From a7699e3da90e9a5d5826cafa218438c999bb4d38 Mon Sep 17 00:00:00 2001
From: Norbert Podhorszki <pnorbert@ornl.gov>
Date: Fri, 3 Mar 2017 17:24:46 -0500
Subject: [PATCH] First try at the C++ API design with a fake example and
doxygen doc
---
doc/API_design/API_example_use.cpp | 350 ++++
doc/API_design/Doxyfile | 2427 ++++++++++++++++++++++++++++
doc/API_design_doc.h | 332 ----
include/ADIOS.h | 421 +----
include/core/Engine.h | 272 +++-
include/core/Method.h | 35 +-
include/core/Variable.h | 43 +-
7 files changed, 3085 insertions(+), 795 deletions(-)
create mode 100644 doc/API_design/API_example_use.cpp
create mode 100644 doc/API_design/Doxyfile
delete mode 100644 doc/API_design_doc.h
diff --git a/doc/API_design/API_example_use.cpp b/doc/API_design/API_example_use.cpp
new file mode 100644
index 000000000..04b198466
--- /dev/null
+++ b/doc/API_design/API_example_use.cpp
@@ -0,0 +1,350 @@
+/* Fake example for Current API by design, incorrect as code but describes most of the ideas */
+#include <mpi.h>
+
+#include "ADIOS.h"
+
+
+void cb_AsyncWriteAdvanceCompleted( std::shared_ptr<adios::Engine> writer )
+{
+ std::cout << "AdvanceAsync() completed. We can modify our zero-copy variables\n";
+}
+
+void cb_AsyncReadAdvanceCompleted( std::shared_ptr<adios::Engine> writer )
+{
+ std::cout << "AdvanceAsync() completed. We have new data to read and we have the lock on it\n";
+}
+
+int main( int argc, char* argv[])
+{
+ //Application variables
+ MPI_Comm comm = MPI_COMM_WORLD;
+ const unsigned int NX = 10;
+ double Temperature[1][NX+2]; // We will want to write only Nx elements, skipping the first and last (think ghost cells)
+ std::vector<float> RaggedArray;
+
+ int Nparts, nproc;
+
+ // Global class/object that serves for init, finalize and provides ADIOS functions
+ adios::ADIOS adios( "config.xml", comm, /*verbose=*/adios::INFO, /*debugflag=*/false );
+
+ /*************
+ * WRITE API
+ *************/
+
+ /* Method
+ * We associate Engines and Transports and user settings into an object called Method.
+ * ADIOS checks if it is defined by the user in the config file, and fills it out if it is.
+ */
+
+ adios::Method& wmethod = adios.DeclareMethod( "WriteMethod" );
+ if( ! wmethod.isUserDefined() )
+ {
+ // if not defined by user, we can change the default settings
+ wmethod.SetEngine( "BP" ); // BP is the default engine
+ wmethod.SetAvailableCores( 1 ); // no threading for data processing (except for staging)
+ wmethod.AddTransport( "File", "lucky=yes" ); // ISO-POSIX file is the default transport
+ wmethod.AddTransport( "Staging" ); //"The" staging method developed in ECP
+ wmethod.SetParameters("have_metadata_file","yes" ); // Passing parameters to the engine
+ wmethod.SetParameters( "Aggregation", (nproc+1)/2 ); // number of aggregators
+ wmethod.SetParameters( "verbose", adios::WARN ); // Verbosity level for this engine and what it calls
+ }
+
+
+ //Define variables with transformations.
+ adios::Variable<unsigned int>& varNX = adios.DefineVariable<unsigned int>( "NX" ); // global single-value across processes
+ auto& varNproc = adios.DefineVariable<int>( "nproc", adios::Dims{adios::GLOBAL_VALUE} ); // same def for global value
+ adios::Variable<int>& varNparts = adios.DefineVariable<int>( "Nparts", adios::Dims{adios::LOCAL_VALUE} ); // a single-value different on every process
+ adios::Variable<double>& var2D = adios.DefineVariable<double>( "Temperature", adios::Dims{nproc,NX} ); // 2D global array, 1D decomposition
+ adios::Variable<float>& varRagged = adios.DefineVariable<float>( "Ragged", adios::Dims{nproc,adios::VARYING_DIMENSION} ); // ragged array
+
+
+ //add transform to variable
+ adios::Transform zfp = adios::transform::ZFP();
+ var2D.AddTransform( zfp, "accuracy=0.001" );
+
+ // open...write.write.write...advance...write.write.write...advance... ...close cycle
+ // "w" create/overwrite on open, "a" append at open, "u" open for update (does not increase step), "r" open for read.
+ std::shared_ptr<adios::Engine> writer = adios.Open( "myNumbers.bp", "w", comm, wmethod, adios::INDEPENDENT_IO);
+
+ if( writer == nullptr )
+ throw std::ios_base::failure( "ERROR: failed to open ADIOS writer\n" );
+
+ // Zero-Copy API: Define a variable with local dimensions now, and make ADIOS allocate it inside its buffers
+ // This requires an engine created. The variable will be deallocated in writer->Close()
+ // Calling varZeroCopy.SetSelection() later should throw an exception, i.e. modification is not allowed
+ // 2D global array, 1D decomposition
+ adios::Variable<double>& varZeroCopy = adios.DefineVariable<double>( "ZC", adios::Dims{nproc,NX}, adios::Dims{1,NX}, adios::Dims{rank,0} );
+ double fillValue = -1.0;
+ double * const myVarZC = writer->AllocateVariable<double>( varZeroCopy, fillValue );
+
+
+ for (int step = 0; step < 10; ++step) {
+ // write scalar value
+ writer->Write<int>( varNparts, Nparts );
+
+ // 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::Selection sel = adios.SelectionBoundingBox( {1,NX}, {rank,NX} ); // local dims and offsets; both as list
+ var2D.SetSelection( sel ); // Shall we call it SetSpaceSelection, SetOutputSelection?
+
+ // Select the area that we want to write from the data pointer we pass to the writer
+ // Think HDF5 memspace, just not hyperslabs yet, only a bounding box selection
+ // Engine will copy this bounding box from the data pointer into the buffer. Size of the bounding box should match the
+ // "space" selection which was given above. Default memspace is the full selection.
+ adios::Selection memspace = adios.SelectionBoundingBox( {1,NX}, {0,1} ); // local dims and offsets; both as list
+ var2D.SetMemorySelection( sel );
+
+ writer->Write<double>( var2D, *Temperature );
+
+ // Indicate we are done for this step.
+ // N-to-M Aggregation, disk I/O will be performed during this call, unless
+ // time aggregation postpones all of that to some later step.
+ // When Advance() returns, user can overwrite its Zero Copy variables.
+ // Internal buffer is freed only if there are no Zero Copy variables and there is no time aggregation going on
+ writer->Advance(); // same as AppendMode
+ writer->Advance( adios::APPEND ); // append new step at next write
+ writer->Advance( adios::UPDATE ); // do not increase step;
+
+ // When AdvanceAsync returns, user need to wait for notification that he can overwrite the Zero Copy variables.
