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Merge pull request #1004 from williamfgc/mgard
MGARD initial integration
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| #------------------------------------------------------------------------------# | ||
| # Distributed under the OSI-approved Apache License, Version 2.0. See | ||
| # accompanying file Copyright.txt for details. | ||
| #------------------------------------------------------------------------------# | ||
| # | ||
| # FindMGARD | ||
| # ----------- | ||
| # | ||
| # Try to find the MGARD library | ||
| # | ||
| # This module defines the following variables: | ||
| # | ||
| # MGARD_FOUND - System has MGARD | ||
| # MGARD_INCLUDE_DIRS - The MGARD include directory | ||
| # MGARD_LIBRARIES - Link these to use MGARD | ||
| # | ||
| # and the following imported targets: | ||
| # MGARD::MGARD - The MGARD compression library target | ||
| # | ||
| # You can also set the following variable to help guide the search: | ||
| # MGARD_ROOT - The install prefix for MGARD containing the | ||
| # include and lib folders | ||
| # Note: this can be set as a CMake variable or an | ||
| # environment variable. If specified as a CMake | ||
| # variable, it will override any setting specified | ||
| # as an environment variable. | ||
|
|
||
| if(NOT MGARD_FOUND) | ||
| if((NOT MGARD_ROOT) AND (NOT (ENV{MGARD_ROOT} STREQUAL ""))) | ||
| set(MGARD_ROOT "$ENV{MGARD_ROOT}") | ||
| endif() | ||
| if(MGARD_ROOT) | ||
| set(MGARD_INCLUDE_OPTS HINTS ${MGARD_ROOT}/include NO_DEFAULT_PATHS) | ||
| set(MGARD_LIBRARY_OPTS | ||
| HINTS ${MGARD_ROOT}/lib ${MGARD_ROOT}/lib64 | ||
| NO_DEFAULT_PATHS | ||
| ) | ||
| endif() | ||
|
|
||
| find_path(MGARD_INCLUDE_DIR mgard.h ${MGARD_INCLUDE_OPTS}) | ||
| find_library(MGARD_LIBRARY NAMES mgard ${MGARD_LIBRARY_OPTS}) | ||
| find_library(ZLIB_LIBRARY NAMES zlib ${SZ_LIBRARY_OPTS}) | ||
|
|
||
| include(FindPackageHandleStandardArgs) | ||
| find_package_handle_standard_args(MGARD | ||
| FOUND_VAR MGARD_FOUND | ||
| REQUIRED_VARS MGARD_LIBRARY ZLIB_LIBRARY MGARD_INCLUDE_DIR | ||
| ) | ||
| if(MGARD_FOUND) | ||
| set(MGARD_INCLUDE_DIRS ${MGARD_INCLUDE_DIR}) | ||
| set(MGARD_LIBRARIES ${MGARD_LIBRARY} ${ZLIB_LIBRARY}) | ||
| if(MGARD_FOUND AND NOT TARGET MGARD::MGARD) | ||
| add_library(MGARD::MGARD UNKNOWN IMPORTED) | ||
| set_target_properties(MGARD::MGARD PROPERTIES | ||
| IMPORTED_LOCATION "${MGARD_LIBRARY}" | ||
| INTERFACE_LINK_LIBRARIES "${MGARD_LIBRARIES}" | ||
| INTERFACE_INCLUDE_DIRECTORIES "${MGARD_INCLUDE_DIR}" | ||
| ) | ||
| endif() | ||
| endif() | ||
| endif() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,149 @@ | ||
| /* | ||
| * Distributed under the OSI-approved Apache License, Version 2.0. See | ||
| * accompanying file Copyright.txt for details. | ||
| * | ||
| * CompressMGARD.cpp : | ||
| * | ||
| * Created on: Aug 3, 2018 | ||
| * Author: William F Godoy godoywf@ornl.gov | ||
| */ | ||
|
|
||
| #include "CompressMGARD.h" | ||
|
|
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| #include <cstring> //std::memcpy | ||
|
|
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| extern "C" { | ||
| #include <mgard_capi.h> | ||
| } | ||
|
|
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| #include "adios2/helper/adiosFunctions.h" | ||
|
|
||
| namespace adios2 | ||
| { | ||
| namespace core | ||
| { | ||
| namespace compress | ||
| { | ||
|
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| CompressMGARD::CompressMGARD(const Params ¶meters, const bool debugMode) | ||
| : Operator("mgard", parameters, debugMode) | ||
| { | ||
| } | ||
|
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| size_t CompressMGARD::Compress(const void *dataIn, const Dims &dimensions, | ||
| const size_t elementSize, const std::string type, | ||
