
@@ -0,0 +1,102 @@
+
+#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;
+}
diff --git a/examples/heatTransfer/write/CMakeLists.txt b/examples/heatTransfer/write/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb72a2af9bd234c09be42c8b00a69ffbca7114e4
--- /dev/null
+++ b/examples/heatTransfer/write/CMakeLists.txt
@@ -0,0 +1,51 @@
+#------------------------------------------------------------------------------#
+# 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()
diff --git a/examples/heatTransfer/HeatTransfer.cpp b/examples/heatTransfer/write/HeatTransfer.cpp
similarity index 99%
rename from examples/heatTransfer/HeatTransfer.cpp
rename to examples/heatTransfer/write/HeatTransfer.cpp
index ac706e4c66d75c5e342faa915ae2edb8aa4519e2..29283fa776a39650cec330d1688402a6b7f83299 100644
--- a/examples/heatTransfer/HeatTransfer.cpp
+++ b/examples/heatTransfer/write/HeatTransfer.cpp
@@ -10,7 +10,6 @@
* Author: Norbert Podhorszki
*
*/
-#include <mpi.h>
#include <iomanip>
#include <iostream>
diff --git a/examples/heatTransfer/HeatTransfer.h b/examples/heatTransfer/write/HeatTransfer.h
similarity index 99%
rename from examples/heatTransfer/HeatTransfer.h
rename to examples/heatTransfer/write/HeatTransfer.h
index 7d48eb558d2db274218e8b0030ad53cc2aa0f7f3..a52acbb742ba6cd617bcd2b7f94e8ec760c13cb9 100644
--- a/examples/heatTransfer/HeatTransfer.h
+++ b/examples/heatTransfer/write/HeatTransfer.h
@@ -12,6 +12,7 @@
#define HEATTRANSFER_H_
#include <mpi.h>
+
#include <vector>
#include "Settings.h"
diff --git a/examples/heatTransfer/IO.h b/examples/heatTransfer/write/IO.h
similarity index 100%
rename from examples/heatTransfer/IO.h
rename to examples/heatTransfer/write/IO.h
index 999866112e471e46f2136f804ed2ee5226bb0a0a..53caaf599fe4e1c2aac8f4cd58c216c7888adf6e 100644
--- a/examples/heatTransfer/IO.h
+++ b/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();
diff --git a/examples/heatTransfer/IO_adios1.cpp b/examples/heatTransfer/write/IO_adios1.cpp
similarity index 100%
rename from examples/heatTransfer/IO_adios1.cpp
rename to examples/heatTransfer/write/IO_adios1.cpp
diff --git a/examples/heatTransfer/write/IO_adios2.cpp b/examples/heatTransfer/write/IO_adios2.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..8af454f718bb406174c7e116018eafb000eb28e4
--- /dev/null
+++ b/examples/heatTransfer/write/IO_adios2.cpp
@@ -0,0 +1,114 @@
+/*
+ * 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
+}
diff --git a/examples/heatTransfer/IO_ascii.cpp b/examples/heatTransfer/write/IO_ascii.cpp
similarity index 100%
rename from examples/heatTransfer/IO_ascii.cpp
rename to examples/heatTransfer/write/IO_ascii.cpp
diff --git a/examples/heatTransfer/IO_hdf5_a.cpp b/examples/heatTransfer/write/IO_hdf5_a.cpp
similarity index 100%
rename from examples/heatTransfer/IO_hdf5_a.cpp
rename to examples/heatTransfer/write/IO_hdf5_a.cpp
diff --git a/examples/heatTransfer/Settings.cpp b/examples/heatTransfer/write/Settings.cpp
similarity index 98%
rename from examples/heatTransfer/Settings.cpp
rename to examples/heatTransfer/write/Settings.cpp
index 4337a00a33f7b3865bceb1feeb569537f1e6271c..4922afd5fdf640d258c110a8b1f3adc38ef613f0 100644
--- a/examples/heatTransfer/Settings.cpp
+++ b/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() {}
diff --git a/examples/heatTransfer/Settings.h b/examples/heatTransfer/write/Settings.h
similarity index 98%
rename from examples/heatTransfer/Settings.h
rename to examples/heatTransfer/write/Settings.h
index 97e85ea310adcd55a2ccc10ca8333346461b3949..20f83f395ce322b97da39edfff0afdd121c2d9e5 100644
--- a/examples/heatTransfer/Settings.h
+++ b/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_ */
diff --git a/examples/heatTransfer/main.cpp b/examples/heatTransfer/write/main.cpp
similarity index 92%
rename from examples/heatTransfer/main.cpp
rename to examples/heatTransfer/write/main.cpp
index 1d1372f401ff641f3dc0da71a1b175b9b5c5b1fb..ff1b6c44c9a5e0cbf836f60b475c3190d7e34e8f 100644
--- a/examples/heatTransfer/main.cpp
+++ b/examples/heatTransfer/write/main.cpp
@@ -10,7 +10,9 @@
* Author: Norbert Podhorszki
*
*/
+#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
+#undef OMPI_SKIP_MPICXX
#include <iostream>
#include <memory>
@@ -64,10 +66,10 @@ int main(int argc, char *argv[])
IO io(settings, mpiHeatTransferComm);
ht.init(true);
- ht.printT("Initialized T:", mpiHeatTransferComm);
+ // ht.printT("Initialized T:", mpiHeatTransferComm);
ht.heatEdges();
- // ht.exchange( mpiHeatTransferComm );
- ht.printT("Heated T:", mpiHeatTransferComm);
+ ht.exchange(mpiHeatTransferComm);
+ // ht.printT("Heated T:", mpiHeatTransferComm);
io.write(0, ht, settings, mpiHeatTransferComm);
for (unsigned int t = 1; t <= settings.steps; ++t)
diff --git a/examples/hello/adios1Writer/CMakeLists.txt b/examples/hello/adios1Writer/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b38cfb90d3a153197efaa99f88295187debcfc1b
--- /dev/null
+++ b/examples/hello/adios1Writer/CMakeLists.txt
@@ -0,0 +1,14 @@
+#------------------------------------------------------------------------------#
+# 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(hello_adios1Writer helloADIOS1Writer.cpp)
+ target_include_directories(hello_adios1Writer PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_adios1Writer adios2 ${MPI_C_LIBRARIES})
+endif()
+
+add_executable(hello_adios1Writer_nompi helloADIOS1Writer_nompi.cpp)
