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SerialIOTest.cpp
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// expose private and protected members for invasive testing
#if openPMD_USE_INVASIVE_TESTS
# define OPENPMD_private public
# define OPENPMD_protected public
#endif
#include "openPMD/auxiliary/Environment.hpp"
#include "openPMD/auxiliary/Filesystem.hpp"
#include "openPMD/auxiliary/StringManip.hpp"
#include "openPMD/openPMD.hpp"
#if openPMD_HAVE_ADIOS2
#include <adios2.h>
#endif
#include <catch2/catch.hpp>
#include <algorithm>
#include <array>
#include <cmath>
#include <complex>
#include <fstream>
#include <iostream>
#include <limits>
#include <list>
#include <memory>
#include <numeric>
#include <sstream>
#include <string>
#include <tuple>
#include <vector>
using namespace openPMD;
std::vector< std::string > testedFileExtensions()
{
auto allExtensions = getFileExtensions();
auto newEnd = std::remove_if(
allExtensions.begin(),
allExtensions.end(),
[]( std::string const & ext )
{ return ext == "sst" || ext == "ssc"; } );
return { allExtensions.begin(), newEnd };
}
#if openPMD_HAVE_ADIOS2
TEST_CASE( "adios2_char_portability", "[serial][adios2]" )
{
/*
* This tests portability of char attributes in ADIOS2 in schema 20210209.
*/
if( auxiliary::getEnvString("OPENPMD_NEW_ATTRIBUTE_LAYOUT", "NOT_SET") == "NOT_SET")
{
/*
* @todo As soon as we have added automatic detection for the new
* layout, this environment variable should be ignore read-side.
* Then we can delete this if condition again.
*/
return;
}
// @todo remove new_attribute_layout key as soon as schema-based versioning
// is merged
std::string const config = R"END(
{
"adios2":
{
"new_attribute_layout": true,
"schema": 20210209
}
})END";
{
adios2::ADIOS adios;
auto IO = adios.DeclareIO( "IO" );
auto engine = IO.Open(
"../samples/adios2_char_portability.bp", adios2::Mode::Write );
engine.BeginStep();
// write default openPMD attributes
auto writeAttribute =
[ &engine, &IO ]( std::string const & name, auto value )
{
using variable_type = decltype( value );
engine.Put( IO.DefineVariable< variable_type >( name ), value );
};
writeAttribute( "/basePath", std::string( "/data/%T/" ) );
writeAttribute( "/date", std::string( "2021-02-22 11:14:00 +0000" ) );
writeAttribute( "/iterationEncoding", std::string( "groupBased" ) );
writeAttribute( "/iterationFormat", std::string( "/data/%T/" ) );
writeAttribute( "/openPMD", std::string( "1.1.0" ) );
writeAttribute( "/openPMDextension", uint32_t( 0 ) );
writeAttribute( "/software", std::string( "openPMD-api" ) );
writeAttribute( "/softwareVersion", std::string( "0.14.0-dev" ) );
IO.DefineAttribute< uint64_t >(
"__openPMD_internal/openPMD2_adios2_schema", 20210209 );
IO.DefineAttribute< unsigned char >( "__openPMD_internal/useSteps", 1 );
// write char things that should be read back properly
std::string baseString = "abcdefghi";
// null termination not necessary, ADIOS knows the size of its variables
std::vector< signed char > signedVector( 9 );
std::vector< unsigned char > unsignedVector( 9 );
for( unsigned i = 0; i < 9; ++i )
{
signedVector[ i ] = baseString[ i ];
unsignedVector[ i ] = baseString[ i ];
}
engine.Put(
IO.DefineVariable< signed char >(
"/signedVector", { 3, 3 }, { 0, 0 }, { 3, 3 } ),
signedVector.data() );
engine.Put(
IO.DefineVariable< unsigned char >(
"/unsignedVector", { 3, 3 }, { 0, 0 }, { 3, 3 } ),
unsignedVector.data() );
engine.Put(
IO.DefineVariable< char >(
"/unspecifiedVector", { 3, 3 }, { 0, 0 }, { 3, 3 } ),
baseString.c_str() );
writeAttribute( "/signedChar", ( signed char )'a' );
writeAttribute( "/unsignedChar", ( unsigned char )'a' );
writeAttribute( "/char", ( char )'a' );
engine.EndStep();