+ writer->AdvanceAsync( adios::APPEND, cb_AsyncWriteAdvanceCompleted );
+
+ }
+
+ // Called once: indicate that we are done with this output for the run
+ // Zero Copy variables will be deallocated
+ writer->Close();
+
+
+
+ /*************
+ * READ API
+ *************/
+ adios::Method& rmethod = adios.DeclareMethod( "ReadMethod" );
+ if( ! rmethod.isUserDefined() )
+ {
+ // if not defined by user, we can change the default settings
+ rmethod.SetEngine( "BP" ); // BP is the default engine
+ rmethod.AddTransport( "Staging" ); //"The" staging method developed in ECP
+ rmethod.SetParameters( "Aggregation", (nproc+1)/2 ); // number of aggregators
+ rmethod.SetParameters( "verbose", adios::WARN ); // Verbosity level for this engine and what it calls
+ }
+
+ // 1. Open a stream, where every reader can see everything in a stream (so that they can read a global array)
+ // Blocking read of a variable
+ try
+ {
+ // These method settings are developer-only, not available to the user
+ rmethod.SetReadMultiplexPattern( adios::GLOBAL_READERS ); // Each reader process sees everything from the stream
+ rmethod.SetStreamOpenMode( adios::WAITFORSTREAM ); // In Open(), wait for the first step appear (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader =
+ adios.Open( "filename.bp", "r", comm, rmethod, adios::COLLECTIVE_IO,
+ /*timeout_sec=*/ 300.0); // wait this long for the stream, return error afterwards
+
+ /* Variable names are available as a vector of strings */
+ std::cout << "List of variables in file: " << reader->VariableNames() << "\n";
+ /* read a Global scalar which has a single value in a step */
+ reader->Read<unsigned int>( "NX", NX );
+
+ // inquiry about a variable, whose name we know
+ adios::Variable<double> var2D = reader->InquireVariableDouble( "Temperature" );
+ std::vector<std::size_t> gdims = var2D.GetGlobalDimensions();
+ int nsteps = var2D.GetSteps();
+
+ struct adios::BlockInfo blocks = reader.InquiryVariableBlockInfo( reader, var2D ); // get per-writer size info
+ // this is adios1 ADIOS_VARBLOCK
+ struct adios::Statistics stats = reader.InquiryVariableStat( reader, var2D, perstepstat, perblockstat ); // get min/max statistics
+ // this is adios1 ADIOS_VARSTAT
+
+ while( true )
+ {
+ // Make a selection to describe the local dimensions of the variable we READ and
+ // its offsets in the global spaces
+ adios::Selection bbsel = adios.SelectionBoundingBox( {1,NX}, {0,0} ); // local dims and offsets; both as list
+ var2D.SetSelection( bbsel );
+ adios::Selection memspace = adios.SelectionBoundingBox( {1,NX}, {0,1} ); // local dims and offsets; both as list
+ var2D.SetMemorySelection( memspace );
+ reader->Read<double>(var2D, *Temperature);
+ //var2D, Temperature );
+
+ // Better for staging to schedule several reads at once
+ reader->ScheduleRead<double>( var2D, *Temperature );
+ reader->PerformReads( adios::BLOCKINGREAD );
+
+ // promise to not read more from this step/item
+ reader->Release();
+
+ // want to move on to the next available step/item
+ reader->Advance(adios::NEXT_AVAILABLE); // default
+ reader->Advance(adios::LATEST_AVAILABLE); // interested only in the latest data
+ }
+ // Close file/stream
+ reader->Close();
+ }
+ catch( adios::end_of_stream& e )
+ {
+ // Reached end of stream, end processing loop
+ // Close file/stream
+ reader->Close();
+ }
+ catch( adios::file_not_found& e )
+ {
+ // File/stream does not exist, quit
+ }
+
+
+
+ // 2. Open a stream, where each item from the writers will get to a single reader only
+ // If the writers are collective, that means a whole steps go to different readers
+ // If the writers are independent, that means each writer's output goes to different readers
+ // Also show here ScheduleRead/PerformRead
+ //try
+ {
+ rmethod.SetReadMultiplexPattern( adios::FIFO_READERS ); // Each reader process sees everything from the stream
+ rmethod.SetStreamOpenMode( adios::WAITFORSTREAM ); // In Open(), wait for the first step appear (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader =
+ adios.Open( "filename.bp", "r", comm, rmethod, adios::INDEPENDENT_IO,
+ /*timeout_sec=*/ 300.0 ); // wait this long for the stream, return error afterwards
+
+ while( true )
+ {
+ // Make a selection to describe the local dimensions of the variable we READ and
+ // its offsets in the global spaces if we know this somehow
+ adios::Selection bbsel = adios.SelectionBoundingBox( {1,NX}, {0,0} ); // local dims and offsets; both as list
+ var2D->SetSelection( bbsel );
+ reader->Read<double>( var2D, *Temperature );
+
+ // Let ADIOS allocate space for the incoming (per-writer) item
+ double * data = reader->Read<double>( var2D );
+
+ // promise to not read more from this step/item
+ reader->Release();
+
+ // want to move on to the next available step/item
+ reader->Advance(); // default
+ reader->Advance(adios::LATEST_AVAILABLE); // This should be an error, or could it make sense?
+ }
+ reader->Close();
+ }
+
+
+ // 3. Open a stream and return immediately, not waiting for data to appear
+ // In this mode we cannot inquiry variables, but can schedule reads
+ //try
+ {
+ rmethod.SetReadMultiplexPattern( adios::GLOBAL_READERS ); // Each reader process sees everything from the stream
+ rmethod.SetStreamOpenMode( adios::NOWAITFORSTREAM ); // In Open(), wait for the first step appear (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader =
+ adios.Open( "filename.bp", "r", comm, rmethod, adios::INDEPENDENT_IO );
+
+ while( true )
+ {
+
+ // Let ADIOS allocate space for the incoming (per-writer) item
+ reader->ScheduleRead(); // read whatever comes
+
+ // One way is to handle the incoming data through a callback (which will be called in a thread)
+ // void cb( const void *data, std::string doid, std::string var, std::string dtype, std::vector<std::size_t> varshape );
+ // void cb( adios::VARCHUNK * chunk ); // see adios1 for VARCHUNK
+ reader->SetReadCallback( cb );
+ reader->PerformReads( adios::NONBLOCKINGREAD );
+
+ // Another way is checking back manually like in adios1 and processing chunks
+ reader->PerformReads( adios::NONBLOCKINGREAD );
+ int ck;
+ adios::VARCHUNK * chunk;
+ try
+ {
+ while ( (ck = reader->CheckReads( &chunk )) > 0) {
+ if (chunk) {
+ // process the chunk first
+ // ...
+ // free memory of chunk (not the data!)
+ adios::FreeChunk(chunk);
+ } else {
+ // no chunk was returned, slow down a little
+ sleep(1);
+ }
+ }
+ }
+ catch( std::exception& e )
+ {
+ // some error happened while getting a chunk
+ }
+
+ reader->Release();
+
+ // When AdvanceAsync returns new data is not yet available.
+ // A callback will tell us when we have the new data (and we have the lock on it to read)
+ writer->AdvanceAsync( adios::NEXT_AVAILABLE, cb_AsyncReadAdvanceCompleted );
+ // Do we need more fine grained control? Like this function does not get the lock and so
+ // do we need to call Advance() to get the lock?
+ }
+ reader->Close();
+ }
+ // Note: chunk reading also works if scheduling reads for specific variables
+
+
+ // 4. Open it as file and see all steps at once.
+ // Allow for reading multiple steps of a variable into a contiguous array
+ try
+ {
+ rmethod.AddTransport( "BP" ); // Set a file engine here. Shall we have RemoveTransport() too?
+
+ // Open a file with all steps immediately available
+ std::shared_ptr<adios::Engine> reader =
+ adios.OpenFileReader( "filename.bp", comm, rmethod, adios::COLLECTIVE_IO );
+
+ /* NX */
+ /* There is a single value for each step. We can read all into a 1D array with a step selection.
+ * Steps are not automatically presented as an array dimension and read does not read it as array.
+ */
+ // We can also just conveniently get the first step with a simple read statement.
+ reader->Read<unsigned int>( "NX", &NX ); // read a Global scalar which has a single value in a step
+ reader->Read<unsigned int>( varNX, &NX ); // read a Global scalar which has a single value in a step
+
+
+ adios::Variable<void> varNXread = reader->InquireVariable("NX");
+ adios::Variable<unsigned int> varNXreadint = reader->InquireVariableInt("NX");
+ std::vector<unsigned int> Nxs( varNXread.GetSteps() ); // number of steps available
+ // make a StepSelection to select multiple steps. Args: From, #of consecutive steps
+ adios::StepSelection stepsNx( 0, varNXread.GetSteps() );
+ // ? How do we make a selection for an arbitrary list of steps ?
+ varNXread.SetStepSelection( stepsNx );
+ reader->Read<unsigned int>( varNXreadint, Nxs.data());
+ reader->Read<void>( varNXread, Nxs.data());
+
+ auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
+ auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
+ if (*itmin != *itmax)
+ {
+ throw std::ios_base::failure( "ERROR: NX is not the same at all steps!\n" );
+ }
+
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of nproc elements.
+ // We can read all steps into a 2D array of nproc * nsteps
+ adios::Variable<void> varNpartsread = reader->InquireVariable("Nparts");
+ std::vector<int> partsV( Nproc * varNpartsread->GetSteps() );
+ varNpartsread->SetStepSelection(
+ adios.StepSelection( 0, varNpartsread.GetSteps() )
+ );
+ reader->Read<int>( "Nparts", partsV.data() );
+ reader->Read<void>( varNpartsread, partsV.data() ); // missing spatial selection = whole array at each step
+
+ // Close file/stream
+ reader->Close();
+ }
+ catch( adios::file_not_found& e )
+ {
+ // File/stream does not exist, quit
+ }
+
+ return 0;
+}
diff --git a/doc/API_design/Doxyfile b/doc/API_design/Doxyfile
new file mode 100644
index 000000000..b5afa02b7
--- /dev/null
+++ b/doc/API_design/Doxyfile
@@ -0,0 +1,2427 @@
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+
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+#
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+PROJECT_NAME = "ADIOS2 API Design"
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+PROJECT_NUMBER =
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+PROJECT_LOGO =
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+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
+# documentation from any documented member that it re-implements.