+target_link_libraries(hello_adios1Writer_nompi adios2)
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer.cpp b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
index 2a7803ab6edac9adc2618699fb3be45c3960b6c7..87101533b4795379e3b2c94966c44d01fea83403 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
@@ -11,7 +11,9 @@
#include <iostream>
#include <vector>
+#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
+#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
index 44d4d5547050e79ef4a3cb3b0222b4d21433438f..5955b33436df32cd835391a75c85bf2bc8f7f53b 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
@@ -16,7 +16,7 @@
int main(int argc, char *argv[])
{
const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
+ adios::ADIOS adios(adios::Verbose::INFO, adiosDebug);
// Application variable
std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index 67e193342b05fe0c7d99881038a69e5233706fda..d208c353979cc633ec57c741583831d27be03081 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -3,6 +3,13 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
+add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
+target_link_libraries(hello_bpWriter_nompi adios2_nompi)
+
+if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bpWriter_nompi COMMAND hello_bpWriter_nompi)
+endif()
+
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
add_executable(hello_bpWriter helloBPWriter.cpp)
@@ -12,12 +19,5 @@ if(ADIOS_USE_MPI)
if(ADIOS_BUILD_TESTING)
add_test( NAME Example::hello::bpWriter COMMAND hello_bpWriter)
endif()
-else()
- add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
- target_link_libraries(hello_bpWriter_nompi adios2)
-
- if(ADIOS_BUILD_TESTING)
- add_test( NAME Example::hello::bpWriter_nompi COMMAND hello_bpWriter_nompi)
- endif()
endif()
diff --git a/examples/hello/datamanReader/CMakeLists.txt b/examples/hello/datamanReader/CMakeLists.txt
index 3aa3e264ad829cf697e9cd91a6336d6fcf8b668d..34db8ffb63b807a029daa91ad67f80614170c736 100644
--- a/examples/hello/datamanReader/CMakeLists.txt
+++ b/examples/hello/datamanReader/CMakeLists.txt
@@ -3,6 +3,16 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
+add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
+target_link_libraries(hello_datamanReader_nompi adios2_nompi)
+
+if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanReader_nompi
+ COMMAND hello_datamanReader_nompi
+ )
+endif()
+
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
@@ -14,15 +24,5 @@ if(ADIOS_USE_MPI)
if(ADIOS_BUILD_TESTING)
add_test(NAME Example::hello::datamanReader COMMAND hello_datamanReader)
endif()
-else()
- add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
- target_link_libraries(hello_datamanReader_nompi adios2)
-
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::datamanReader_nompi
- COMMAND hello_datamanReader_nompi
- )
- endif()
endif()
diff --git a/examples/hello/datamanWriter/CMakeLists.txt b/examples/hello/datamanWriter/CMakeLists.txt
index 7defd6c40b3bd2eba1802a4e6e99dd41f5de1697..c9268d31c761aac93069bee68adcae9fa2289530 100644
--- a/examples/hello/datamanWriter/CMakeLists.txt
+++ b/examples/hello/datamanWriter/CMakeLists.txt
@@ -3,6 +3,16 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
+add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
+target_link_libraries(hello_datamanWriter_nompi adios2_nompi)
+
+if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanWriter_nompi
+ COMMAND hello_datamanWriter_nompi
+ )
+endif()
+
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
@@ -14,15 +24,5 @@ if(ADIOS_USE_MPI)
if(ADIOS_BUILD_TESTING)
add_test(NAME Example::hello::datamanWriter COMMAND hello_datamanWriter)
endif()
-else()
- add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
- target_link_libraries(hello_datamanWriter_nompi adios2)
-
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::datamanWriter_nompi
- COMMAND hello_datamanWriter_nompi
- )
- endif()
endif()
diff --git a/examples/hello/timeBP/CMakeLists.txt b/examples/hello/timeBP/CMakeLists.txt
index d86828c90625a3a4e34952730fcd6ed9631c2949..949e8145e18683463df84e4b555e065901bc9e03 100644
--- a/examples/hello/timeBP/CMakeLists.txt
+++ b/examples/hello/timeBP/CMakeLists.txt
@@ -3,6 +3,16 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
+add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
+target_link_libraries(hello_timeBPWriter_nompi adios2_nompi)
+
+if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::timeBPWriter_nompi
+ COMMAND hello_timeBPWriter_nompi
+ )
+endif()
+
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
add_executable(hello_timeBPWriter timeBPWriter.cpp)
@@ -13,14 +23,4 @@ if(ADIOS_USE_MPI)
if(ADIOS_BUILD_TESTING)
add_test(NAME Example::hello::timeBPWriter COMMAND hello_timeBPWriter)
endif()
-else()
- add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
- target_link_libraries(hello_timeBPWriter_nompi adios2)
-
- if(ADIOS_BUILD_TESTING)
- add_test(
- NAME Example::hello::timeBPWriter_nompi
- COMMAND hello_timeBPWriter_nompi
- )
- endif()
endif()
diff --git a/include/core/VariableBase.h b/include/core/VariableBase.h
index fb223613bc157057d50123f1540bc6b2a10f3f74..49bb98a1e45e55f95664ec18d84326d220f6bf70 100644
--- a/include/core/VariableBase.h
+++ b/include/core/VariableBase.h
@@ -12,14 +12,16 @@
#define VARIABLEBASE_H_
/// \cond EXCLUDE_FROM_DOXYGEN
+#include <exception>
#include <iterator>
#include <sstream>
#include <string>
