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ADIOS2IOHandler.cpp
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/* Copyright 2017-2021 Franz Poeschel, Fabian Koller and Axel Huebl
*
* This file is part of openPMD-api.
*
* openPMD-api is free software: you can redistribute it and/or modify
* it under the terms of of either the GNU General Public License or
* the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* openPMD-api is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License and the GNU Lesser General Public License
* for more details.
*
* You should have received a copy of the GNU General Public License
* and the GNU Lesser General Public License along with openPMD-api.
* If not, see <http://www.gnu.org/licenses/>.
*/
#include "openPMD/IO/ADIOS/ADIOS2IOHandler.hpp"
#include "openPMD/IO/ADIOS/ADIOS2File.hpp"
#include "openPMD/Datatype.hpp"
#include "openPMD/Error.hpp"
#include "openPMD/IO/ADIOS/ADIOS2Auxiliary.hpp"
#include "openPMD/IO/ADIOS/ADIOS2FilePosition.hpp"
#include "openPMD/IO/ADIOS/ADIOS2IOHandler.hpp"
#include "openPMD/IterationEncoding.hpp"
#include "openPMD/auxiliary/Environment.hpp"
#include "openPMD/auxiliary/Filesystem.hpp"
#include "openPMD/auxiliary/JSON_internal.hpp"
#include "openPMD/auxiliary/Mpi.hpp"
#include "openPMD/auxiliary/StringManip.hpp"
#include "openPMD/auxiliary/TypeTraits.hpp"
#include <algorithm>
#include <cctype> // std::tolower
#include <iostream>
#include <iterator>
#include <memory>
#include <set>
#include <sstream>
#include <stdexcept>
#include <string>
#include <type_traits>
namespace openPMD
{
#if openPMD_USE_VERIFY
#define VERIFY(CONDITION, TEXT) \
{ \
if (!(CONDITION)) \
throw std::runtime_error((TEXT)); \
}
#else
#define VERIFY(CONDITION, TEXT) \
do \
{ \
(void)sizeof(CONDITION); \
} while (0);
#endif
#define VERIFY_ALWAYS(CONDITION, TEXT) \
{ \
if (!(CONDITION)) \
throw std::runtime_error((TEXT)); \
}
#if openPMD_HAVE_ADIOS2
std::optional<size_t> joinedDimension(adios2::Dims const &dims)
{
for (size_t i = 0; i < dims.size(); ++i)
{
if (dims[i] == adios2::JoinedDim)
{
return i;
}
}
return std::nullopt;
}
#if openPMD_HAVE_MPI
ADIOS2IOHandlerImpl::ADIOS2IOHandlerImpl(
AbstractIOHandler *handler,
MPI_Comm communicator,
json::TracingJSON cfg,
std::string engineType,
std::string specifiedExtension)
: AbstractIOHandlerImplCommon(handler)
, m_ADIOS{communicator}
, m_communicator{communicator}
, m_engineType(std::move(engineType))
, m_userSpecifiedExtension{std::move(specifiedExtension)}
{
init(
std::move(cfg),
/* callbackWriteAttributesFromRank = */
[communicator, this](nlohmann::json const &attribute_writing_ranks) {
int rank = 0;
MPI_Comm_rank(communicator, &rank);
auto throw_error = []() {
throw error::BackendConfigSchema(
{"adios2", "attribute_writing_ranks"},
"Type must be either an integer or an array of integers.");
};
if (attribute_writing_ranks.is_array())
{
m_writeAttributesFromThisRank = false;
for (auto const &val : attribute_writing_ranks)
{
if (!val.is_number())
{
throw_error();
}
if (val.get<int>() == rank)
{
m_writeAttributesFromThisRank = true;
break;
}
}
}
else if (attribute_writing_ranks.is_number())
{
m_writeAttributesFromThisRank =
attribute_writing_ranks.get<int>() == rank;
}
else
{
throw_error();
}
});
}
#endif // openPMD_HAVE_MPI
ADIOS2IOHandlerImpl::ADIOS2IOHandlerImpl(
AbstractIOHandler *handler,
json::TracingJSON cfg,
std::string engineType,
std::string specifiedExtension)
: AbstractIOHandlerImplCommon(handler)
, m_ADIOS{}
, m_engineType(std::move(engineType))
, m_userSpecifiedExtension(std::move(specifiedExtension))
{
init(std::move(cfg), [](auto const &...) {});
}
ADIOS2IOHandlerImpl::~ADIOS2IOHandlerImpl()
{
/*
* m_fileData is an unordered_map indexed by pointer addresses
* to the fileState member of InvalidatableFile.