+# The default value is: YES.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
+# page for each member. If set to NO, the documentation of a member will be part
+# of the file/class/namespace that contains it.
+# The default value is: NO.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
+# uses this value to replace tabs by spaces in code fragments.
+# Minimum value: 1, maximum value: 16, default value: 4.
+
+TAB_SIZE = 4
+
+# This tag can be used to specify a number of aliases that act as commands in
+# the documentation. An alias has the form:
+# name=value
+# For example adding
+# "sideeffect=@par Side Effects:\n"
+# will allow you to put the command \sideeffect (or @sideeffect) in the
+# documentation, which will result in a user-defined paragraph with heading
+# "Side Effects:". You can put \n's in the value part of an alias to insert
+# newlines.
+
+ALIASES =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding "class=itcl::class"
+# will allow you to use the command class in the itcl::class meaning.
+
+TCL_SUBST =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
+# only. Doxygen will then generate output that is more tailored for C. For
+# instance, some of the names that are used will be different. The list of all
+# members will be omitted, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
+# Python sources only. Doxygen will then generate output that is more tailored
+# for that language. For instance, namespaces will be presented as packages,
+# qualified scopes will look different, etc.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources. Doxygen will then generate output that is tailored for Fortran.
+# The default value is: NO.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for VHDL.
+# The default value is: NO.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension, and
+# language is one of the parsers supported by doxygen: IDL, Java, Javascript,
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
+#
+# Note: For files without extension you can use no_extension as a placeholder.
+#
+# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
+# the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
+# according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you can
+# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
+# case of backward compatibilities issues.
+# The default value is: YES.
+
+MARKDOWN_SUPPORT = YES
+
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+# The default value is: YES.
+
+AUTOLINK_SUPPORT = YES
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should set this
+# tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string);
+# versus func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+# The default value is: NO.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+# The default value is: NO.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
+# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen
+# will parse them like normal C++ but will assume all classes use public instead
+# of private inheritance when no explicit protection keyword is present.
+# The default value is: NO.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES will make
+# doxygen to replace the get and set methods by a property in the documentation.
+# This will only work if the methods are indeed getting or setting a simple
+# type. If this is not the case, or you want to show the methods anyway, you
+# should set this option to NO.
+# The default value is: YES.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+# The default value is: NO.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# If one adds a struct or class to a group and this option is enabled, then also
+# any nested class or struct is added to the same group. By default this option
+# is disabled and one has to add nested compounds explicitly via \ingroup.
+# The default value is: NO.
+
+GROUP_NESTED_COMPOUNDS = NO
+
+# Set the SUBGROUPING tag to YES to allow class member groups of the same type
+# (for instance a group of public functions) to be put as a subgroup of that
+# type (e.g. under the Public Functions section). Set it to NO to prevent
+# subgrouping. Alternatively, this can be done per class using the
+# \nosubgrouping command.
+# The default value is: YES.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
+# are shown inside the group in which they are included (e.g. using \ingroup)
+# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
+# and RTF).
+#
+# Note that this feature does not work in combination with
+# SEPARATE_MEMBER_PAGES.
+# The default value is: NO.
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
+# with only public data fields or simple typedef fields will be shown inline in
+# the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST = YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT = ../../include ../../include/core
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
+# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+
+FILE_PATTERNS = ADIOS.h Variable.h Method.h Engine.h
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS = YES
+
+# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# generated with the -Duse-libclang=ON option for CMake.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# If clang assisted parsing is enabled you can provide the compiler with command
+# line options that you would normally use when invoking the compiler. Note that
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE = NO
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
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diff --git a/doc/API_design_doc.h b/doc/API_design_doc.h
deleted file mode 100644
index 7f3b65369..000000000
--- a/doc/API_design_doc.h
+++ /dev/null
@@ -1,332 +0,0 @@
-/* Current API by design, incorrect as code but describes all the ideas */
-
-#include "ADIOS.h"
-
-
-namespace adios
-{
-typedef enum {
- VARYING_DIMENSION = -1,
- LOCAL_VALUE = 0,
- GLOBAL_VALUE = 1
-};
-
-typedef enum { ERROR = 0, WARN = 1, INFO = 2, DEBUG = 3 } VerboseFlag;
-
-typedef enum {
- COLLECTIVE_WRITERS = 0, INDEPENDENT_WRITERS = 1,
- GLOBAL_READERS = 2, ROUNDROBIN_READERS = 3, FIFO_READERS = 4,
- OPEN_ALL_STEPS = 5
-} OpenMode;
-
-typedef enum { NOWAITFORSTREAM = 0, WAITFORSTREAM = 1 } StreamOpenMode; // default: wait for stream
-
-typedef enum {
- APPEND = 0, UPDATE = 1, // writer advance modes
- NEXT_AVAILABLE = 2, LATEST_AVAILABLE = 3, // reader advance modes
-} AdvanceMode;
-
-typedef enum { NONBLOCKINGREAD = 0, BLOCKINGREAD = 1 } ReadMode;
-
-} // namespace adios
-
-void dummy()
-{
- //Application variables
- std::vector<double> Temperature;
- std::vector<float> RaggedArray;
- unsigned int Nx;
- int Nparts, nproc;
-
- // Global class/object that serves for init, finalize and provides ADIOS functions
- adios::ADIOS adios( std::string configfile, MPI_Comm comm, adios::verboseflag flag, bool debugflag );
-
-
- /*************
- * WRITE API
- *************/
-
- /* Method
- * We associate Engines and Transports and user settings into an object called Method.
- * ADIOS check if it is defined by the user in the config file, and fills it out if it is.
- */
-
- std::shared_ptr<adios::Method> method = adios.DeclareMethod( "MethodName" );
- if( ! method.isDefinedInConfig() )
- {
- // if not defined by user, we can change the default settings
- method.SetEngine( "BP" ); // BP is the default engine
- method.AddTransport( "File", "lucky=yes" ); // ISO-POSIX file is the default transport
- method.AddTransport( "Staging" ); //"The" staging method developed in ECP
- method.SetParameters("have_metadata_file","yes" ); // Passing parameters to the engine
- method.SetParameters( "Aggregation", (nproc+1)/2 ); // number of aggregators
- method.SetParameters( "verbose", adios::WARN ); // Verbosity level for this engine and what it calls
- }
-
-
- //Define variables with transformations.
- adios::Variable<unsigned int>& varNX = adios.DefineVariable<unsigned int>( "NX" ); // global single-value across processes
- adios::Variable<int>& varNproc = adios.DefineVariable<int>( "nproc", adios::GLOBAL_VALUE ); // same def for global value
- adios::Variable<int>& varNparts = adios.DefineVariable<int>( "Nparts", adios::LOCAL_VALUE ); // a single-value different on every process
- adios::Variable<double>& var1D = adios.DefineVariable<double>( "Temperature", {nproc*Nx} ); // 1D global array
- adios::Variable<float>& varRagged = adios.DefineVariable<float>( "Ragged", {nproc,adios::VARYING_DIMENSION} ); // ragged array
-
- // Define a variable with local dimensions now, and make ADIOS allocate it inside its buffers (zero-copy API)
- adios::Variable<double>& varZeroCopy = adios.DefineVariable<double>( "ZC", {nproc,Nx}, {1,NX}, {rank,0} ); // 2D global array, 1D decomposition
- double *myVarZC = adios.AllocateVar( varZeroCopy );
-
- //add transform to variable
- adios::Transform bzip2 = adios::transform::BZIP2( );
- var1D->AddTransform( bzip2, 1 );
-
- // open...write.write.write...advance...write.write.write...advance... ...close cycle
- // "w" create/overwrite on open, "a" append at open, "u" open for update (does not increase step), "r" open for read.