#include <vector>
/// \endcond
-#include "functions/adiosFunctions.h" //GetTotalSize, DimsToCSV
-#include "functions/adiosTemplates.h" //GetType<T>
+#include "functions/adiosFunctions.h" //GetTotalSize, DimsToCSV, ConvertUint64VectorToSizetVector
+#include "functions/adiosTemplates.h" //GetType<T>
+#include "selection/SelectionBoundingBox.h" //Selection
namespace adios
{
@@ -42,10 +44,13 @@ public:
Dims m_LocalDimensions; ///< dimensions per rank (MPI)
Dims m_GlobalDimensions; ///< total dimensions across MPI
Dims m_Offsets; ///< selections offset
+ Dims m_MemoryDimensions; ///< array of memory dimensions
+ Dims m_MemoryOffsets; ///< array of memory offsets
bool m_IsScalar = false;
const bool m_IsDimension = false;
+ const bool m_DebugMode = false;
- VariableBase(const std::string name, const std::string type,
+ VariableBase(const std::string &name, const std::string type,
const std::size_t elementSize, const Dims localDimensions,
const Dims globalDimensions, const Dims offsets,
const bool debugMode)
@@ -80,9 +85,55 @@ public:
return GetTotalSize(m_LocalDimensions);
}
- // protected: off for now
- const bool m_DebugMode = false;
+ /**
+ * Set the local dimension and global offset of the variable using a
+ * selection
+ * Only bounding boxes are allowed
+ */
+ void SetSelection(const SelectionBoundingBox &sel)
+ {
+ if (m_GlobalDimensions.size() == 0)
+ {
+ throw std::invalid_argument("Variable.SetSelection() is an invalid "
+ "call for single value variables\n");
+ }
+ if (m_GlobalDimensions.size() != sel.m_Count.size())
+ {
+ throw std::invalid_argument("Variable.SetSelection() bounding box "
+ "dimension must equal the global "
+ "dimension of the variable\n");
+ }
+
+ ConvertUint64VectorToSizetVector(sel.m_Count, m_LocalDimensions);
+ ConvertUint64VectorToSizetVector(sel.m_Start, m_Offsets);
+ }
+
+ /**
+ * Set the local dimension and global offset of the variable using a
+ * selection
+ * Only bounding boxes are allowed
+ */
+ void SetMemorySelection(const SelectionBoundingBox &sel)
+ {
+ if (m_GlobalDimensions.size() == 0)
+ {
+ throw std::invalid_argument(
+ "Variable.SetMemorySelection() is an invalid "
+ "call for single value variables\n");
+ }
+ if (m_GlobalDimensions.size() != sel.m_Count.size())
+ {
+ throw std::invalid_argument(
+ "Variable.SetMemorySelection() bounding box "
+ "dimension must equal the global "
+ "dimension of the variable\n");
+ }
+
+ ConvertUint64VectorToSizetVector(sel.m_Count, m_MemoryDimensions);
+ ConvertUint64VectorToSizetVector(sel.m_Start, m_MemoryOffsets);
+ }
};
-}
+
+} // end namespace
#endif /* VARIABLEBASE_H_ */
diff --git a/include/engine/adios1/ADIOS1Reader.h b/include/engine/adios1/ADIOS1Reader.h
index e2abe89bef8c73d2d398be33644a099c0ff83566..53fb32bec3f8cf8c09ef7584c4f06213ed47bfba 100644
--- a/include/engine/adios1/ADIOS1Reader.h
+++ b/include/engine/adios1/ADIOS1Reader.h
@@ -23,6 +23,14 @@
namespace adios
{
+#ifndef ADIOS_HAVE_MPI
+#define _NOMPI 1
+#endif
+#include "adios_read_v2.h" // this is adios 1.x header file
+#ifndef ADIOS_HAVE_MPI
+#undef _NOMPI
+#endif
+
class ADIOS1Reader : public Engine
{
@@ -44,65 +52,40 @@ public:
~ADIOS1Reader();
- Variable<void> *InquireVariable(const std::string &variableName,
+ Variable<void> *InquireVariable(const std::string &name,
const bool readIn = true);
-
- Variable<char> *InquireVariableChar(const std::string &variableName,
+ Variable<char> *InquireVariableChar(const std::string &name,
const bool readIn = true);
-
- Variable<unsigned char> *
- InquireVariableUChar(const std::string &variableName,
- const bool readIn = true);
-
- Variable<short> *InquireVariableShort(const std::string &variableName,
+ Variable<unsigned char> *InquireVariableUChar(const std::string &name,
+ const bool readIn = true);
+ Variable<short> *InquireVariableShort(const std::string &name,
const bool readIn = true);
-
- Variable<unsigned short> *
- InquireVariableUShort(const std::string &variableName,
- const bool readIn = true);
-
- Variable<int> *InquireVariableInt(const std::string &variableName,
+ Variable<unsigned short> *InquireVariableUShort(const std::string &name,
+ const bool readIn = true);
+ Variable<int> *InquireVariableInt(const std::string &name,
const bool readIn = true);
-
- Variable<unsigned int> *InquireVariableUInt(const std::string &variableName,
+ Variable<unsigned int> *InquireVariableUInt(const std::string &name,
const bool readIn = true);
-
- Variable<long int> *InquireVariableLInt(const std::string &variableName,
+ Variable<long int> *InquireVariableLInt(const std::string &name,
const bool readIn = true);
-
- Variable<unsigned long int> *
- InquireVariableULInt(const std::string &variableName,
- const bool readIn = true);
-
- Variable<long long int> *
- InquireVariableLLInt(const std::string &variableName,
- const bool readIn = true);
-
+ Variable<unsigned long int> *InquireVariableULInt(const std::string &name,
+ const bool readIn = true);
+ Variable<long long int> *InquireVariableLLInt(const std::string &name,
+ const bool readIn = true);
Variable<unsigned long long int> *
- InquireVariableULLInt(const std::string &variableName,
- const bool readIn = true);
-
- Variable<float> *InquireVariableFloat(const std::string &variableName,
+ InquireVariableULLInt(const std::string &name, const bool readIn = true);
+ Variable<float> *InquireVariableFloat(const std::string &name,
const bool readIn = true);
-