* This means that destruction order is nondeterministic.
* Let's determinize it (necessary if computing in parallel).
*/
using file_t = std::unique_ptr<detail::ADIOS2File>;
std::vector<file_t> sorted;
sorted.reserve(m_fileData.size());
for (auto &pair : m_fileData)
{
sorted.push_back(std::move(pair.second));
}
m_fileData.clear();
/*
* Technically, std::sort() is sufficient here, since file names are unique.
* Use std::stable_sort() for two reasons:
* 1) On some systems (clang 13.0.1, libc++ 13.0.1), std::sort() leads to
* weird inconsistent segfaults here.
* 2) Robustness against future changes. stable_sort() might become needed
* in future, and debugging this can be hard.
* 3) It does not really matter, this is just the destructor, so we can take
* the extra time.
*/
std::stable_sort(
sorted.begin(), sorted.end(), [](auto const &left, auto const &right) {
return left->m_file <= right->m_file;
});
// run the destructors
for (auto &file : sorted)
{
// std::unique_ptr interface
file.reset();
}
}
template <typename Callback>
void ADIOS2IOHandlerImpl::init(
json::TracingJSON cfg, Callback &&callbackWriteAttributesFromRank)
{
if (auto unsupported_engine_cfg =
auxiliary::getEnvString("OPENPMD_ADIOS2_PRETEND_ENGINE", "");
!unsupported_engine_cfg.empty())
{
auxiliary::lowerCase(unsupported_engine_cfg);
pretendEngine(std::move(unsupported_engine_cfg));
}
// allow overriding through environment variable
realEngineType() =
auxiliary::getEnvString("OPENPMD_ADIOS2_ENGINE", m_engineType);
auxiliary::lowerCase(realEngineType());
// environment-variable based configuration
if (int groupTableViaEnv =
auxiliary::getEnvNum("OPENPMD2_ADIOS2_USE_GROUP_TABLE", -1);
groupTableViaEnv != -1)
{
m_useGroupTable =
groupTableViaEnv == 0 ? UseGroupTable::No : UseGroupTable::Yes;
}
if (cfg.json().contains("adios2"))
{
m_config = cfg["adios2"];
if (m_config.json().contains("use_group_table"))
{
m_useGroupTable = m_config["use_group_table"].json().get<bool>()
? UseGroupTable::Yes
: UseGroupTable::No;
}
if (m_config.json().contains("use_span_based_put"))
{
m_useSpanBasedPutByDefault =
m_config["use_span_based_put"].json().get<bool>() ? UseSpan::Yes
: UseSpan::No;
}
if (m_config.json().contains("modifiable_attributes"))
{
m_modifiableAttributes =
m_config["modifiable_attributes"].json().get<bool>()
? ModifiableAttributes::Yes
: ModifiableAttributes::No;
}
if (m_config.json().contains("attribute_writing_ranks"))
{
callbackWriteAttributesFromRank(
m_config["attribute_writing_ranks"].json());
}
auto engineConfig = config(adios_defaults::str_engine);
if (!engineConfig.json().is_null())
{
auto engineTypeConfig =
config(adios_defaults::str_type, engineConfig).json();
if (!engineTypeConfig.is_null())
{
// convert to string
auto maybeEngine =
json::asLowerCaseStringDynamic(engineTypeConfig);