engine.Close();
}
{
if( auxiliary::getEnvString( "OPENPMD_BP_BACKEND", "ADIOS2" ) !=
"ADIOS2" )
{
return;
}
Series read(
"../samples/adios2_char_portability.bp",
Access::READ_ONLY,
config );
auto signedVectorAttribute = read.getAttribute( "signedVector" );
REQUIRE( signedVectorAttribute.dtype == Datatype::VEC_STRING );
auto unsignedVectorAttribute = read.getAttribute( "unsignedVector" );
REQUIRE( unsignedVectorAttribute.dtype == Datatype::VEC_STRING );
auto unspecifiedVectorAttribute =
read.getAttribute( "unspecifiedVector" );
REQUIRE( unspecifiedVectorAttribute.dtype == Datatype::VEC_STRING );
std::vector< std::string > desiredVector{ "abc", "def", "ghi" };
REQUIRE(
signedVectorAttribute.get< std::vector< std::string > >() ==
desiredVector );
REQUIRE(
unsignedVectorAttribute.get< std::vector< std::string > >() ==
desiredVector );
REQUIRE(
unspecifiedVectorAttribute.get< std::vector< std::string > >() ==
desiredVector );
auto signedCharAttribute = read.getAttribute( "signedChar" );
// we don't have that datatype yet
// REQUIRE(unsignedCharAttribute.dtype == Datatype::SCHAR);
auto unsignedCharAttribute = read.getAttribute( "unsignedChar" );
REQUIRE( unsignedCharAttribute.dtype == Datatype::UCHAR );
auto charAttribute = read.getAttribute( "char" );
// might currently report Datatype::UCHAR on some platforms
// REQUIRE(unsignedCharAttribute.dtype == Datatype::CHAR);
REQUIRE( signedCharAttribute.get< char >() == char( 'a' ) );
REQUIRE( unsignedCharAttribute.get< char >() == char( 'a' ) );
REQUIRE( charAttribute.get< char >() == char( 'a' ) );
}
}
#endif
void
write_and_read_many_iterations( std::string const & ext ) {
constexpr unsigned int nIterations = 1000;
std::string filename = "../samples/many_iterations/many_iterations_%T." + ext;
std::vector<float> data(10);
std::iota(data.begin(), data.end(), 0.);
Dataset ds{Datatype::FLOAT, {10}};
{
Series write(filename, Access::CREATE);
for (unsigned int i = 0; i < nIterations; ++i) {
// std::cout << "Putting iteration " << i << std::endl;
Iteration it = write.iterations[i];
auto E_x = it.meshes["E"]["x"];
E_x.resetDataset(ds);
E_x.storeChunk(data, {0}, {10});
it.close();
}
// ~Series intentionally not yet called
Series read( filename, Access::READ_ONLY, "{\"defer_iteration_parsing\": true}" );
for( auto iteration : read.iterations )
{
iteration.second.open();
// std::cout << "Reading iteration " << iteration.first <<
// std::endl;
auto E_x = iteration.second.meshes["E"]["x"];
auto chunk = E_x.loadChunk<float>({0}, {10});
iteration.second.close();
auto array = chunk.get();
for (size_t i = 0; i < 10; ++i) {
REQUIRE(array[i] == float(i));
}
}
}
Series list( filename, Access::READ_ONLY );
helper::listSeries( list );
}
TEST_CASE( "write_and_read_many_iterations", "[serial]" )
{
if( auxiliary::directory_exists( "../samples/many_iterations" ) )
auxiliary::remove_directory( "../samples/many_iterations" );
for( auto const & t : testedFileExtensions() )
{
write_and_read_many_iterations( t );
}
}
TEST_CASE( "multi_series_test", "[serial]" )
{
std::list< Series > allSeries;
auto myfileExtensions = testedFileExtensions();
// this test demonstrates an ADIOS1 (upstream) bug, comment this section to trigger it
auto const rmEnd = std::remove_if( myfileExtensions.begin(), myfileExtensions.end(), [](std::string const & beit) {
return beit == "bp" &&
determineFormat("test.bp") == Format::ADIOS1;
});
myfileExtensions.erase(rmEnd, myfileExtensions.end());
// have multiple serial series alive at the same time
for (auto const sn : {1, 2, 3}) {
for (auto const & t: myfileExtensions)
{
auto const file_ending = t;
std::cout << file_ending << std::endl;
allSeries.emplace_back(
std::string("../samples/multi_open_test_").