- std::shared_ptr<adios::Engine> writer = adios.Open( "myNumbers.bp", "w", method, adios::INDEPENDENT_WRITERS );
- if( writer == nullptr )
- throw std::ios_base::failure( "ERROR: failed to open ADIOS writer\n" );
-
- for (int step = 0; step < 10; ++step) {
- // write scalar value
- writer->Write<int>( varNparts, Nparts );
-
- // Make a selection to describe the local dimensions of the variable we write and
- // its offsets in the global spaces
- adios::Selection& sel = adios.SelectionBoundingBox( {Nx}, {rank*Nx} ); // local dims and offsets; both as list
- var1D.SetSelection( sel );
- writer->Write<double>( var1D, Temperature.data() );
-
- // Indicate we are done for this step.
- // N-to-M Aggregation, disk I/O will be performed during this call, unless
- // time aggregation postpones all of that to some later step.
- // When Advance() returns, user can overwrite its Zero Copy variables.
- // Internal buffer is freed only if there are no Zero Copy variables and there is no time aggregation going on
- writer->Advance(); // same as AppendMode
- writer->Advance( adios::APPEND ); // append new step at next write
- writer->Advance( adios::UPDATE ); // do not increase step; ? should this cause error in staging ?
-
- // When AdvanceAsync returns, user need to wait for notification that he can overwrite the Zero Copy variables.
- writer->AdvanceAsync( callback_func_to_notify_me() );
- }
-
- // Called once: indicate that we are done with this output for the run
- // Zero Copy variables will be deallocated
- writer->Close();
-
-
-
- /*************
- * READ API
- *************/
-
- // 1. Open a stream, where every reader can see everything in a stream (so that they can read a global array)
- // Blocking read of a variable
- try
- {
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader =
- adios.Open( "filename.bp", "r", method,
- adios::GLOBAL_READERS, // Each reader process sees everything from the stream
- adios::WAITFORSTREAM, // wait for the first step appear (default)
- timeout ); // wait this long for the stream, return error afterwards
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << reader->VariableNames << "\n";
- /* read a Global scalar which has a single value in a step */
- reader->Read<unsigned int>( "NX", Nx );
-
- // inquiry about a variable, whose name we know
- adios::Variable var1D = reader.InquiryVariable( "Temperature" );
- vector<uint64_t> gdims = var1D->GetGlobalDimensions();
- int step = varID->GetStep();
-
- struct adios::BlockInfo blocks = reader.InquiryVariableBlockInfo( reader, var1D ); // get per-writer size info
- // this is adios1 ADIOS_VARBLOCK
- struct adios::Statistics stats = reader.InquiryVariableStat( reader, var1D, perstepstat, perblockstat ); // get min/max statistics
- // this is adios1 ADIOS_VARSTAT
-
- while( true )
- {
- // Make a selection to describe the local dimensions of the variable we READ and
- // its offsets in the global spaces
- adios::Selection bbsel = adios.SelectionBoundingBox( {ldim}, {offs} ); // local dims and offsets; both as list
- var1D->SetSelection( bbsel );
- reader->Read<double>( var1D, Temperature.data() );
-
- // Better for staging to schedule several reads at once
- reader->ScheduleRead<double>( var1D, Temperature.data() );
- reader->PerformRead( adios::BLOCKINGREAD );
-
- // promise to not read more from this step/item
- reader->Release();
-
- // want to move on to the next available step/item
- reader->Advance(adios::NEXT_AVAILABLE); // default
- reader->Advance(adios::LATEST_AVAILABLE); // interested only in the latest data
- }
- // Close file/stream
- reader->Close();
- }
- catch( adios::end_of_stream& e )
- {
- // Reached end of stream, end processing loop
- // Close file/stream
- bpReader->Close();
- }
- catch( adios::file_not_found& e )
- {
- // File/stream does not exist, quit
- }
-
-
-
- // 2. Open a stream, where each item from the writers will get to a single reader only
- // If the writers are collective, that means a whole steps go to different readers
- // If the writers are independent, that means each writer's output goes to different readers
- // Also show here ScheduleRead/PerformRead
- //try
- {
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader =
- adios.Open( "filename.bp", "r", method,
- adios::FIFO_READERS, // Each reader process sees everything from the stream
- adios::WAITFORSTREAM, // wait for the first step appear (default)
- timeout ); // wait this long for the stream, return error afterwards
-
- while( true )
- {
- // Make a selection to describe the local dimensions of the variable we READ and
- // its offsets in the global spaces if we know this somehow
- adios::Selection bbsel = adios.SelectionBoundingBox( {ldim}, {offs} ); // local dims and offsets; both as list
- var1D->SetSelection( bbsel );
- reader->Read<double>( var1D, Temperature.data() );
-
- // Let ADIOS allocate space for the incoming (per-writer) item
- double * data = reader->Read<double>( var1D );
-
- // promise to not read more from this step/item
- reader->Release();
-
- // want to move on to the next available step/item
- reader->Advance(); // default
- reader->Advance(adios::LATEST_AVAILABLE); // This should be an error, or could it make sense?
- }
- reader->Close();
- }
-
-
- // 3. Open a stream and return immediately, not waiting for data to appear
- // In this mode we cannot inquiry variables, but can schedule reads
- //try
- {
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader =
- adios.Open( "filename.bp", "r", method,
- adios::GLOBAL_READERS, // Each reader process sees everything from the stream
- adios::NOWAITFORSTREAM // wait for the first step appear (default)
- );
-
- while( true )
- {
-
- // Let ADIOS allocate space for the incoming (per-writer) item
- reader->ScheduleRead<void>(); // read whatever comes
-
- // One way is to handle the incoming data through a callback (which will be called in a thread)
- // void cb( const void *data, std::string doid, std::string var, std::string dtype, std::vector<std::size_t> varshape );
- // void cb( adios::VARCHUNK * chunk ); // see adios1 for VARCHUNK
- reader->SetReadCallback( cb );
- reader->PerformRead( adios::NONBLOCKINGREAD );
-
- // Another way is checking back manually like in adios1 and processing chunks
- reader->PerformRead( adios::NONBLOCKINGREAD );
- int ck;
- adios::VARCHUNK * chunk;
- try
- {
- while ( (ck = reader->CheckReads( &chunk )) > 0) {
- if (chunk) {
- // process the chunk first
- // ...
- // free memory of chunk (not the data!)
- adios::FreeChunk(chunk);
- } else {
- // no chunk was returned, slow down a little
- sleep(1);
- }
- }
- }
- catch( std::exception& e )
- {
- // some error happened while getting a chunk
- }
-
- reader->Release();
- reader->Advance();
- }
- reader->Close();
- }
-
-
- // 4. Open it as file and see all steps at once.
- // Allow for reading multiple steps of a variable into a contiguous array
- try
- {
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader =
- adios.Open( "filename.bp", "r", method,
- adios::OPEN_ALL_STEPS, //File mode, no advance
- );
-
- /* NX */
- /* There is a single value for each step. We can read all into a 1D array with a step selection.
- * Steps are not automatically presented as an array dimension and read does not read it as array.
- */
- // We can also just conveniently get the first step with a simple read statement.
- reader->Read<unsigned int>( "NX", &Nx ); // read a Global scalar which has a single value in a step
-
-
- adios::Variable<void> varNx = bpReader.InquiryVariable("Nx");
- std::vector<int> Nxs( varNx->GetSteps() ); // number of steps available
- // make a StepSelection to select multiple steps. Args: From, #of consecutive steps
- adios::StepSelection stepsNx( 0, varNx->GetSteps() );
- // ? How do we make a selection for an arbitrary list of steps ?
- varNX.SetStepSelection( stepsNx );
- reader->Read<unsigned int>( varNx, Nxs.data() );
-
- auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
- auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
- if (*itmin != *itmax)
- {
- throw std::ios_base::failure( "ERROR: NX is not the same at all steps!\n" );
- }
-
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of nproc elements.