if (maybeEngine.has_value())
{
// override engine type by JSON/TOML configuration
realEngineType() = std::move(maybeEngine.value());
}
else
{
throw error::BackendConfigSchema(
{"adios2", "engine", "type"},
"Must be convertible to string type.");
}
}
if (engineConfig.json().contains(
adios_defaults::str_treat_unsupported_engine_like))
{
auto maybeEngine = json::asLowerCaseStringDynamic(
engineConfig
[adios_defaults::str_treat_unsupported_engine_like]
.json());
if (!maybeEngine.has_value())
{
throw error::BackendConfigSchema(
{"adios2",
adios_defaults::str_engine,
adios_defaults::str_treat_unsupported_engine_like},
"Must be convertible to string type.");
}
pretendEngine(std::move(*maybeEngine));
}
}
auto operators = getOperators();
if (operators)
{
defaultOperators = std::move(operators.value());
}
}
#if !openPMD_HAS_ADIOS_2_9
if (m_modifiableAttributes == ModifiableAttributes::Yes)
{
throw error::OperationUnsupportedInBackend(
m_handler->backendName(),
"Modifiable attributes require ADIOS2 >= v2.9.");
}
if (m_useGroupTable.has_value() &&
m_useGroupTable.value() == UseGroupTable::Yes)
{
throw error::OperationUnsupportedInBackend(
m_handler->backendName(),
"ADIOS2 group table feature requires ADIOS2 >= v2.9.");
}
#endif
}
std::optional<std::vector<ADIOS2IOHandlerImpl::ParameterizedOperator>>
ADIOS2IOHandlerImpl::getOperators(json::TracingJSON cfg)
{
using ret_t = std::optional<std::vector<ParameterizedOperator>>;
std::vector<ParameterizedOperator> res;
if (!cfg.json().contains("dataset"))
{
return ret_t();
}
auto datasetConfig = cfg["dataset"];
if (!datasetConfig.json().contains("operators"))
{
return ret_t();
}
auto _operators = datasetConfig["operators"];
nlohmann::json const &operators = _operators.json();
for (auto operatorIterator = operators.begin();
operatorIterator != operators.end();
++operatorIterator)
{
nlohmann::json const &op = operatorIterator.value();
std::string const &type = op["type"];
adios2::Params adiosParams;
if (op.contains("parameters"))
{
nlohmann::json const ¶ms = op["parameters"];
for (auto paramIterator = params.begin();
paramIterator != params.end();
++paramIterator)
{
auto maybeString = json::asStringDynamic(paramIterator.value());
if (maybeString.has_value())
{
adiosParams[paramIterator.key()] =
std::move(maybeString.value());
}
else
{
throw error::BackendConfigSchema(
{"adios2", "dataset", "operators", paramIterator.key()},
"Must be convertible to string type.");
}
}
}
std::optional<adios2::Operator> adiosOperator =
getCompressionOperator(type);
if (adiosOperator)
{
res.emplace_back(ParameterizedOperator{
adiosOperator.value(), std::move(adiosParams)});
}
}
_operators.declareFullyRead();
return std::make_optional(std::move(res));
}
std::optional<std::vector<ADIOS2IOHandlerImpl::ParameterizedOperator>>