append(std::to_string(sn)).append(".").append(file_ending),
Access::CREATE
);
allSeries.back().iterations[sn].setAttribute("wululu", sn);
allSeries.back().flush();
}
}
// skip some series: sn=1
auto it = allSeries.begin();
std::for_each( myfileExtensions.begin(), myfileExtensions.end(), [&it](std::string const &){
it++;
});
// remove some series: sn=2
std::for_each( myfileExtensions.begin(), myfileExtensions.end(), [&it, &allSeries](std::string const &){
it = allSeries.erase(it);
});
// write from last series: sn=3
std::for_each( myfileExtensions.begin(), myfileExtensions.end(), [&it](std::string const &){
it->iterations[10].setAttribute("wululu", 10);
it->flush();
it++;
});
// remove all leftover series
allSeries.clear();
}
TEST_CASE( "available_chunks_test_json", "[serial][json]" )
{
/*
* This test is JSON specific
* Our JSON backend does not store chunks explicitly,
* so the JSON backend will simply go through the multidimensional array
* and gather the data items into chunks
* Example dataset:
*
* 0123
* 0 ____
* 1 ____
* 2 ****
* 3 ****
* 4 ****
* 5 ****
* 6 ****
* 7 **__
* 8 **_*
* 9 ___*
*
* Will be read as three chunks:
* 1. (2,0) -- (5,4) (offset -- extent)
* 2. (7,0) -- (2,2) (offset -- extent)
* 3. (8,3) -- (2,1) (offset -- extent)
*
* Since the chunks are reconstructed, they won't necessarily
* correspond with the way that the chunks were written.
* As an example, let's write the first chunk in the above depiction
* line by line.
*/
constexpr unsigned height = 10;
std::string name = "../samples/available_chunks.json";
std::vector< int > data{ 2, 4, 6, 8 };
{
Series write( name, Access::CREATE );
Iteration it0 = write.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { height, 4 } } );
for( unsigned line = 2; line < 7; ++line )
{
E_x.storeChunk( data, { line, 0 }, { 1, 4 } );
}
for( unsigned line = 7; line < 9; ++line )
{
E_x.storeChunk( data, { line, 0 }, { 1, 2 } );
}
E_x.storeChunk( data, { 8, 3 }, { 2, 1 } );
auto E_y = it0.meshes[ "E" ][ "y" ];
E_y.resetDataset( { Datatype::INT, { height, 4 } } );
E_y.makeConstant( 1234 );
it0.close();
}
{
Series read( name, Access::READ_ONLY );
Iteration it0 = read.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
ChunkTable table = E_x.availableChunks();
REQUIRE( table.size() == 3 );
/*
* Explicitly convert things to bool, so Catch doesn't get the splendid
* idea to print the Chunk struct.