- // We can read all steps into a 2D array of nproc * nsteps
- adios::Variable<void> varNparts = bpReader.InquiryVariable("Nparts");
- std::vector<int> partsV( Nproc * varNparts->GetSteps() );
- varNparts->SetStepSelection(
- adios.StepSelection( 0, varNparts->GetSteps() )
- );
- bpReader->Read<int>( varNparts, partsV.data() ); // missing spatial selection = whole array at each step
-
- // Close file/stream
- reader->Close();
- }
- catch( adios::end_of_stream& e )
- {
- // Reached end of stream, end processing loop
- // Close file/stream
- bpReader->Close();
- }
- catch( adios::file_not_found& e )
- {
- // File/stream does not exist, quit
- }
-
-}
diff --git a/include/ADIOS.h b/include/ADIOS.h
index e0e4e19bf..0d506d744 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -35,6 +35,19 @@
namespace adios
{
+/** Use these values in Dims() when defining variables
+ */
+typedef enum {
+ VARYING_DIMENSION = -1,//!< VARYING_DIMENSION
+ LOCAL_VALUE = 0, //!< LOCAL_VALUE
+ GLOBAL_VALUE = 1 //!< GLOBAL_VALUE
+};
+
+typedef enum { ERROR = 0, WARN = 1, INFO = 2, DEBUG = 3 } VerboseFlag;
+
+typedef enum { INDEPENDENT_IO = 0, COLLECTIVE_IO = 1 } IOMode;
+
+
class Engine;
/**
@@ -45,21 +58,10 @@ class ADIOS
public: // PUBLIC Constructors and Functions define the User Interface with ADIOS
- #ifdef HAVE_MPI
- MPI_Comm m_MPIComm = MPI_COMM_NULL; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
- #else
- MPI_Comm m_MPIComm = 0; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
- #endif
-
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
-
- std::string m_HostLanguage = "C++";
-
/**
* @brief ADIOS empty constructor. Used for non XML config file API calls.
*/
- ADIOS( const bool debugMode = false );
+ ADIOS( const adios::VerboseFlag verbose = WARN, const bool debugMode = false );
/**
@@ -67,7 +69,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param configFileName passed to m_ConfigFile
* @param debugMode true: on throws exceptions and do additional checks, false: off (faster, but unsafe)
*/
- ADIOS( const std::string configFileName, const bool debugMode = false );
+ ADIOS( const std::string configFileName, const adios::VerboseFlag verbose = WARN, const bool debugMode = false );
/**
@@ -76,7 +78,7 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param mpiComm MPI communicator ...const to be discussed
* @param debugMode true: on, false: off (faster, but unsafe)
*/
- ADIOS( const std::string configFileName, const MPI_Comm mpiComm, const bool debugMode = false );
+ ADIOS( const std::string configFileName, const MPI_Comm mpiComm, const adios::VerboseFlag verbose = WARN, const bool debugMode = false );
/**
@@ -84,16 +86,13 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
* @param mpiComm MPI communicator passed to m_MPIComm*
* @param debugMode true: on, false: off (faster)
*/
- ADIOS( const MPI_Comm mpiComm, const bool debugMode = false );
+ ADIOS( const MPI_Comm mpiComm, const adios::VerboseFlag verbose = WARN, const bool debugMode = false );
~ADIOS( ); ///< empty, using STL containers for memory management
- void InitMPI( ); ///< sets rank and size in m_rank and m_Size, respectively.
-
-
- /**
+ /**
* Look for template specialization
* @param name
* @param dimensions
@@ -129,10 +128,15 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
VariableCompound& GetVariableCompound( const std::string name );
+
/**
- * Declares a new method
- * @param name must be unique
- * @param type supported type : "Writer" (default), "DataMan"...future: "Sirius"
+ * Declares a new method. If the method is defined in the user config file,
+ * it will be already created during processing the config file,
+ * the method is set up with the user settings and this function just returns that method.
+ * Otherwise it will create and return a new Method with default settings.
+ * Use method.isUserDefined() to distinguish between the two cases.
+ * @param methodName must be unique
+ * @param type supported type : "BP" (default), "DataMan"...future: "Sirius"
*/
Method& DeclareMethod( const std::string methodName, const std::string type = "" );
@@ -140,52 +144,67 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
/**
* @brief Open to Write, Read. Creates a new engine from previously defined method
* @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or "update"
* @param mpiComm option to modify communicator from ADIOS class constructor
* @param method looks for corresponding Method object in ADIOS to initialize the engine
- * @param cores optional parameter for threaded operations
+ * @param iomode Independent or collective open/advance by writers/readers? Write() operations are always independent.
* @return Derived class of base Engine depending on Method parameters, shared_ptr for potential flexibility
*/
std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode, MPI_Comm mpiComm,
- const Method& method, const unsigned int cores = 1 );
-
+ const Method& method, const enum IOMode iomode );
+ /**
+ * @brief Open to Read with a timeout value specified. Creates a new engine from previously defined method
+ * @param streamName unique stream or file name
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or "update"
+ * @param mpiComm option to modify communicator from ADIOS class constructor
+ * @param method looks for corresponding Method object in ADIOS to initialize the engine
+ * @param iomode Independent or collective open/advance by writers/readers? Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream (i.e. wait for it for a while)
+ * @return Derived class of base Engine depending on Method parameters, shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode, MPI_Comm mpiComm,
+ const Method& method, const enum IOMode iomode,
+ const float timeout_sec );
/**
* @brief Open to Write, Read. Creates a new engine from previously defined method.
* Reuses MPI communicator from ADIOS constructor.
* @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or "update"
* @param method contains engine parameters
- * @param cores optional parameter for threaded operations
+ * @param iomode Independent or collective open/advance by writers/readers? Write() operations are always independent.
* @return Derived class of base Engine depending on Method parameters, shared_ptr for potential flexibility
*/
std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode, const Method& method,
- const unsigned int cores = 1 );
+ const enum IOMode iomode );
/**
- * Version required by the XML config file implementation, searches method inside ADIOS through a unique name
+ * @brief Open to Read with a timeout value specified. Creates a new engine from previously defined method
+ * Reuses MPI communicator from ADIOS constructor.
* @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
- * @param mpiComm mpi Communicator
- * @param methodName used to search method object inside ADIOS object
- * @param cores optional parameter for threaded operations
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or "update"
+ * @param method looks for corresponding Method object in ADIOS to initialize the engine
+ * @param iomode Independent or collective open/advance by writers/readers? Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream (i.e. wait for it for a while)
* @return Derived class of base Engine depending on Method parameters, shared_ptr for potential flexibility
*/
- std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode, MPI_Comm mpiComm,
- const std::string methodName, const unsigned int cores = 1 );
+ std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode, const Method& method,
+ const enum IOMode iomode,
+ const float timeout_sec );
+
/**
- * Version required by the XML config file implementation, searches method inside ADIOS through a unique name.
- * Reuses ADIOS MPI Communicator from constructor.
- * @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
- * @param methodName used to search method object inside ADIOS object
- * @param cores optional parameter for threaded operations
+ * @brief Open to Read all steps from a file. No streaming, advancing is possible here. All steps in the file
+ * are immediately available for reading. Creates a new engine from previously defined method.
+ * @param fileName file name
+ * @param mpiComm option to modify communicator from ADIOS class constructor
+ * @param method looks for corresponding Method object in ADIOS to initialize the engine
+ * @param iomode Independent or collective open/advance by writers/readers? Write() operations are always independent.
* @return Derived class of base Engine depending on Method parameters, shared_ptr for potential flexibility
*/
- std::shared_ptr<Engine> Open( const std::string streamName, const std::string accessMode,
- const std::string methodName, const unsigned int cores = 1 );
+ std::shared_ptr<Engine> OpenFileReader( const std::string streamName, MPI_Comm mpiComm,
+ const Method& method, const enum IOMode iomode );
/**
* @brief Dumps groups information to a file stream or standard output.
@@ -198,322 +217,8 @@ public: // PUBLIC Constructors and Functions define the User Interface with ADIO
private: //no const to allow default empty and copy constructors
- std::vector< Variable<char> > m_Char; ///< Key: variable name, Value: variable of type char
- std::vector< Variable<unsigned char> > m_UChar; ///< Key: variable name, Value: variable of type unsigned char
- std::vector< Variable<short> > m_Short; ///< Key: variable name, Value: variable of type short
- std::vector< Variable<unsigned short> > m_UShort; ///< Key: variable name, Value: variable of type unsigned short
- std::vector< Variable<int> > m_Int; ///< Key: variable name, Value: variable of type int
- std::vector< Variable<unsigned int> > m_UInt; ///< Key: variable name, Value: variable of type unsigned int
- std::vector< Variable<long int> > m_LInt; ///< Key: variable name, Value: variable of type long int
- std::vector< Variable<unsigned long int> > m_ULInt; ///< Key: variable name, Value: variable of type unsigned long int
- std::vector< Variable<long long int> > m_LLInt; ///< Key: variable name, Value: variable of type long long int
- std::vector< Variable<unsigned long long int> > m_ULLInt; ///< Key: variable name, Value: variable of type unsigned long long int
- std::vector< Variable<float> > m_Float; ///< Key: variable name, Value: variable of type float
- std::vector< Variable<double> > m_Double; ///< Key: variable name, Value: variable of type double
- std::vector< Variable<long double> > m_LDouble; ///< Key: variable name, Value: variable of type double
- std::vector< Variable<std::complex<float>> > m_CFloat; ///< Key: variable name, Value: variable of type complex<float>
- std::vector< Variable<std::complex<double>> > m_CDouble; ///< Key: variable name, Value: variable of type complex<float>
- std::vector< Variable<std::complex<long double>> > m_CLDouble; ///< Key: variable name, Value: variable of type complex<float>
- std::vector< VariableCompound > m_Compound; ///< Key: variable name, Value: compound type variable
-
- std::string m_ConfigFile; ///< XML File to be read containing configuration information
- bool m_DebugMode = false; ///< if true will do more checks, exceptions, warnings, expect slower code
-
- //Variables
- std::map< std::string, std::pair< std::string, unsigned int > > m_Variables; ///< Makes variable name unique, key: variable name, value: pair.first = type, pair.second = index in corresponding vector of Variable
-
- std::vector< std::shared_ptr<Transform> > m_Transforms; ///< transforms associated with ADIOS run
-
-
- /**
- * @brief List of Methods (engine metadata) defined from either ADIOS XML configuration file or the DeclareMethod function.