ADIOS2IOHandlerImpl::getOperators()
{
return getOperators(m_config);
}
using AcceptedEndingsForEngine = std::map<std::string, std::string>;
std::string ADIOS2IOHandlerImpl::fileSuffix(bool verbose) const
{
// SST engine adds its suffix unconditionally
// so we don't add it
#if openPMD_HAVE_ADIOS2_BP5 && openPMD_HAS_ADIOS_2_9
constexpr char const *const default_file_ending = ".bp5";
#else
constexpr char const *const default_file_ending = ".bp4";
#endif
if (m_realEngineType.has_value())
{
// unknown engine type, use whatever ending the user specified
return m_userSpecifiedExtension;
}
static std::map<std::string, AcceptedEndingsForEngine> const endings{
{"sst", {{"", ""}, {".sst", ""}, {".%E", ""}}},
{"staging", {{"", ""}, {".sst", ""}, {".%E", ""}}},
{"filestream",
{{".bp", ".bp"},
{".bp4", ".bp4"},
{".bp5", ".bp5"},
{".%E", default_file_ending}}},
{"bp4", {{".bp4", ".bp4"}, {".bp", ".bp"}, {".%E", ".bp4"}}},
{"bp5", {{".bp5", ".bp5"}, {".bp", ".bp"}, {".%E", ".bp5"}}},
{"bp3", {{".bp", ".bp"}, {".%E", ".bp"}}},
{"file",
{{".bp", ".bp"},
{".bp4", ".bp4"},
{".bp5", ".bp5"},
{".%E", default_file_ending}}},
{"hdf5", {{".h5", ".h5"}, {".%E", ".h5"}}},
{"nullcore",
{{".nullcore", ".nullcore"}, {".bp", ".bp"}, {".%E", ".nullcore"}}},
{"ssc", {{".ssc", ".ssc"}, {".%E", ".ssc"}}}};
if (auto engine = endings.find(m_engineType); engine != endings.end())
{
auto const &acceptedEndings = engine->second;
if (auto ending = acceptedEndings.find(m_userSpecifiedExtension);
ending != acceptedEndings.end())
{
if (verbose &&
(m_engineType == "file" || m_engineType == "filestream") &&
(m_userSpecifiedExtension == ".bp3" ||
m_userSpecifiedExtension == ".bp4" ||
m_userSpecifiedExtension == ".bp5"))
{
std::cerr
<< "[ADIOS2] Explicit ending '" << m_userSpecifiedExtension
<< "' was specified in combination with generic file "
"engine '"
<< m_engineType
<< "'. ADIOS2 will pick a default file ending "
"independent of specified suffix. (E.g. 'simData.bp5' "
"might actually be written as a BP4 dataset.)"
<< std::endl;
}
return ending->second;
}
else if (m_userSpecifiedExtension.empty())
{
std::cerr << "[ADIOS2] No file ending specified. Will not add one."
<< std::endl;
if (verbose && m_engineType == "bp3")
{
std::cerr
<< "Note that the ADIOS2 BP3 engine will add its "
"ending '.bp' if not specified (e.g. 'simData.bp3' "
"will appear on disk as 'simData.bp3.bp')."
<< std::endl;
}
return "";
}
else
{
if (verbose)
{
std::cerr << "[ADIOS2] Specified ending '"
<< m_userSpecifiedExtension
<< "' does not match the selected engine '"
<< m_engineType
<< "'. Will use the specified ending anyway."
<< std::endl;
if (m_engineType == "bp3")
{
std::cerr
<< "Note that the ADIOS2 BP3 engine will add its "
"ending '.bp' if not specified (e.g. 'simData.bp3' "
"will appear on disk as 'simData.bp3.bp')."