| void *bufferOut, const Params ¶meters) const | ||
| { | ||
| const size_t ndims = dimensions.size(); | ||
| if (m_DebugMode) | ||
| { | ||
| if (ndims != 2) | ||
| { | ||
| throw std::invalid_argument( | ||
| "ERROR: ADIOS2 MGARD compression: no more " | ||
| "than 2-dimensions is supported.\n"); | ||
| } | ||
| } | ||
|
|
||
| // set type | ||
| int mgardType = -1; | ||
| if (type == "float") | ||
| { | ||
| if (m_DebugMode) | ||
| { | ||
| throw std::invalid_argument( | ||
| "ERROR: ADIOS2 operator " | ||
| "MGARD only supports double precision, in call to Put\n"); | ||
| } | ||
| } | ||
| else if (type == "double") | ||
| { | ||
| mgardType = 1; | ||
| } | ||
|
|
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| int r[ndims]; | ||
|
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| for (auto i = 0; i < ndims; i++) | ||
| { | ||
| r[ndims - i - 1] = static_cast<int>(dimensions[i]); | ||
| } | ||
|
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||
| // Parameters | ||
| auto itTolerance = parameters.find("tolerance"); | ||
| if (m_DebugMode) | ||
| { | ||
| if (itTolerance == parameters.end()) | ||
| { | ||
| throw std::invalid_argument("ERROR: missing mandatory parameter " | ||
| "tolerance for MGARD compression " | ||
| "operator, in call to Put\n"); | ||
| } | ||
| } | ||
|
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| double tolerance = std::stod(itTolerance->second); | ||
|
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| int sizeOut = 0; | ||
| unsigned char *dataOutPtr = | ||
| mgard_compress(mgardType, const_cast<void *>(dataIn), &sizeOut, r[0], | ||
| r[1], &tolerance); | ||
|
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| const size_t sizeOutT = static_cast<size_t>(sizeOut); | ||
| std::memcpy(bufferOut, dataOutPtr, sizeOutT); | ||
|
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| return sizeOutT; | ||
| } | ||
|
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| size_t CompressMGARD::Decompress(const void *bufferIn, const size_t sizeIn, | ||
| void *dataOut, const Dims &dimensions, | ||
| const std::string type, | ||
| const Params & /*parameters*/) const | ||
| { | ||
| int mgardType = -1; | ||
| size_t elementSize = 0; | ||
|
|
||
| if (type == "float") | ||
| { | ||
| if (m_DebugMode) | ||
| { | ||
| throw std::invalid_argument( | ||
| "ERROR: ADIOS2 operator " | ||
| "MGARD only supports double precision, in call to Get\n"); | ||
| } | ||
| } | ||
| else if (type == "double") | ||
| { | ||
| mgardType = 1; | ||
| elementSize = 8; | ||
| } | ||
| else | ||
| { | ||
| if (m_DebugMode) | ||
| { | ||
| throw std::invalid_argument( | ||
| "ERROR: ADIOS2 operator " | ||
| "MGARD only supports double precision, in call to Get\n"); | ||
| } | ||
| } | ||
|
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| const size_t ndims = dimensions.size(); | ||
| int r[ndims]; | ||
|
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| for (auto i = 0; i < ndims; i++) | ||
| { | ||
| r[ndims - i - 1] = static_cast<int>(dimensions[i]); | ||
| } | ||
|
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| void *dataPtr = mgard_decompress( | ||
| mgardType, | ||
| reinterpret_cast<unsigned char *>(const_cast<void *>(bufferIn)), | ||
| static_cast<int>(sizeIn), r[0], r[1]); | ||
|
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| const size_t dataSizeBytes = helper::GetTotalSize(dimensions) * elementSize; | ||
| std::memcpy(dataOut, dataPtr, dataSizeBytes); | ||
|
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| return static_cast<size_t>(dataSizeBytes); | ||
| } | ||
|
|
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| } // end namespace compress | ||
| } // end namespace core | ||
| } // end namespace adios2 |
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