- * <pre>
- * Key: std::string unique method name
- * Value: Method class
- * </pre>
- */
- std::map< std::string, Method > m_Methods;
- std::set< std::string > m_EngineNames; ///< set used to check Engine name uniqueness in debug mode
-
- /**
- * @brief Checks for group existence in m_Groups, if failed throws std::invalid_argument exception
- * @param itGroup m_Groups iterator, usually from find function
- * @param groupName unique name, passed for thrown exception only
- * @param hint adds information to thrown exception
- */
- void CheckVariableInput( const std::string name, const Dims& dimensions ) const;
-
- /**
- * Checks for variable name, if not found throws an invalid exception
- * @param itVariable iterator pointing to the variable name in m_Variables
- * @param name variable name
- * @param hint message to be thrown for debugging purporses
- */
- void CheckVariableName( std::map< std::string, std::pair< std::string, unsigned int > >::const_iterator itVariable,
- const std::string name, const std::string hint ) const;
-
- /**
- * @brief Checks for method existence in m_Methods, if failed throws std::invalid_argument exception
- * @param itMethod m_Methods iterator, usually from find function
- * @param methodName unique name, passed for thrown exception only
- * @param hint adds information to thrown exception
- */
- void CheckMethod( std::map< std::string, Method >::const_iterator itMethod,
- const std::string methodName, const std::string hint ) const;
-
- template< class T >
- unsigned int GetVariableIndex( const std::string name )
- {
- auto itVariable = m_Variables.find( name );
- CheckVariableName( itVariable, name, "in call to GetVariable<" + GetType<T>() + ">, or call to GetVariableCompound if <T> = <compound>\n" );
- return itVariable->second.second;
- }
-
};
-//template specializations of DefineVariable:
-template<> inline
-Variable<char>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_Char.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<char>(), m_Char.size()-1 ) );
- return m_Char.back();
-}
-
-
-template<> inline
-Variable<unsigned char>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_UChar.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), m_UChar.size()-1 ) );
- return m_UChar.back();
-}
-
-
-template<> inline
-Variable<short>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_Short.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned char>(), m_Short.size()-1 ) );
- return m_Short.back();
-}
-
-
-template<> inline
-Variable<unsigned short>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_UShort.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned short>(), m_UShort.size()-1 ) );
- return m_UShort.back();
-}
-
-
-template<> inline
-Variable<int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_Int.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<int>(), m_Int.size()-1 ) );
- return m_Int.back();
-}
-
-
-template<> inline
-Variable<unsigned int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_UInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned int>(), m_UInt.size()-1 ) );
- return m_UInt.back();
-}
-
-
-template<> inline
-Variable<long int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_LInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<long int>(), m_LInt.size()-1 ) );
- return m_LInt.back();
-}
-
-
-template<> inline
-Variable<unsigned long int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_ULInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned long int>(), m_ULInt.size()-1 ) );
- return m_ULInt.back();
-}
-
-
-template<> inline
-Variable<long long int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_LLInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<long long int>(), m_LLInt.size()-1 ) );
- return m_LLInt.back();
-}
-
-
-template<> inline
-Variable<unsigned long long int>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_ULLInt.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<unsigned long long int>(), m_ULLInt.size()-1 ) );
- return m_ULLInt.back();
-}
-
-template<> inline
-Variable<float>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_Float.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<float>(), m_Float.size()-1 ) );
- return m_Float.back();
-}
-
-
-template<> inline
-Variable<double>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_Double.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<double>(), m_Double.size()-1 ) );
- return m_Double.back();
-}
-
-
-template<> inline
-Variable<long double>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_LDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<long double>(), m_LDouble.size()-1 ) );
- return m_LDouble.back();
-}
-
-
-template<> inline
-Variable<std::complex<float>>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_CFloat.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<std::complex<float>>(), m_CFloat.size()-1 ) );
- return m_CFloat.back();
-}
-
-
-template<> inline
-Variable<std::complex<double>>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_CDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<std::complex<double>>(), m_CDouble.size()-1 ) );
- return m_CDouble.back();
-}
-
-
-template<> inline
-Variable<std::complex<long double>>& ADIOS::DefineVariable( const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets )
-{
- CheckVariableInput( name, dimensions );
- m_CLDouble.emplace_back( name, dimensions, globalDimensions, globalOffsets, m_DebugMode );
- m_Variables.emplace( name, std::make_pair( GetType<std::complex<double>>(), m_CLDouble.size()-1 ) );
- return m_CLDouble.back();
-}
-
-
-//Get template specialization
-template<> inline
-Variable<char>& ADIOS::GetVariable( const std::string name )
-{ return m_Char[ GetVariableIndex<char>(name) ]; }
-
-template<> inline
-Variable<unsigned char>& ADIOS::GetVariable( const std::string name )
-{ return m_UChar[ GetVariableIndex<unsigned char>(name) ]; }
-
-template<> inline
-Variable<short>& ADIOS::GetVariable( const std::string name )
-{ return m_Short[ GetVariableIndex<short>(name) ]; }
-
-template<> inline
-Variable<unsigned short>& ADIOS::GetVariable( const std::string name )
-{ return m_UShort[ GetVariableIndex<unsigned short>(name) ]; }
-
-template<> inline
-Variable<int>& ADIOS::GetVariable( const std::string name )
-{ return m_Int[ GetVariableIndex<int>(name) ]; }
-
-template<> inline
-Variable<unsigned int>& ADIOS::GetVariable( const std::string name )
-{ return m_UInt[ GetVariableIndex<unsigned int>(name) ]; }
-
-template<> inline
-Variable<long int>& ADIOS::GetVariable( const std::string name )
-{ return m_LInt[ GetVariableIndex<unsigned int>(name) ]; }
-
-template<> inline
-Variable<unsigned long int>& ADIOS::GetVariable( const std::string name )
-{ return m_ULInt[ GetVariableIndex<unsigned long int>(name) ]; }
-
-template<> inline
-Variable<long long int>& ADIOS::GetVariable( const std::string name )
-{ return m_LLInt[ GetVariableIndex<long long int>(name) ]; }
-
-template<> inline
-Variable<unsigned long long int>& ADIOS::GetVariable( const std::string name )
-{ return m_ULLInt[ GetVariableIndex<unsigned long long int>(name) ]; }
-
-template<> inline
-Variable<float>& ADIOS::GetVariable( const std::string name )
-{ return m_Float[ GetVariableIndex<float>(name) ]; }
-
-template<> inline
-Variable<double>& ADIOS::GetVariable( const std::string name )
-{ return m_Double[ GetVariableIndex<double>(name) ]; }
-
-template<> inline
-Variable<long double>& ADIOS::GetVariable( const std::string name )
-{ return m_LDouble[ GetVariableIndex<long double>(name) ]; }
-
-template<> inline
-Variable<std::complex<float>>& ADIOS::GetVariable( const std::string name )
-{ return m_CFloat[ GetVariableIndex<std::complex<float>>(name) ]; }
-
-template<> inline
-Variable<std::complex<double>>& ADIOS::GetVariable( const std::string name )
-{ return m_CDouble[ GetVariableIndex<std::complex<double>>(name) ]; }
-
-template<> inline
-Variable<std::complex<long double>>& ADIOS::GetVariable( const std::string name )
-{ return m_CLDouble[ GetVariableIndex<std::complex<long double>>(name) ]; }
-
-
-
} //end namespace
diff --git a/include/core/Engine.h b/include/core/Engine.h
index e5e8f16ca..90c20a019 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -36,6 +36,14 @@
namespace adios
{
+typedef enum { NONBLOCKINGREAD = 0, BLOCKINGREAD = 1 } PerformReadMode;
+
+
+typedef enum {
+ APPEND = 0, UPDATE = 1, // writer advance modes
+ NEXT_AVAILABLE = 2, LATEST_AVAILABLE = 3, // reader advance modes
+} AdvanceMode;
+
/**
* Base class for Engine operations managing shared-memory, and buffer and variables transform and transport operations
*/
@@ -44,24 +52,9 @@ class Engine
public:
- #ifdef HAVE_MPI
- MPI_Comm m_MPIComm = MPI_COMM_NULL; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
- #else
- MPI_Comm m_MPIComm = 0; ///< only used as reference to MPI communicator passed from parallel constructor, MPI_Comm is a pointer itself. Public as called from C
- #endif
-
- const std::string m_EngineType; ///< from derived class
- const std::string m_Name; ///< name used for this engine
- const std::string m_AccessMode; ///< accessMode for buffers used by this engine
- const Method& m_Method; ///< associated method containing engine metadata
-
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
-
- const std::string m_HostLanguage = "C++";
-
/**
* Unique constructor
+ * @param adios
* @param engineType
* @param name
* @param accessMode
@@ -78,11 +71,29 @@ public:
virtual ~Engine( );
- /**
+ /** @brief Let ADIOS allocate memory for a variable, which can be used by the user.