<< std::endl;
}
}
return m_userSpecifiedExtension;
}
}
else
{
throw error::WrongAPIUsage(
"[ADIOS2] Specified engine '" + m_engineType +
"' is not supported by ADIOS2 backend.");
}
}
using FlushTarget = adios_defs::FlushTarget;
static FlushTarget &
overrideFlushTarget(FlushTarget &inplace, FlushTarget new_val)
{
auto allowsOverride = [](FlushTarget ft) {
switch (ft)
{
case FlushTarget::Buffer:
case FlushTarget::Disk:
case FlushTarget::NewStep:
return true;
case FlushTarget::Buffer_Override:
case FlushTarget::Disk_Override:
case FlushTarget::NewStep_Override:
return false;
}
return true;
};
if (allowsOverride(inplace))
{
inplace = new_val;
}
else
{
if (!allowsOverride(new_val))
{
inplace = new_val;
}
// else { keep the old value, no-op }
}
return inplace;
}
std::future<void>
ADIOS2IOHandlerImpl::flush(internal::ParsedFlushParams &flushParams)
{
auto res = AbstractIOHandlerImpl::flush();
detail::ADIOS2File::ADIOS2FlushParams adios2FlushParams{
flushParams.flushLevel, m_flushTarget};
if (flushParams.backendConfig.json().contains("adios2"))
{
auto adios2Config = flushParams.backendConfig["adios2"];
if (adios2Config.json().contains("engine"))
{
auto engineConfig = adios2Config["engine"];
if (engineConfig.json().contains(adios_defaults::str_flushtarget))
{
auto target = json::asLowerCaseStringDynamic(
engineConfig[adios_defaults::str_flushtarget].json());
if (!target.has_value())
{
throw error::BackendConfigSchema(
{"adios2", "engine", adios_defaults::str_flushtarget},
"Flush target must be either 'disk' or 'buffer', but "
"was non-literal type.");
}
overrideFlushTarget(
adios2FlushParams.flushTarget,
adios_defs::flushTargetFromString(target.value()));
}
}
if (auto shadow = adios2Config.invertShadow(); shadow.size() > 0)
{
switch (adios2Config.originallySpecifiedAs)
{
case json::SupportedLanguages::JSON:
std::cerr << "Warning: parts of the backend configuration for "
"ADIOS2 remain unused:\n"
<< shadow << std::endl;
break;
case json::SupportedLanguages::TOML: {
auto asToml = json::jsonToToml(shadow);
std::cerr << "Warning: parts of the backend configuration for "
"ADIOS2 remain unused:\n"
<< json::format_toml(asToml) << std::endl;
break;
}
}
}
}
for (auto const &file : m_dirty)
{
auto file_data = m_fileData.find(file);
if (file_data == m_fileData.end())
{
throw error::Internal(
"[ADIOS2 backend] No associated data found for file'" + *file +
"'.");
}
file_data->second->flush(
adios2FlushParams, /* writeLatePuts = */ false);
}
m_dirty.clear();
return res;
}
/*
* If the iteration encoding is variableBased, we default to using a group
* table, since it is the only reliable way to recover currently active
* groups.
* If group-based encoding is used without group table, then
* READ_LINEAR is forbidden as it will be unreliable in reporting
* currently available data.
* Use AbstractIOHandler::m_encoding for implementing this logic.
*/
static constexpr char const *warningADIOS2NoGroupbasedEncoding = &R"(
[Warning] Use of group-based encoding in ADIOS2 is discouraged as it can lead
to drastic performance issues, no matter if I/O steps are used or not.
* If not using I/O steps: A crash will corrupt all data since there is only
one atomic logical write operation upon closing the file.
Memory performance can be pathological depending on the setup.
* If using I/O steps: Each step will add new variables and attributes instead
of reusing those from earlier steps. ADIOS2 is not optimized for this and
especially the BP5 engine will show a quadratic increase in metadata size
as the number of steps increase.
We advise you to pick either file-based encoding or variable-based encoding
(variable-based encoding is not yet feature-complete in the openPMD-api).