- Variable<double> *InquireVariableDouble(const std::string &variableName,
+ Variable<double> *InquireVariableDouble(const std::string &name,
const bool readIn = true);
-
- Variable<long double> *
- InquireVariableLDouble(const std::string &variableName,
- const bool readIn = true);
-
+ Variable<long double> *InquireVariableLDouble(const std::string &name,
+ const bool readIn = true);
Variable<std::complex<float>> *
- InquireVariableCFloat(const std::string &variableName,
- const bool readIn = true);
-
+ InquireVariableCFloat(const std::string &name, const bool readIn = true);
Variable<std::complex<double>> *
- InquireVariableCDouble(const std::string &variableName,
- const bool readIn = true);
-
+ InquireVariableCDouble(const std::string &name, const bool readIn = true);
Variable<std::complex<long double>> *
- InquireVariableCLDouble(const std::string &variableName,
- const bool readIn = true);
+ InquireVariableCLDouble(const std::string &name, const bool readIn = true);
/**
* Not implemented
@@ -110,32 +93,20 @@ public:
* @param readIn
* @return
*/
- VariableCompound *InquireVariableCompound(const std::string name,
+ VariableCompound *InquireVariableCompound(const std::string &name,
const bool readIn = true);
void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- // format::BP1Writer m_BP1Writer; ///< format object will provide the
- // required
- // BP functionality to be applied on m_Buffer and m_Transports
-
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
+ void Init(); ///< called from constructor, gets the selected ADIOS1
+ /// transport method from settings
template <class T>
- Variable<T> *InquireVariableCommon(const std::string name,
+ Variable<T> *InquireVariableCommon(const std::string &name,
const bool readIn)
{
- std::cout << "Hello BPReaderCommon\n";
+ std::cout << "Hello ADIOS1Reader::InquireVariableCommon\n";
// here read variable metadata (dimensions, type, etc.)...then create a
// Variable like below:
@@ -144,8 +115,10 @@ private:
// return &variable; //return address if success
return nullptr; // on failure
}
+
+ enum ADIOS_READ_METHOD read_method = ADIOS_READ_METHOD_BP;
};
} // end namespace adios
-#endif /* BPFILEREADER_H_ */
+#endif /* ADIOS1READER_H_ */
diff --git a/include/engine/adios1/ADIOS1Writer.h b/include/engine/adios1/ADIOS1Writer.h
index d783c02f7bf675d4db4d11ae84211151cafae6d8..17553a885b454697507d8645a767fbf72c39ed2b 100644
--- a/include/engine/adios1/ADIOS1Writer.h
+++ b/include/engine/adios1/ADIOS1Writer.h
@@ -18,11 +18,11 @@
namespace adios
{
-#ifdef ADIOS_NOMPI
+#ifndef ADIOS_HAVE_MPI
#define _NOMPI
#endif
#include "adios.h" // this is adios 1.x header file
-#ifdef ADIOS_NOMPI
+#ifndef ADIOS_HAVE_MPI
#undef _NOMPI
#endif
diff --git a/include/external/adios_selection.h b/include/external/adios_selection.h
new file mode 100644
index 0000000000000000000000000000000000000000..551d72ee5f8ea6297f5367e12b3759abdb6fdb1a
--- /dev/null
+++ b/include/external/adios_selection.h
@@ -0,0 +1,240 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ */
+
+/*
+ * Streaming/Chunking/Selection Read API in C for ADIOS BP format
+ *
+ * A SELECTION is the data ranges resulting from a QUERY over a file and
+ * variable(s).
+ *
+ * A SELECTION can be a list of bounding boxes and point-sets. Other data
+ * structures
+ * are not supported. Any query will result in such a selection.
+ * Other selections are the write-block and auto.
+ *
+ * Write block is a block of data written
+ * by a writer process, it is identified by an index. If each writer outputs
+ * one block
+ * then the index equals to the rank of the write process. With multi-var
+ * writing and
+ * multiple steps in a file, index runs from 0 as rank 0 process' first block.
+ *
+ * Auto selection lets the read method to automatically choose what to return.
+ * It will
+ * be a block / blocks of selected writers.
+ *
+ * If a query is a simple bounding box, the selection is the bounding box
+ * itself, so
+ * the application does not need to retrieve the selection to work on the read
+ * data.
+ */
+#ifndef __ADIOS_SELECTION_C_H__
+#define __ADIOS_SELECTION_C_H__
+
+#include <stdint.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*************************/
+/* Types used in the API */
+/*************************/
+
+typedef struct ADIOS_SELECTION_STRUCT ADIOS_SELECTION;
+
+/* Type of selection */
+enum ADIOS_SELECTION_TYPE
+{
+ ADIOS_SELECTION_BOUNDINGBOX = 0, /* Contiguous block of data defined by
+ offsets and counts in each dimension */
+ ADIOS_SELECTION_POINTS = 1, /* List of individual points */
+ ADIOS_SELECTION_WRITEBLOCK =
+ 2, /* Selection of an individual block written by a writer process */
+ ADIOS_SELECTION_AUTO = 3 /* Let the method decide what to return */
+};
+
+/* A Bounding Box */
+typedef struct
+{
+ int ndim;
+ uint64_t *start;
+ uint64_t *count;
+} ADIOS_SELECTION_BOUNDINGBOX_STRUCT;
+
+/* A list of points.
+ * It is a 1D array of indices, linearized for all dimension
+ * (e.g. [i1,j1,k1,i2,j2,k2,...,in,jn,kn] for n points in a 3D space.
+ * If a container selection is given, points are relative coordinates/offsets in
+ * the
+ * container box/writeblock.
+ * 1D offsets in N-dimensional container are allowed. Such selections are
+ * returned by
+ * FASTBIT and ALACRITY query method. File reading is supported for such
+ * selections.
+ * adios_selection_points_1DtoND() can be used to convert 1D to N-D points.