*/
REQUIRE( bool( table[ 0 ] == WrittenChunkInfo( { 2, 0 }, { 5, 4 } ) ) );
REQUIRE( bool( table[ 1 ] == WrittenChunkInfo( { 7, 0 }, { 2, 2 } ) ) );
REQUIRE( bool( table[ 2 ] == WrittenChunkInfo( { 8, 3 }, { 2, 1 } ) ) );
auto E_y = it0.meshes[ "E" ][ "y" ];
table = E_y.availableChunks();
REQUIRE( table.size() == 1 );
REQUIRE(
bool( table[ 0 ] == WrittenChunkInfo( { 0, 0 }, { height, 4 } ) ) );
}
}
TEST_CASE( "multiple_series_handles_test", "[serial]" )
{
/*
* First test: No premature flushes through destructor when another copy
* is still around
*/
{
std::unique_ptr< openPMD::Series > series_ptr;
{
openPMD::Series series(
"sample%T.json", openPMD::AccessType::CREATE );
series_ptr = std::make_unique< openPMD::Series >( series );
/*
* we have two handles for the same Series instance now:
* series and series_ptr
* series goes out of scope before series_ptr
* destructor should only do a flush after both of them go out of
* scope, but it will currently run directly after this comment
* since no iteration has been written yet, an error will be thrown
*/
}
series_ptr->iterations[ 0 ].meshes[ "E" ][ "x" ].makeEmpty< int >( 1 );
}
/*
* Second test: A Series handle should remain accessible even if the
* original handle is destroyed
*/
{
std::unique_ptr< openPMD::Series > series_ptr;
{
openPMD::Series series(
"sample%T.json", openPMD::AccessType::CREATE );
series_ptr = std::make_unique< openPMD::Series >( series );
series_ptr->iterations[ 0 ].meshes[ "E" ][ "x" ].makeEmpty< int >(
1 );
}
/*
* series_ptr is still in scope, but the original Series instance
* has been destroyed
* since internal pointers actually refer to the original *handle*,
* doing anything with series_ptr now (such as flushing it) yields
* nullpointer accesses
*/
series_ptr->flush();
}
}
void
close_iteration_test( std::string file_ending )
{
std::string name = "../samples/close_iterations_%T." + file_ending;
std::vector<int> data{2, 4, 6, 8};
// { // we do *not* need these parentheses
Series write(name, Access::CREATE);
bool isAdios1 = write.backend() == "ADIOS1";
{
Iteration it0 = write.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { 2, 2 } } );
E_x.storeChunk( data, { 0, 0 }, { 2, 2 } );
it0.close( /* flush = */ false );
}
write.flush();
// }
if (isAdios1)
{
// run a simplified test for Adios1 since Adios1 has issues opening
// twice in the same process
REQUIRE( auxiliary::file_exists( "../samples/close_iterations_0.bp" ) );
}
else
{
Series read( name, Access::READ_ONLY );
Iteration it0 = read.iterations[ 0 ];
auto E_x_read = it0.meshes[ "E" ][ "x" ];
auto chunk = E_x_read.loadChunk< int >( { 0, 0 }, { 2, 2 } );
it0.close( /* flush = */ false );
read.flush();
for( size_t i = 0; i < data.size(); ++i )
{
REQUIRE( data[ i ] == chunk.get()[ i ] );
}
}
{
Iteration it1 = write.iterations[1];
auto E_x = it1.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { 2, 2 } } );