For more details, refer to
https://openpmd-api.readthedocs.io/en/latest/usage/concepts.html#iteration-and-series)"
[1];
void ADIOS2IOHandlerImpl::createFile(
Writable *writable, Parameter<Operation::CREATE_FILE> const ¶meters)
{
VERIFY_ALWAYS(
access::write(m_handler->m_backendAccess),
"[ADIOS2] Creating a file in read-only mode is not possible.");
if (!writable->written)
{
std::string name = parameters.name + fileSuffix();
auto res_pair = getPossiblyExisting(name);
InvalidatableFile shared_name = InvalidatableFile(name);
VERIFY_ALWAYS(
!(m_handler->m_backendAccess == Access::READ_WRITE &&
(!std::get<PE_NewlyCreated>(res_pair) ||
auxiliary::file_exists(
fullPath(std::get<PE_InvalidatableFile>(res_pair))))),
"[ADIOS2] Can only overwrite existing file in CREATE mode.");
if (!std::get<PE_NewlyCreated>(res_pair))
{
auto file = std::get<PE_InvalidatableFile>(res_pair);
m_dirty.erase(file);
dropFileData(file);
file.invalidate();
}
std::string const dir(m_handler->directory);
if (!auxiliary::directory_exists(dir))
{
auto success = auxiliary::create_directories(dir);
VERIFY(success, "[ADIOS2] Could not create directory.");
}
associateWithFile(writable, shared_name);
this->m_dirty.emplace(shared_name);
writable->written = true;
writable->abstractFilePosition = std::make_shared<ADIOS2FilePosition>();
// enforce opening the file
// lazy opening is deathly in parallel situations
auto &fileData =
getFileData(shared_name, IfFileNotOpen::OpenImplicitly);
if (!printedWarningsAlready.noGroupBased &&
m_writeAttributesFromThisRank &&
m_handler->m_encoding == IterationEncoding::groupBased)
{
// For a peaceful phase-out of group-based encoding in ADIOS2,
// print this warning only in the new layout (with group table)
if (m_useGroupTable.value_or(UseGroupTable::No) ==
UseGroupTable::Yes)
{
std::cerr << warningADIOS2NoGroupbasedEncoding << std::endl;
printedWarningsAlready.noGroupBased = true;
}
fileData.m_IO.DefineAttribute(
adios_defaults::str_groupBasedWarning,
std::string("Consider using file-based or variable-based "
"encoding instead in ADIOS2."));
}
}
}
void ADIOS2IOHandlerImpl::checkFile(
Writable *, Parameter<Operation::CHECK_FILE> ¶meters)
{
std::string name =
fullPath(parameters.name + fileSuffix(/* verbose = */ false));
using FileExists = Parameter<Operation::CHECK_FILE>::FileExists;
*parameters.fileExists = checkFile(name) ? FileExists::Yes : FileExists::No;
}
bool ADIOS2IOHandlerImpl::checkFile(std::string fullFilePath) const
{
if (realEngineType() == "bp3")
{
if (!auxiliary::ends_with(fullFilePath, ".bp"))
{
/*
* BP3 will add this ending if not specified
*/
fullFilePath += ".bp";
}
}
else if (realEngineType() == "sst")
{
/*
* SST will add this ending indiscriminately
*/
fullFilePath += ".sst";
}
bool fileExists = auxiliary::directory_exists(fullFilePath) ||
auxiliary::file_exists(fullFilePath);
#if openPMD_HAVE_MPI
if (m_communicator.has_value())
{
bool fileExistsRes = false;
int status = MPI_Allreduce(
&fileExists,
&fileExistsRes,
1,
MPI_C_BOOL,
MPI_LOR, // logical or
m_communicator.value());
if (status != 0)
{
throw std::runtime_error("MPI Reduction failed!");
}
fileExists = fileExistsRes;
}
#endif
return fileExists;
}
void ADIOS2IOHandlerImpl::createPath(
Writable *writable, const Parameter<Operation::CREATE_PATH> ¶meters)
{
std::string path;
auto file = refreshFileFromParent(writable, /* preferParentFile = */ true);
/* Sanitize path */
if (!auxiliary::starts_with(parameters.path, '/'))
{
path = filePositionToString(setAndGetFilePosition(writable)) + "/" +
auxiliary::removeSlashes(parameters.path);
}
else
{
path = "/" + auxiliary::removeSlashes(parameters.path);
}
/* ADIOS has no concept for explicitly creating paths.