+ *
+ * To decrease the cost of copying memory, a user may let ADIOS allocate the memory for a user-variable,
+ * according to the definition of an ADIOS-variable. The memory will be part of the ADIOS buffer used
+ * by the engine and it lives until the engine (file, stream) is closed.
+ * A variable that has been allocated this way (cannot have its local dimensions changed, and AdvanceAsync() should be
+ * used instead of Advance() and the user-variable must not be modified by the application until the notification arrives.
+ * This is required so that any reader can access the written data before the application overwrites it.
+ * @param var Variable with defined local dimensions and offsets in global space
+ * @param fillValue Fill the allocated array with this value
+ * @return A constant pointer to the non-constant allocated array. User should not deallocate this pointer.
+ */
+ template<class T> inline
+ T * const AllocateVariable( Variable<T>& var, T fillValue = 0 )
+ {
+ throw std::invalid_argument( "ERROR: type not supported for variable " + var->name + " in call to GetVariable\n" );
+ }
+
+ /*
* Needed for DataMan Engine
* @param callback
*/
- virtual void SetCallBack( std::function<void( const void*, std::string, std::string, std::string, Dims )> callback );
+ //virtual void SetCallBack( std::function<void( const void*, std::string, std::string, std::string, Dims )> callback );
/**
* Write function that adds static checking on the variable to be passed by values
@@ -176,76 +187,199 @@ public:
virtual void Write( const std::string variableName, const void* values );
/**
- * Indicates that a new step is going to be written as new variables come in.
+ * Read function that adds static checking on the variable to be passed by values
+ * It then calls its corresponding derived class virtual function
+ * This version uses m_Group to look for the variableName.
+ * @param variable name of variable to the written
+ * @param values pointer passed from the application, nullptr not allowed, must use Read(variable) instead intentionally
*/
- virtual void Advance( );
+ template< class T >
+ void Read( Variable<T>& variable, const T* values )
+ {
+ Read( variable, values );
+ }
+ /**
+ * String version
+ * @param variableName
+ * @param values
+ */
+ template< class T >
+ void Read( const std::string variableName, const T* values )
+ {
+ Read( variableName, values );
+ }
- //Read API
/**
- * Inquires and (optionally) allocates and copies the contents of a variable
- * If success: it returns a pointer to the internal stored variable object in ADIOS class.
- * If failure: it returns nullptr
- * @param name variable name to look for
- * @param readIn if true: reads the full variable and payload, allocating values in memory, if false: internal payload is nullptr
- * @return success: it returns a pointer to the internal stored variable object in ADIOS class, failure: nullptr
+ * Single value version
+ * @param variable
+ * @param values
*/
- virtual Variable<void>* InquireVariable( const std::string name, const bool readIn = true );
- virtual Variable<char>* InquireVariableChar( const std::string name, const bool readIn = true );
- virtual Variable<unsigned char>* InquireVariableUChar( const std::string name, const bool readIn = true );
- virtual Variable<short>* InquireVariableShort( const std::string name, const bool readIn = true );
- virtual Variable<unsigned short>* InquireVariableUShort( const std::string name, const bool readIn = true );
- virtual Variable<int>* InquireVariableInt( const std::string name, const bool readIn = true );
- virtual Variable<unsigned int>* InquireVariableUInt( const std::string name, const bool readIn = true );
- virtual Variable<long int>* InquireVariableLInt( const std::string name, const bool readIn = true );
- virtual Variable<unsigned long int>* InquireVariableULInt( const std::string name, const bool readIn = true );
- virtual Variable<long long int>* InquireVariableLLInt( const std::string name, const bool readIn = true );
- virtual Variable<unsigned long long int>* InquireVariableULLInt( const std::string name, const bool readIn = true );
- virtual Variable<float>* InquireVariableFloat( const std::string name, const bool readIn = true );
- virtual Variable<double>* InquireVariableDouble( const std::string name, const bool readIn = true );
- virtual Variable<long double>* InquireVariableLDouble( const std::string name, const bool readIn = true );
- virtual Variable<std::complex<float>>* InquireVariableCFloat( const std::string name, const bool readIn = true );
- virtual Variable<std::complex<double>>* InquireVariableCDouble( const std::string name, const bool readIn = true );
- virtual Variable<std::complex<long double>>* InquireVariableCLDouble( const std::string name, const bool readIn = true );
- virtual VariableCompound* InquireVariableCompound( const std::string name, const bool readIn = true );
+ template< class T >
+ void Read( Variable<T>& variable, const T& values)
+ {
+ Read( variable, &values );
+ }
- virtual void Close( const int transportIndex = -1 ) = 0; ///< Closes a particular transport, or all if -1
+ /**
+ * Single value version using string as variable handlers
+ * @param variableName
+ * @param values
+ */
+ template< class T >
+ void Read( const std::string variableName, const T& values )
+ {
+ Read( variableName, &values );
+ }
+ /**
+ * Unallocated version, ADIOS will allocate space for incoming data
+ * @param variable
+ */
+ template< class T >
+ void Read( Variable<T>& variable )
+ {
+ Read( variable, nullptr );
+ }
-protected:
+ /**
+ * Unallocated version, ADIOS will allocate space for incoming data
+ * @param variableName
+ */
+ template< class T >
+ void Read( const std::string variableName )
+ {
+ Read( variableName, nullptr );
+ }
- ADIOS& m_ADIOS; ///< reference to ADIOS object that creates this Engine at Open
- std::vector< std::shared_ptr<Transport> > m_Transports; ///< transports managed
- const bool m_DebugMode = false; ///< true: additional checks, false: by-pass checks
- unsigned int m_Cores = 1;
- const std::string m_EndMessage; ///< added to exceptions to improve debugging
- std::set<std::string> m_WrittenVariables; ///< contains the names of the variables that are being written
+ virtual void Read( Variable<double>& variable, const double* values );
- virtual void Init( ); ///< Initialize m_Capsules and m_Transports, called from constructor
- virtual void InitCapsules( ); ///< Initialize transports from Method, called from Init in constructor.
- virtual void InitTransports( ); ///< Initialize transports from Method, called from Init in constructor.
/**
- * Used to verify parameters in m_Method containers
- * @param itParam iterator to a certain parameter
- * @param parameters map of parameters, from m_Method
- * @param parameterName used if exception is thrown to provide debugging information
- * @param hint used if exception is thrown to provide debugging information
+ * Read function that adds static checking on the variable to be passed by values
+ * It then calls its corresponding derived class virtual function
+ * This version uses m_Group to look for the variableName.