+ */
+typedef struct
+{
+ int ndim;
+ int _free_points_on_delete; // user provided points are not copied, won't
+ // free either
+ uint64_t npoints;
+ uint64_t *points;
+ ADIOS_SELECTION
+ *container_selection; // a writeblock, a bounding box, or NULL
+} ADIOS_SELECTION_POINTS_STRUCT;
+
+/* A selected block produced by a writer
+ * Identified with an index in current versions.
+ */
+typedef struct
+{
+ int index;
+
+ /* NCSU ALACRITY-ADIOS:
+ * Adding timestep-relative vs. absolute writeblock selections, as
+ * well as sub-PG selection support. Both of these are currently only
+ * used by the transform layer
+ */
+ int is_absolute_index; /* 0 if 'index' is relative to the current timestep,
+ != 0
+ otherwise (i.e., absolute index) */
+ int is_sub_pg_selection; /* Whether this writeblock selection contains
+ sub-PG bounds.
+ The following fields only matter if this is != 0
+ */
+
+ /* Reads the linear range of elements in [element_offset, element_offset +
+ * nelements) */
+ uint64_t element_offset;
+ uint64_t nelements;
+} ADIOS_SELECTION_WRITEBLOCK_STRUCT;
+
+/* Let the read method decide what to return to each reading client.
+ * Hints are method-dependent parameters to influence what and how to
+ * return (e.g. the ordering of returned chunks, decomposition among
+ * read processes, etc.)
+ */
+typedef struct
+{
+ char *hints;
+} ADIOS_SELECTION_AUTO_STRUCT;
+
+/** Selection for reading a subset of a variable.
+ * A selection is an additive list of bounding boxes and point-sets
+ */
+struct ADIOS_SELECTION_STRUCT
+{
+ enum ADIOS_SELECTION_TYPE type; /* Type of selection */
+ union {
+ ADIOS_SELECTION_BOUNDINGBOX_STRUCT bb;
+ ADIOS_SELECTION_POINTS_STRUCT points;
+ ADIOS_SELECTION_WRITEBLOCK_STRUCT block;
+ ADIOS_SELECTION_AUTO_STRUCT autosel;
+ } u;
+ // ADIOS_SELECTION *next;
+};
+
+#ifndef __INCLUDED_FROM_FORTRAN_API__
+
+/** Boundingbox selection to read a subset of a non-scalar variable.
+ * IN:
+ * ndim Number of dimensions
+ * start array of offsets to start reading in each dimension
+ * count number of data elements to read in each dimension
+ * RETURN: A selection which can be used to read variables
+ */
+ADIOS_SELECTION *adios_selection_boundingbox(int ndim, const uint64_t *start,
+ const uint64_t *count);
+
+/** Selection for a selection of an enumeration of positions.
+ * IN:
+ * ndim Number of dimensions
+ * npoints Number of points of the selection
+ * points 1D array of indices, compacted for all dimension
+ * (e.g. [i1,j1,k1,i2,j2,k2,...,in,jn,kn] for
+ * n points in a 3D space.
+ */
+ADIOS_SELECTION *adios_selection_points(int ndim, uint64_t npoints,
+ const uint64_t *points);
+
+/** Selection for a block of data coming from a certain producer.
+ *
+ * IN:
+ * index Identifier of the written block, starting from 0 for the
+ * first block
+ * written by producer rank 0. If each writer outputs one block
+ * then the index equals to the rank of the write process.
+ * With multi-var writing and multiple steps in a file, index
+ * should be
+ * calculated by the reading application using outside
+ * information beyond
+ * what is provided by the ADIOS Read API.
+ */
+ADIOS_SELECTION *adios_selection_writeblock(int index);
+
+/** Let the method decide what data gets to what reader process.
+ * This selection enables each reading method to provide an 'optimal'
+ * data transfer from writers to readers. It depends on the method and the
+ * circumstances, what this selection actually means.
+ *
+ * E.g. in situ processing: readers on a compute node will receive all data
+ * from the writers on the same compute node.
+ *
+ * IN:
+ * hints Method dependent parameters to influence what and how to
+ * return (e.g. decomposition; ordering of returned chunks)
+ */
+ADIOS_SELECTION *adios_selection_auto(char *hints);
+
+/** Make a strided hyperslab selection the same way as in HDF5.
+ * IN:
+ * ndim Number of dimentsions
+ * start array of offsets to start reading in each dimension
+ * strides striding steps, NULL=1 in all dimensions (= boundingbox)
+ * count number of data elements to read in each dimension
+ * blocks block size at each stride, NULL=1 in all dimensions
+ */
+/*
+ No support: Klasky, Podhorszki
+ Support:
+
+ADIOS_SELECTION* adios_selection_hyperslab (uint64_t ndim, uint64_t *start,
+uint64_t *strides,
+ uint64_t *count, uint64_t *blocks);
+*/
+
+/** Delete a selection and free up memory used by the selection.
+ * IN: selection
+ * RESULT: None
+ * The ADIOS_SELECTION object can be simply freed by free(), too.
+ */
+void adios_selection_delete(ADIOS_SELECTION *selection);
+
+/* Convert one selection of 1D point offsets in a bounding box,
+ * returned by FASTBIT and ALACRITY query methods, to N-dimensional points.
+ * This function works only if there is a bounding box in
+ * pointsinbox1D->u.points.container!
+ * It allocates memory for the result selection, after which the original can be
+ * freed.
+ * Return:
+ * If global==0, the points will be relative to the container, if not, the
+ * points will be
+ * global coordinates (container's starting offsets added to each point) and
+ * result's container
+ * will be NULL.