E_x.storeChunk( data, { 0, 0 }, { 2, 2 } );
it1.close( /* flush = */ true );
// illegally access iteration after closing
E_x.storeChunk( data, { 0, 0 }, { 2, 2 } );
REQUIRE_THROWS( write.flush() );
}
if (isAdios1)
{
// run a simplified test for Adios1 since Adios1 has issues opening
// twice in the same process
REQUIRE( auxiliary::file_exists( "../samples/close_iterations_1.bp" ) );
}
else
{
Series read( name, Access::READ_ONLY );
Iteration it1 = read.iterations[ 1 ];
auto E_x_read = it1.meshes[ "E" ][ "x" ];
auto chunk = E_x_read.loadChunk< int >( { 0, 0 }, { 2, 2 } );
it1.close( /* flush = */ true );
for( size_t i = 0; i < data.size(); ++i )
{
REQUIRE( data[ i ] == chunk.get()[ i ] );
}
auto read_again = E_x_read.loadChunk< int >( { 0, 0 }, { 2, 2 } );
REQUIRE_THROWS( read.flush() );
}
{
Series list{ name, Access::READ_ONLY };
helper::listSeries( list );
}
}
TEST_CASE( "close_iteration_test", "[serial]" )
{
for( auto const & t : testedFileExtensions() )
{
close_iteration_test( t );
}
}
void
close_and_copy_attributable_test( std::string file_ending )
{
using position_t = double;
// open file for writing
Series series( "electrons." + file_ending, Access::CREATE );
Datatype datatype = determineDatatype< position_t >();
constexpr unsigned long length = 10ul;
Extent global_extent = { length };
Dataset dataset = Dataset( datatype, global_extent );
std::shared_ptr< position_t > local_data(
new position_t[ length ],
[]( position_t const * ptr ) { delete[] ptr; } );
std::unique_ptr< Iteration > iteration_ptr;
for( size_t i = 0; i < 100; ++i )
{
if( iteration_ptr )
{
*iteration_ptr = series.iterations[ i ];
}
else
{
// use copy constructor
iteration_ptr =
std::make_unique< Iteration >( series.iterations[ i ] );
}
Record electronPositions =
iteration_ptr->particles[ "e" ][ "position" ];
// TODO set this automatically to zero if not provided
Record electronPositionsOffset =
iteration_ptr->particles[ "e" ][ "positionOffset" ];
std::iota( local_data.get(), local_data.get() + length, i * length );
for( auto const & dim : { "x", "y", "z" } )
{
RecordComponent pos = electronPositions[ dim ];
pos.resetDataset( dataset );
pos.storeChunk( local_data, Offset{ 0 }, global_extent );
RecordComponent posOff = electronPositionsOffset[ dim ];
posOff.resetDataset( dataset );
posOff.makeConstant( position_t( 0.0 ) );
}
iteration_ptr->close();
// force re-flush of previous iterations
series.flush();
}
}
TEST_CASE( "close_and_copy_attributable_test", "[serial]" )
{
// demonstrator for https://github.com/openPMD/openPMD-api/issues/765
for( auto const & t : testedFileExtensions() )
{
close_and_copy_attributable_test( t );
}
}
#if openPMD_HAVE_ADIOS2
TEST_CASE( "close_iteration_throws_test", "[serial]" )
{
/*
* Iterations should not be accessed any more after closing.
* Test that the openPMD API detects that case and throws.