* They are implicitly created with the paths of variables/attributes. */
writable->written = true;
writable->abstractFilePosition =
std::make_shared<ADIOS2FilePosition>(path, GroupOrDataset::GROUP);
switch (useGroupTable())
{
case UseGroupTable::No:
break;
case UseGroupTable::Yes:
getFileData(file, IfFileNotOpen::ThrowError).markActive(writable);
break;
}
}
void ADIOS2IOHandlerImpl::createDataset(
Writable *writable, const Parameter<Operation::CREATE_DATASET> ¶meters)
{
if (access::readOnly(m_handler->m_backendAccess))
{
throw std::runtime_error(
"[ADIOS2] Creating a dataset in a file opened as read "
"only is not possible.");
}
#if !openPMD_HAS_ADIOS_2_9
if (parameters.joinedDimension.has_value())
{
error::throwOperationUnsupportedInBackend(
"ADIOS2", "Joined Arrays require ADIOS2 >= v2.9");
}
#endif
if (!writable->written)
{
/* Sanitize name */
std::string name = auxiliary::removeSlashes(parameters.name);
auto const file =
refreshFileFromParent(writable, /* preferParentFile = */ true);
writable->abstractFilePosition.reset();
auto filePos = setAndGetFilePosition(writable, name);
filePos->gd = GroupOrDataset::DATASET;
auto const varName = nameOfVariable(writable);
std::vector<ParameterizedOperator> operators;
json::TracingJSON options =
json::parseOptions(parameters.options, /* considerFiles = */ false);
if (options.json().contains("adios2"))
{
json::TracingJSON datasetConfig(options["adios2"]);
auto datasetOperators = getOperators(datasetConfig);
operators = datasetOperators ? std::move(datasetOperators.value())
: defaultOperators;
}
else
{
operators = defaultOperators;
}
parameters.warnUnusedParameters(
options,
"adios2",
"Warning: parts of the backend configuration for ADIOS2 dataset '" +
varName + "' remain unused:\n");
// cast from openPMD::Extent to adios2::Dims
adios2::Dims shape(parameters.extent.begin(), parameters.extent.end());
if (auto jd = parameters.joinedDimension; jd.has_value())
{
shape[jd.value()] = adios2::JoinedDim;
}
auto &fileData = getFileData(file, IfFileNotOpen::ThrowError);
#define HAS_BP5_BLOSC2_BUG \
(ADIOS2_VERSION_MAJOR * 100 + ADIOS2_VERSION_MINOR == 209 && \
ADIOS2_VERSION_PATCH <= 1)
#if HAS_BP5_BLOSC2_BUG
std::string engineType = fileData.getEngine().Type();
std::transform(
engineType.begin(),
engineType.end(),
engineType.begin(),
[](unsigned char c) { return std::tolower(c); });
if (!printedWarningsAlready.blosc2bp5 && engineType == "bp5writer")
{
for (auto const &op : operators)
{
std::string operatorType = op.op.Type();
std::transform(
operatorType.begin(),
operatorType.end(),
operatorType.begin(),
[](unsigned char c) { return std::tolower(c); });
if (operatorType == "blosc")
{
std::cerr << &R"(
[Warning] Use BP5+Blosc with care in ADIOS2 v2.9.0 and v2.9.1.
Unreadable data might be created, to mitigate either deactivate Blosc or use BP4+Blosc.
For further details see
https://github.com/ornladios/ADIOS2/issues/3504.