+ */
+ADIOS_SELECTION *adios_selection_points_1DtoND(ADIOS_SELECTION *pointsinbox1D,
+ int global);
+
+#endif /*__INCLUDED_FROM_FORTRAN_API__*/
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*__ADIOS_SELECTION_C_H__*/
diff --git a/include/functions/adiosFunctions.h b/include/functions/adiosFunctions.h
index c9b88a03ed124a5c828d85709630b0b6e3790b6f..418a075781663a6e0abcfd60094fb4f73bccf141 100644
--- a/include/functions/adiosFunctions.h
+++ b/include/functions/adiosFunctions.h
@@ -182,6 +182,12 @@ BuildParametersMap(const std::vector<std::string> ¶meters,
*/
std::vector<int> CSVToVectorInt(const std::string csv);
+/** Convert a vector of uint64_t elements to a vector of std::size_t elements
+ * @param input vector of uint64_t elements
+ * @param output vector of std::size_t elements
+ */
+void ConvertUint64VectorToSizetVector(const std::vector<std::uint64_t> &in,
+ std::vector<std::size_t> &out);
/**
* Converts a vector of dimensions to a CSV string
* @param dims vector of dimensions
@@ -197,7 +203,8 @@ std::string DimsToCSV(const std::vector<std::size_t> &dims);
* buffers ( default = 1.5 )
* @param maxBufferSize user provided maximum buffer size
* @param buffer to be reallocated
- * @return true: must do a transport flush, false: buffer sizes are enough to
+ * @return true: must do a transport flush, false: buffer sizes are enough
+ * to
* contain incoming data, no need for transport flush
*/
bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
diff --git a/include/selection/Selection.h b/include/selection/Selection.h
new file mode 100644
index 0000000000000000000000000000000000000000..70d4c831409cb0e1cd7beeee0e121470acf39d1f
--- /dev/null
+++ b/include/selection/Selection.h
@@ -0,0 +1,70 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ */
+
+/*
+ * Selection API in C++
+ *
+ * A SELECTION is the data ranges resulting from a QUERY over a file and
+ * variable(s).
+ *
+ * A SELECTION can be a list of bounding boxes and point-sets. Other data
+ * structures
+ * are not supported. Any query will result in such a selection.
+ * Other selections are the write-block and auto.
+ *
+ * Write block is a block of data written
+ * by a writer process, it is identified by an index. If each writer outputs
+ * one block
+ * then the index equals to the rank of the write process. With multi-var
+ * writing and
+ * multiple steps in a file, index runs from 0 as rank 0 process' first block.
+ *
+ * Auto selection lets the read method to automatically choose what to return.
+ * It will
+ * be a block / blocks of selected writers.
+ *
+ * If a query is a simple bounding box, the selection is the bounding box
+ * itself, so
+ * the application does not need to retrieve the selection to work on the read
+ * data.
+ */
+#ifndef __ADIOS_SELECTION_H__
+#define __ADIOS_SELECTION_H__
+
+/// \cond EXCLUDE_FROM_DOXYGEN
+#include "external/adios_selection.h"
+#include <stdint.h>
+/// \endcond
+
+namespace adios
+{
+
+/*************************/
+/* Types used in the API */
+/*************************/
+/* Type of selection */
+enum class SelectionType
+{
+ // Contiguous block of data defined by offsets and counts in each
+ // dimension
+ BoundingBox = ADIOS_SELECTION_BOUNDINGBOX,
+ // List of individual points
+ Points = ADIOS_SELECTION_POINTS,
+ // Selection of an individual block written by a writer process
+ WriteBlock = ADIOS_SELECTION_WRITEBLOCK,
+ // Let the method decide what to return
+ Auto = ADIOS_SELECTION_AUTO
+};
+
+class Selection
+{
+public:
+ Selection(const SelectionType t) : m_Type(t){};
+ const SelectionType m_Type;
+};
+
+} // namespace adios
+
+#endif /*__ADIOS_SELECTION_H__*/
diff --git a/include/selection/SelectionBoundingBox.h b/include/selection/SelectionBoundingBox.h
new file mode 100644
index 0000000000000000000000000000000000000000..b110fd96e517a2ee7854db1bad92d422dfd3d5e1
--- /dev/null
+++ b/include/selection/SelectionBoundingBox.h
@@ -0,0 +1,38 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ */
+
+#ifndef __ADIOS_SELECTION_BOUNDINGBOX_H__
+#define __ADIOS_SELECTION_BOUNDINGBOX_H__
+
+/// \cond EXCLUDE_FROM_DOXYGEN
+#include <cstdint>
+/// \endcond
+
+#include "selection/Selection.h"
+
+namespace adios
+{
+
+/** Boundingbox selection to read a subset of a non-scalar variable.
+ * @param start array of offsets to start reading in each dimension
+ * @param count number of data elements to read in each dimension
+ */
+class SelectionBoundingBox : public Selection
+{
+public:
+ SelectionBoundingBox(const std::vector<std::uint64_t> start,
+ const std::vector<std::uint64_t> count)
+ : Selection(SelectionType::BoundingBox), m_Start(start), m_Count(count)
+ {
+ }
+ ~SelectionBoundingBox(){};
+
+ std::vector<std::uint64_t> m_Start;
+ std::vector<std::uint64_t> m_Count;
+};
+
+} // namespace adios
+
+#endif /*__ADIOS_SELECTION_BOUNDINGBOX_H__*/
diff --git a/include/selection/SelectionPoints.h b/include/selection/SelectionPoints.h
new file mode 100644
index 0000000000000000000000000000000000000000..13fa951cbaa587c2f1592e64dd9eeb46601d29cd
--- /dev/null
+++ b/include/selection/SelectionPoints.h
@@ -0,0 +1,55 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ */
+
+#ifndef __ADIOS_SELECTION_POINTS_H__
+#define __ADIOS_SELECTION_POINTS_H__
+
+/// \cond EXCLUDE_FROM_DOXYGEN
+#include <cstdint>
+/// \endcond
+
+#include "selection/Selection.h"
+#include "selection/SelectionBoundingBox.h"
+
+namespace adios
+{
+
+/** Selection for a selection of an enumeration of positions.
+ * @param ndim Number of dimensions
+ * @param npoints Number of points of the selection
+ * @param points 1D array of indices, compacted for all dimension
+ * (e.g. [i1,j1,k1,i2,j2,k2,...,in,jn,kn] for
+ * n points in a 3D space.