*/
{
Series series(
"../samples/close_iteration_throws_1.bp", Access::CREATE );
auto it0 = series.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { 5 } } );
std::vector< int > data{ 0, 1, 2, 3, 4 };
E_x.storeChunk( data, { 0 }, { 5 } );
it0.close();
auto B_y = it0.meshes[ "B" ][ "y" ];
B_y.resetDataset( { Datatype::INT, { 5 } } );
B_y.storeChunk( data, { 0 }, { 5 } );
REQUIRE_THROWS( series.flush() );
}
{
Series series(
"../samples/close_iteration_throws_2.bp", Access::CREATE );
auto it0 = series.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { 5 } } );
std::vector< int > data{ 0, 1, 2, 3, 4 };
E_x.storeChunk( data, { 0 }, { 5 } );
it0.close();
auto e_position_x = it0.particles[ "e" ][ "position" ][ "x" ];
e_position_x.resetDataset( { Datatype::INT, { 5 } } );
e_position_x.storeChunk( data, { 0 }, { 5 } );
REQUIRE_THROWS( series.flush() );
}
{
Series series(
"../samples/close_iteration_throws_3.bp", Access::CREATE );
auto it0 = series.iterations[ 0 ];
auto E_x = it0.meshes[ "E" ][ "x" ];
E_x.resetDataset( { Datatype::INT, { 5 } } );
std::vector< int > data{ 0, 1, 2, 3, 4 };
E_x.storeChunk( data, { 0 }, { 5 } );
it0.close();
it0.setTimeUnitSI( 2.0 );
REQUIRE_THROWS( series.flush() );
}
}
#endif
inline void
empty_dataset_test( std::string file_ending )
{
{
Series series(
"../samples/empty_datasets." + file_ending, Access::CREATE );
auto makeEmpty_dim_7_int =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_int" ];
auto makeEmpty_dim_7_long =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_bool" ];
auto makeEmpty_dim_7_int_alt =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_int_alt" ];
auto makeEmpty_dim_7_long_alt =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_bool_alt" ];
auto makeEmpty_resetDataset_dim3 =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_resetDataset_dim3" ];
auto makeEmpty_resetDataset_dim3_notallzero =
series.iterations[ 1 ]
.meshes[ "rho" ][ "makeEmpty_resetDataset_dim3_notallzero" ];
makeEmpty_dim_7_int.makeEmpty< int >( 7 );
makeEmpty_dim_7_long.makeEmpty< long >( 7 );
makeEmpty_dim_7_int_alt.makeEmpty( Datatype::INT, 7 );
makeEmpty_dim_7_long_alt.makeEmpty( Datatype::LONG, 7 );
makeEmpty_resetDataset_dim3.resetDataset(
Dataset( Datatype::LONG, Extent( 3, 0 ) ) );
makeEmpty_resetDataset_dim3_notallzero.resetDataset(
Dataset( Datatype::LONG_DOUBLE, Extent{ 1, 2, 0 } ) );
series.flush();
}
{
Series series(
"../samples/empty_datasets." + file_ending, Access::READ_ONLY );
REQUIRE(series.iterations.contains(1));
REQUIRE(series.iterations.count(1) == 1);
REQUIRE(series.iterations.count(123456) == 0);
REQUIRE(series.iterations[1].meshes.contains("rho"));
REQUIRE(series.iterations[1].meshes["rho"].contains("makeEmpty_dim_7_int"));
auto makeEmpty_dim_7_int =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_int" ];
auto makeEmpty_dim_7_long =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_bool" ];
auto makeEmpty_dim_7_int_alt =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_int_alt" ];
auto makeEmpty_dim_7_long_alt =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_dim_7_bool_alt" ];
auto makeEmpty_resetDataset_dim3 =
series.iterations[ 1 ].meshes[ "rho" ][ "makeEmpty_resetDataset_dim3" ];
auto makeEmpty_resetDataset_dim3_notallzero =
series.iterations[ 1 ]
.meshes[ "rho" ][ "makeEmpty_resetDataset_dim3_notallzero" ];
REQUIRE(makeEmpty_dim_7_int.getDimensionality() == 7);