+ * @param variable name of variable to the written
+ * @param values pointer passed from the application
*/
- void CheckParameter( const std::map<std::string, std::string>::const_iterator itParam,
- const std::map<std::string, std::string>& parameters,
- const std::string parameterName,
- const std::string hint ) const;
+ template< class T >
+ void ScheduleRead( Variable<T>& variable, const T* values )
+ {
+ ScheduleRead( variable, values );
+ }
- bool TransportNamesUniqueness( ) const; ///< checks if transport names are unique among the same types (file I/O)
+ /**
+ * String version
+ * @param variableName
+ * @param values
+ */
+ template< class T >
+ void ScheduleRead( const std::string variableName, const T* values )
+ {
+ ScheduleRead( variableName, values );
+ }
+ /**
+ * Single value version
+ * @param variable
+ * @param values
+ */
+ template< class T >
+ void ScheduleRead( Variable<T>& variable, const T& values )
+ {
+ ScheduleRead( variable, &values );
+ }
/**
- * Throws an exception in debug mode if transport index is out of range.
- * @param transportIndex must be in the range [ -1 , m_Transports.size()-1 ]
+ * Single value version using string as variable handlers
+ * @param variableName
+ * @param values
+ */
+ template< class T >
+ void ScheduleRead( const std::string variableName, const T& values )
+ {
+ ScheduleRead( variableName, &values );
+ }
+
+ /**
+ * Single value version using string as variable handlers
*/
- void CheckTransportIndex( const int transportIndex );
+ void ScheduleRead();
+
+
+ virtual void ScheduleRead( Variable<double>& variable, const double* values );
+
+ /**
+ * Perform all scheduled reads, either blocking until all reads completed, or return immediately.
+ * @param mode Blocking or non-blocking modes
+ */
+ void PerformReads( PerformReadMode mode );
+
+
+ /**
+ * Reader application indicates that no more data will be read from the current stream before advancing.
+ * This is necessary to allow writers to advance as soon as possible.
+ */
+ virtual void Release( );
+
+ /**
+ * Indicates that a new step is going to be written as new variables come in.
+ */
+ virtual void Advance( float timeout_sec=0.0 );
+
+ /**
+ * Indicates that a new step is going to be written as new variables come in.
+ * @param mode Advance mode, there are different options for writers and readers
+ */
+ virtual void Advance( AdvanceMode mode, float timeout_sec=0.0 );
+
+ /** @brief Advance asynchronously and get a callback when readers release access to the buffered step.
+ *
+ * User variables that were allocated through AllocateVariable()
+ * must not be modified until advance is completed.
+ * @param mode Advance mode, there are different options for writers and readers
+ * @param callback Will be called when advance is completed.
+ */
+ virtual void AdvanceAsync ( AdvanceMode mode, std::function<void( std::shared_ptr<adios::Engine> )> callback );
+
+
+ //Read API
+ /**
+ * Inquires and (optionally) allocates and copies the contents of a variable
+ * If success: it returns a pointer to the internal stored variable object in ADIOS class.
+ * If failure: it returns nullptr
+ * @param name variable name to look for
+ * @param readIn if true: reads the full variable and payload, allocating values in memory, if false: internal payload is nullptr
+ * @return success: it returns a pointer to the internal stored variable object in ADIOS class, failure: nullptr
+ */
+ virtual Variable<void> InquireVariable( const std::string name, const bool readIn = true );
+ virtual Variable<char> InquireVariableChar( const std::string name, const bool readIn = true );
+ virtual Variable<unsigned char> InquireVariableUChar( const std::string name, const bool readIn = true );
+ virtual Variable<short> InquireVariableShort( const std::string name, const bool readIn = true );
+ virtual Variable<unsigned short> InquireVariableUShort( const std::string name, const bool readIn = true );
+ virtual Variable<int> InquireVariableInt( const std::string name, const bool readIn = true );
+ virtual Variable<unsigned int> InquireVariableUInt( const std::string name, const bool readIn = true );
+ virtual Variable<long int> InquireVariableLInt( const std::string name, const bool readIn = true );
+ virtual Variable<unsigned long int> InquireVariableULInt( const std::string name, const bool readIn = true );
+ virtual Variable<long long int> InquireVariableLLInt( const std::string name, const bool readIn = true );
+ virtual Variable<unsigned long long int> InquireVariableULLInt( const std::string name, const bool readIn = true );
+ virtual Variable<float> InquireVariableFloat( const std::string name, const bool readIn = true );
+ virtual Variable<double> InquireVariableDouble( const std::string name, const bool readIn = true );
+ virtual Variable<long double> InquireVariableLDouble( const std::string name, const bool readIn = true );
+ virtual Variable<std::complex<float>> InquireVariableCFloat( const std::string name, const bool readIn = true );
+ virtual Variable<std::complex<double>> InquireVariableCDouble( const std::string name, const bool readIn = true );
+ virtual Variable<std::complex<long double>> InquireVariableCLDouble( const std::string name, const bool readIn = true );
+ virtual VariableCompound InquireVariableCompound( const std::string name, const bool readIn = true );
+
+
+ /** Return the names of all variables present in a stream/file opened for reading
+ *
+ * @return a vector of strings
+ */
+ std::vector<std::string> VariableNames();
+
+ virtual void Close( const int transportIndex = -1 ) = 0; ///< Closes a particular transport, or all if -1
};
diff --git a/include/core/Method.h b/include/core/Method.h
index 84ed0f95e..bf0593cde 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -19,6 +19,13 @@
namespace adios
{
+typedef enum {
+ GLOBAL_READERS = 2, ROUNDROBIN_READERS = 3, FIFO_READERS = 4,
+ OPEN_ALL_STEPS = 5
+} ReadMultiplexPattern;
+
+typedef enum { NOWAITFORSTREAM = 0, WAITFORSTREAM = 1 } StreamOpenMode; // default: wait for stream
+
/**
* Serves as metadata to define an engine
*/
@@ -34,12 +41,33 @@ public:
/**
* Constructor
- * @param type must be an engine type
+ * @param name is a label that can be used in the config file to set up the method at runtime
*/
- Method( const std::string type, const bool debugMode = false );
+ Method( const std::string name, const bool debugMode = false );
~Method( );
+ /** Check if the method was defined by the user in the config file.
+ * @return true if the method was user-defined, false otherwise when method is set with default parameters
+ */
+ bool isUserDefined();
+
+
+ /**
+ * Define the engine type
+ * @param type must be a valid engine type
+ */
+ void SetEngine( const std::string type );
+
+
+ /**
+ * Tell how many cores the engine can use for its operations.
+ * If only 1 core is specified, no extra threads will be created during the ADIOS calls, except
+ * that staging always creates an extra thread for communication.
+ * @param number of cores, minimum 1 is required
+ */
+ void SetAvailableCores( const int nCores );
+
/**
* Sets parameters for the method in "parameter=value" format
* @param args list of parameters with format "parameter1=value1", ..., "parameterN=valueN"
@@ -63,6 +91,9 @@ public:
AddTransportParameters( type, parameters );
}
+ void SetReadMultiplexPattern( const ReadMultiplexPattern pattern ); // How to split stream content among readers
+ void SetStreamOpenMode( const StreamOpenMode mode); // In Read mode, should Open() wait for the first step appear (default)
+
private:
diff --git a/include/core/Variable.h b/include/core/Variable.h
index 95532571c..81f552ac4 100644
--- a/include/core/Variable.h
+++ b/include/core/Variable.h
@@ -58,40 +58,15 @@ public:
m_Transforms.emplace_back( transform, BuildParametersMap( parameters, m_DebugMode ) ); //need to check
}
- void Monitor( std::ostream& logInfo ) const noexcept
- {
- logInfo << "Variable: " << m_Name << "\n";
- logInfo << "Type: " << m_Type << "\n";
- logInfo << "Size: " << TotalSize() << " elements\n";
- logInfo << "Payload: " << PayLoadSize() << " bytes\n";
-
- if( m_AppValues != nullptr )
- {
- logInfo << "Values (first 10 or max_size): \n";
- std::size_t size = TotalSize();
- if( size > 10 )
- size = 10;
-
- if( m_Type.find("complex") != m_Type.npos ) //it's complex
- {
- for( unsigned int i = 0; i < size; ++i )
- {
- logInfo << "( " << std::real( m_AppValues[i] ) << " , " << std::imag( m_AppValues[i] ) << " ) ";
- }
- }
- else
- {
- for( unsigned int i = 0; i < size; ++i )
- {
- logInfo << m_AppValues[i] << " ";
- }
- }
-
- logInfo << " ...";
- }
- logInfo << "\n";
- }
-
+ /** Return the global dimensions of the variable
+ * @return vector of std::size_t values
+ */
+ std::vector<std::size_t> GetGlobalDimensions();
+
+ /** Return the number of steps available for the variable
+ * @return Number of steps
+ */
+ int GetSteps();
};
--
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