+ */
+class SelectionPoints : public Selection
+{
+public:
+ SelectionPoints(std::size_t ndim, std::size_t npoints,
+ std::vector<std::uint64_t> &points)
+ : Selection(SelectionType::Points), m_Ndim(ndim), m_Npoints(npoints),
+ m_Points(points)
+ {
+ }
+
+ ///< C-style constructor to be used in the C-to-C++ wrapper
+ SelectionPoints(std::size_t ndim, std::size_t npoints, uint64_t *points)
+ : Selection(SelectionType::Points), m_Ndim(ndim), m_Npoints(npoints),
+ m_Points(std::vector<std::uint64_t>()), m_PointsC(points)
+ {
+ }
+
+ ~SelectionPoints(){};
+
+ const std::size_t m_Ndim;
+ const std::size_t m_Npoints;
+ std::vector<std::uint64_t> &m_Points;
+ ///< C-to-C++ wrapper needs a pointer to hold the points created by the C
+ /// application
+ std::uint64_t *m_PointsC = nullptr;
+};
+
+} // namespace adios
+
+#endif /*__ADIOS_SELECTION_POINTS_H__*/
diff --git a/scripts/developer/git/setup-aliases b/scripts/developer/git/setup-aliases
index 2d996582b0284debddf288a85708702053f53270..bf2f6c298365f828675fe64fd687482d4592534f 100755
--- a/scripts/developer/git/setup-aliases
+++ b/scripts/developer/git/setup-aliases
@@ -1,15 +1,15 @@
#!/usr/bin/env bash
echo "Setting up git aliases..."
-if ! which clang-format 2>1 1>/dev/null
+if ! which clang-format 1>/dev/null 2>&1
then
echo "Warning: ADIOS uses clang-format to enforce style guidelines but no"
- echo " clang-format binary was found in tyour path"
+ echo " clang-format binary was found in your path"
fi
if ! git config alias.clang-format "!scripts/developer/git/git-clang-format"
then
- echo "Error adding clang-format alias"
+ echo "Waring: Error adding clang-format alias"
fi
exit 0
diff --git a/scripts/developer/git/setup-remotes b/scripts/developer/git/setup-remotes
index 17cac1b31d0abba2b48886f23ba531eb21616776..1071260393482dd3f3d084b43d02b5b2c186c459 100755
--- a/scripts/developer/git/setup-remotes
+++ b/scripts/developer/git/setup-remotes
@@ -1,27 +1,50 @@
#!/usr/bin/env bash
-echo "Checking GitHub username..."
-GHUSER=$(git remote get-url origin | sed 's|.*[:/]\([^/]*\)/adios2.git|\1|')
-if [ -z "${GHUSER}" ]
+GH_UPSTREAM_URL=$(git remote show origin | grep "Fetch URL" | sed 's|.*: \(.*\)|\1|')
+BRANCH="$(git branch | sed -n 's|^\* \(.*\)|\1|p')"
+if [ "${GH_UPSTREAM_URL}" != "https://github.com/ornladios/adios2.git" ] || \
+ [ "${BRANCH}" != "master" ]
then
- echo " Warning: Unable to determine GitHub username. Are you sure you"
- echo " cloned your fork?"
+ echo " Warning: This script is intended to run off of the master branch"
+ echo " of the upstream repository. Setup might not work as"
+ echo " expected otherwise."
+fi
+
+read -p "Enter your GitHub username: " GH_USERNAME
+if [ -z "${GH_USERNAME}" ]
+then
+ echo " Error: GitHub username cannot be empty."
exit 1
fi
-echo "Using GitHub user ${GHUSER}"
+git remote set-url origin https://github.com/${GH_USERNAME}/adios2.git
+read -p "Setup SSH push access? [(y)/n] " GH_USE_SSH
+GH_USE_SSH="${GH_USE_SSH,,}"
+if [ -z "${GH_USE_SSH}" ]
+then
+ echo " Empty entry. Using 'y' as default"
+ GH_USE_SSH="y"
+elif [ "${GH_USE_SSH}" != "y" ] && [ "${GH_USE_SSH}" != "n" ]
+then
+ echo " Invalid entry. Using 'y' by default"
+ GH_USE_SSH="y"
+fi
+if [ "${GH_USE_SSH}" == "y" ]
+then
+ git config remote.origin.pushurl "git@github.com:${GH_USERNAME}/adios2.git"
+fi
+
-echo "Adding upstream remote..."
if git remote show upstream > /dev/null 2>&1
then
- echo " Warning: upstream remote already exists; skipping"
-else
- git remote add upstream https://github.com/ornladios/adios2.git
+ echo " Warning: upstream remote already exists; replacing..."