REQUIRE(makeEmpty_dim_7_int.getExtent() == Extent(7, 0));
REQUIRE(isSame(makeEmpty_dim_7_int.getDatatype(), determineDatatype< int >()));
REQUIRE(makeEmpty_dim_7_long.getDimensionality() == 7);
REQUIRE(makeEmpty_dim_7_long.getExtent() == Extent(7, 0));
REQUIRE(isSame(makeEmpty_dim_7_long.getDatatype(), determineDatatype< long >()));
REQUIRE(makeEmpty_dim_7_int_alt.getDimensionality() == 7);
REQUIRE(makeEmpty_dim_7_int_alt.getExtent() == Extent(7, 0));
REQUIRE(isSame(makeEmpty_dim_7_int_alt.getDatatype(), determineDatatype< int >()));
REQUIRE(makeEmpty_dim_7_long_alt.getDimensionality() == 7);
REQUIRE(makeEmpty_dim_7_long_alt.getExtent() == Extent(7, 0));
REQUIRE(isSame(makeEmpty_dim_7_long_alt.getDatatype(), determineDatatype< long >()));
REQUIRE(makeEmpty_resetDataset_dim3.getDimensionality() == 3);
REQUIRE(makeEmpty_resetDataset_dim3.getExtent() == Extent(3, 0));
REQUIRE(isSame(makeEmpty_resetDataset_dim3.getDatatype(), Datatype::LONG));
REQUIRE(makeEmpty_resetDataset_dim3_notallzero.getDimensionality() == 3);
REQUIRE(makeEmpty_resetDataset_dim3_notallzero.getExtent() == Extent{1,2,0});
REQUIRE(isSame(makeEmpty_resetDataset_dim3_notallzero.getDatatype(), Datatype::LONG_DOUBLE));
}
{
Series list{ "../samples/empty_datasets." + file_ending, Access::READ_ONLY };
helper::listSeries( list );
}
}
TEST_CASE( "empty_dataset_test", "[serial]" )
{
for (auto const & t: testedFileExtensions())
{
empty_dataset_test( t );
}
}
inline
void constant_scalar(std::string file_ending)
{
Mesh::Geometry const geometry = Mesh::Geometry::spherical;
std::string const geometryParameters = "dummyGeometryParameters";
Mesh::DataOrder const dataOrder = Mesh::DataOrder::F;
std::vector< double > const gridSpacing { 1.0, 2.0, 3.0 };
std::vector< double > const gridGlobalOffset{ 11.0, 22.0, 33.0 };
double const gridUnitSI = 3.14;
std::vector< std::string > const axisLabels { "x", "y", "z" };
std::map< UnitDimension, double > const unitDimensions{
{UnitDimension::I, 1.0},
{UnitDimension::J, 2.0}
};
double const timeOffset = 1234.0;
{
// constant scalar
Series s = Series("../samples/constant_scalar." + file_ending, Access::CREATE);
auto rho = s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR];
REQUIRE(s.iterations[1].meshes["rho"].scalar());
rho.resetDataset(Dataset(Datatype::CHAR, {1, 2, 3}));
rho.makeConstant(static_cast< char >('a'));
REQUIRE(rho.constant());
// mixed constant/non-constant
auto E_x = s.iterations[1].meshes["E"]["x"];
E_x.resetDataset(Dataset(Datatype::FLOAT, {1, 2, 3}));
E_x.makeConstant(static_cast< float >(13.37));
auto E_y = s.iterations[1].meshes["E"]["y"];
E_y.resetDataset(Dataset(Datatype::UINT, {1, 2, 3}));
std::shared_ptr< unsigned int > E(new unsigned int[6], [](unsigned int const *p){ delete[] p; });
unsigned int e{0};
std::generate(E.get(), E.get() + 6, [&e]{ return e++; });
E_y.storeChunk(E, {0, 0, 0}, {1, 2, 3});
// store a number of predefined attributes in E
Mesh & E_mesh = s.iterations[1].meshes["E"];
E_mesh.setGeometry( geometry );
E_mesh.setGeometryParameters( geometryParameters );
E_mesh.setDataOrder( dataOrder );
E_mesh.setGridSpacing( gridSpacing );
E_mesh.setGridGlobalOffset( gridGlobalOffset );
E_mesh.setGridUnitSI( gridUnitSI );
E_mesh.setAxisLabels( axisLabels );
E_mesh.setUnitDimension(unitDimensions);
E_mesh.setTimeOffset( timeOffset );
// constant scalar
auto pos = s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR];
pos.resetDataset(Dataset(Datatype::DOUBLE, {3, 2, 1}));