)"[1] << std::endl;
printedWarningsAlready.blosc2bp5 = true;
}
}
}
#endif
#undef HAS_BP5_BLOSC2_BUG
switchAdios2VariableType<detail::VariableDefiner>(
parameters.dtype, fileData.m_IO, varName, operators, shape);
fileData.invalidateVariablesMap();
writable->written = true;
m_dirty.emplace(file);
}
}
namespace detail
{
struct DatasetExtender
{
template <typename T, typename... Args>
static void call(
adios2::IO &IO, std::string const &variable, Extent const &newShape)
{
auto var = IO.InquireVariable<T>(variable);
if (!var)
{
throw std::runtime_error(
"[ADIOS2] Unable to retrieve variable for resizing: '" +
variable + "'.");
}
adios2::Dims dims;
dims.reserve(newShape.size());
for (auto ext : newShape)
{
dims.push_back(ext);
}
var.SetShape(dims);
}
static constexpr char const *errorMsg = "ADIOS2: extendDataset()";
};
} // namespace detail
void ADIOS2IOHandlerImpl::extendDataset(
Writable *writable, const Parameter<Operation::EXTEND_DATASET> ¶meters)
{
VERIFY_ALWAYS(
access::write(m_handler->m_backendAccess),
"[ADIOS2] Cannot extend datasets in read-only mode.");
setAndGetFilePosition(writable);
auto file = refreshFileFromParent(writable, /* preferParentFile = */ false);
std::string name = nameOfVariable(writable);
auto &filedata = getFileData(file, IfFileNotOpen::ThrowError);
Datatype dt = detail::fromADIOS2Type(filedata.m_IO.VariableType(name));
switchAdios2VariableType<detail::DatasetExtender>(
dt, filedata.m_IO, name, parameters.extent);
}
void ADIOS2IOHandlerImpl::openFile(
Writable *writable, Parameter<Operation::OPEN_FILE> ¶meters)
{
if (!auxiliary::directory_exists(m_handler->directory))
{
throw error::ReadError(
error::AffectedObject::File,
error::Reason::Inaccessible,
"ADIOS2",
"Supplied directory is not valid: " + m_handler->directory);
}
std::string name = parameters.name + fileSuffix();
auto file = std::get<PE_InvalidatableFile>(getPossiblyExisting(name));
associateWithFile(writable, file);
writable->written = true;
writable->abstractFilePosition = std::make_shared<ADIOS2FilePosition>();
// enforce opening the file
// lazy opening is deathly in parallel situations
auto &fileData = getFileData(file, IfFileNotOpen::OpenImplicitly);
*parameters.out_parsePreference = fileData.parsePreference;
m_dirty.emplace(std::move(file));
}
void ADIOS2IOHandlerImpl::closeFile(
Writable *writable, Parameter<Operation::CLOSE_FILE> const &)
{
auto fileIterator = m_files.find(writable);
if (fileIterator != m_files.end())
{
// do not invalidate the file
// it still exists, it is just not open
auto it = m_fileData.find(fileIterator->second);
if (it != m_fileData.end())
{
/*
* No need to finalize unconditionally, destructor will take care
* of it.
*/
it->second->flush(
FlushLevel::UserFlush,
[](detail::ADIOS2File &ba, adios2::Engine &) { ba.finalize(); },
/* writeLatePuts = */ true,
/* flushUnconditionally = */ false);
m_fileData.erase(it);
}
m_dirty.erase(fileIterator->second);
m_files.erase(fileIterator);
}
}
void ADIOS2IOHandlerImpl::openPath(
Writable *writable, const Parameter<Operation::OPEN_PATH> ¶meters)
{
/* Sanitize path */
auto file = refreshFileFromParent(writable, /* preferParentFile = */ true);
std::string prefix =
filePositionToString(setAndGetFilePosition(writable->parent));
std::string suffix = auxiliary::removeSlashes(parameters.path);
std::string infix =
suffix.empty() || auxiliary::ends_with(prefix, '/') ? "" : "/";
/* ADIOS has no concept for explicitly creating paths.
* They are implicitly created with the paths of variables/attributes. */
writable->abstractFilePosition = std::make_shared<ADIOS2FilePosition>(
prefix + infix + suffix, GroupOrDataset::GROUP);
writable->written = true;
switch (useGroupTable())
{
case UseGroupTable::No:
break;
case UseGroupTable::Yes:
getFileData(file, IfFileNotOpen::ThrowError).markActive(writable);
break;
}
}
void ADIOS2IOHandlerImpl::openDataset(
Writable *writable, Parameter<Operation::OPEN_DATASET> ¶meters)
{
auto name = auxiliary::removeSlashes(parameters.name);
writable->abstractFilePosition.reset();
auto pos = setAndGetFilePosition(writable, name);
pos->gd = GroupOrDataset::DATASET;
auto file = refreshFileFromParent(writable, /* preferParentFile = */ true);
auto varName = nameOfVariable(writable);
auto &fileData = getFileData(file, IfFileNotOpen::ThrowError);
*parameters.dtype =
detail::fromADIOS2Type(fileData.m_IO.VariableType(varName));