+ git remote rm upstream
fi
-git fetch --all -p
+git remote add upstream https://github.com/ornladios/adios2.git
echo "Re-configuring local master branch to use upstream"
git config branch.master.remote upstream
git config branch.master.mergeOptions "--ff-only"
git config merge.log 100
+git fetch --all -p
exit 0
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index 611c256c9213d76580bd770496c162a3a9e9a000..766c5dec17a3689dfdac3c9d55faa5b4827b6064 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -2,71 +2,81 @@
# Distributed under the OSI-approved Apache License, Version 2.0. See
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-
-add_library(adios2
- ADIOS.cpp ADIOS_inst.cpp
- #ADIOS_C.cpp
-
- capsule/heap/STLVector.cpp
- capsule/shmem/ShmSystemV.cpp
-
- core/Capsule.cpp
- core/Engine.cpp
- core/Method.cpp
- core/Support.cpp
- core/Transform.cpp
- core/Transport.cpp
-
- engine/bp/BPFileReader.cpp
- engine/bp/BPFileWriter.cpp
-
- utilities/format/bp1/BP1Base.cpp
- utilities/format/bp1/BP1Aggregator.cpp
- utilities/format/bp1/BP1Writer.cpp
- utilities/profiling/iochrono/Timer.cpp
-
- functions/adiosFunctions.cpp
+set(adios2_targets adios2_nompi)
+if(ADIOS_USE_MPI)
+ list(APPEND adios2_targets adios2)
+endif()
+
+foreach(adios2_target IN LISTS adios2_targets)
+ add_library(${adios2_target}
+ ADIOS.cpp ADIOS_inst.cpp
+ #ADIOS_C.cpp
+
+ capsule/heap/STLVector.cpp
+ capsule/shmem/ShmSystemV.cpp
+
+ core/Capsule.cpp
+ core/Engine.cpp
+ core/Method.cpp
+ core/Support.cpp
+ core/Transform.cpp
+ core/Transport.cpp
+
+ engine/bp/BPFileReader.cpp
+ engine/bp/BPFileWriter.cpp
+
+ format/BP1.cpp
+ format/BP1Aggregator.cpp
+ format/BP1Writer.cpp
+
+ functions/adiosFunctions.cpp
+
+ transport/file/FStream.cpp
+ transport/file/FileDescriptor.cpp
+ transport/file/FilePointer.cpp
+ )
+ target_include_directories(${adios2_target}
+ PUBLIC ${ADIOS_SOURCE_DIR}/include
+ )
+
+ if(ADIOS_USE_DataMan)
+ find_package(DataMan REQUIRED)
+ target_sources(${adios2_target} PRIVATE
+ engine/dataman/DataManReader.cpp
+ engine/dataman/DataManWriter.cpp
+ transport/wan/MdtmMan.cpp
+ )
+ target_compile_definitions(${adios2_target} PRIVATE ADIOS_HAVE_DATAMAN)
+ target_link_libraries(${adios2_target} PRIVATE DataMan::DataMan)
+ endif()
+
+ if(ADIOS_USE_BZip2)
+ find_package(BZip2 REQUIRED)
+ target_sources(${adios2_target} PRIVATE transform/BZip2.cpp)
+ target_compile_definitions(${adios2_target} PRIVATE ADIOS_HAVE_BZIP2)
+ target_link_libraries(${adios2_target} PRIVATE BZip2::BZip2)
+ endif()
+endforeach()
- transport/file/FStream.cpp
- transport/file/FileDescriptor.cpp
- transport/file/FilePointer.cpp
-)
-target_include_directories(adios2 PUBLIC ${ADIOS_SOURCE_DIR}/include)
+target_sources(adios2_nompi PRIVATE mpidummy.cpp)
+if(CMAKE_CXX_COMPILER_WRAPPER STREQUAL CrayPrgEnv)
+ target_compile_options(adios2_nompi PRIVATE --cray-bypass-pkgconfig)
+endif()
if(ADIOS_USE_MPI)
find_package(MPI COMPONENTS C REQUIRED)
target_include_directories(adios2 PUBLIC ${MPI_C_INCLUDE_PATH})
target_compile_definitions(adios2 PUBLIC ADIOS_HAVE_MPI)
target_link_libraries(adios2 PUBLIC ${MPI_C_LIBRARIES})
-else()
- target_sources(adios2 PRIVATE mpidummy.cpp)
-endif()
-
-if(ADIOS_USE_ADIOS1)
- find_package(ADIOS REQUIRED)
- target_sources(adios2 PRIVATE
- engine/adios1/ADIOS1Reader.cpp
- engine/adios1/ADIOS1Writer.cpp
- )
- target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_ADIOS1)
- target_link_libraries(adios2 PRIVATE adios::adios)
-endif()
-
-if(ADIOS_USE_DataMan)
- find_package(DataMan REQUIRED)
- target_sources(adios2 PRIVATE
- engine/dataman/DataManReader.cpp
- engine/dataman/DataManWriter.cpp
- transport/wan/MdtmMan.cpp
- )
- target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_DATAMAN)
- target_link_libraries(adios2 PRIVATE DataMan::DataMan)
-endif()
-if(ADIOS_USE_BZip2)
- find_package(BZip2 REQUIRED)
- target_sources(adios2 PRIVATE transform/BZip2.cpp)
- target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_BZIP2)
- target_link_libraries(adios2 PRIVATE BZip2::BZip2)
+ if(ADIOS_USE_ADIOS1)
+ find_package(ADIOS1 REQUIRED)
+ target_sources(adios2 PRIVATE
+ engine/adios1/ADIOS1Reader.cpp
+ engine/adios1/ADIOS1Writer.cpp
+ )
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_ADIOS1)
+ target_link_libraries(adios2 PRIVATE adios1::adios)
+ endif()
endif()
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index a840d404a869e093bd1413fd735fa1844a315a01..55a745a0e7370a437665321105cc3ecafd5e9f26 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -22,8 +22,7 @@ ADIOS1Reader::ADIOS1Reader(ADIOS &adios, const std::string &name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method)
: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method,
- " BPFileReader constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+ " BPFileReader constructor (or call to ADIOS Open).\n")
{
Init();
}
@@ -170,15 +169,9 @@ void BPFileReader::Init()
", in call to ADIOS Open or BPFileReader constructor\n");
}
- InitCapsules();
InitTransports();
}
-void BPFileReader::InitCapsules()
-{
- // here init memory capsules
-}
-
void BPFileReader::InitTransports() // maybe move this?
{
if (m_DebugMode == true)
diff --git a/source/functions/adiosFunctions.cpp b/source/functions/adiosFunctions.cpp
index dcd7ece82e64b26677570205196da389e5bdac1b..47ab64cac7c6d82195b1449fc954900249052c31 100644
--- a/source/functions/adiosFunctions.cpp
+++ b/source/functions/adiosFunctions.cpp
@@ -650,6 +650,17 @@ std::string DimsToCSV(const std::vector<std::size_t> &dims)
return dimsCSV;
}
+void ConvertUint64VectorToSizetVector(const std::vector<std::uint64_t> &in,
+ std::vector<std::size_t> &out)
+{
+ out.clear();
+ out.reserve(in.size());
+ for (const auto inElement : in)
+ {
+ out.push_back(static_cast<std::size_t>(inElement));
+ }
+}
+
bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
const std::size_t maxBufferSize,
std::vector<char> &buffer)