pos.makeConstant(static_cast< double >(42.));
auto posOff = s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR];
posOff.resetDataset(Dataset(Datatype::INT, {3, 2, 1}));
posOff.makeConstant(static_cast< int >(-42));
// mixed constant/non-constant
auto vel_x = s.iterations[1].particles["e"]["velocity"]["x"];
vel_x.resetDataset(Dataset(Datatype::SHORT, {3, 2, 1}));
vel_x.makeConstant(static_cast< short >(-1));
auto vel_y = s.iterations[1].particles["e"]["velocity"]["y"];
vel_y.resetDataset(Dataset(Datatype::ULONGLONG, {3, 2, 1}));
std::shared_ptr< unsigned long long > vel(new unsigned long long[6], [](unsigned long long const *p){ delete[] p; });
unsigned long long v{0};
std::generate(vel.get(), vel.get() + 6, [&v]{ return v++; });
vel_y.storeChunk(vel, {0, 0, 0}, {3, 2, 1});
}
{
Series s = Series("../samples/constant_scalar." + file_ending, Access::READ_ONLY);
REQUIRE(s.iterations[1].meshes.count("rho") == 1);
REQUIRE(s.iterations[1].meshes["rho"].count(MeshRecordComponent::SCALAR) == 1);
REQUIRE(s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR].containsAttribute("shape"));
REQUIRE(s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR].getAttribute("shape").get< std::vector< uint64_t > >() == Extent{1, 2, 3});
REQUIRE(s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR].containsAttribute("value"));
REQUIRE(s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR].getAttribute("value").get< char >() == 'a');
REQUIRE(s.iterations[1].meshes["rho"].scalar());
REQUIRE(s.iterations[1].meshes["rho"][MeshRecordComponent::SCALAR].constant());
REQUIRE(s.iterations[1].meshes.count("E") == 1);
REQUIRE(!s.iterations[1].meshes["E"].scalar());
REQUIRE(s.iterations[1].meshes["E"].count("x") == 1);
REQUIRE(s.iterations[1].meshes["E"]["x"].constant());
REQUIRE(s.iterations[1].meshes["E"]["x"].containsAttribute("shape"));
REQUIRE(s.iterations[1].meshes["E"]["x"].getAttribute("shape").get< std::vector< uint64_t > >() == Extent{1, 2, 3});
REQUIRE(s.iterations[1].meshes["E"]["x"].containsAttribute("value"));
REQUIRE(s.iterations[1].meshes["E"]["x"].getAttribute("value").get< float >() == static_cast< float >(13.37));
REQUIRE(!s.iterations[1].meshes["E"]["y"].constant());
REQUIRE(s.iterations[1].meshes["E"]["y"].getExtent() == Extent{1, 2, 3});
REQUIRE(s.iterations[1].meshes["E"].count("y") == 1);
REQUIRE(!s.iterations[1].meshes["E"]["y"].containsAttribute("shape"));
REQUIRE(!s.iterations[1].meshes["E"]["y"].containsAttribute("value"));
REQUIRE(s.iterations[1].meshes["E"]["y"].getExtent() == Extent{1, 2, 3});
REQUIRE(s.iterations[1].particles.count("e") == 1);
REQUIRE(s.iterations[1].particles["e"].count("position") == 1);
REQUIRE(s.iterations[1].particles["e"]["position"].count(RecordComponent::SCALAR) == 1);
REQUIRE(s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR].containsAttribute("shape"));
REQUIRE(s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR].getAttribute("shape").get< std::vector< uint64_t > >() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR].containsAttribute("value"));
REQUIRE(s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR].getAttribute("value").get< double >() == 42.);
REQUIRE(s.iterations[1].particles["e"]["position"][RecordComponent::SCALAR].getExtent() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"].count("positionOffset") == 1);
REQUIRE(s.iterations[1].particles["e"]["positionOffset"].count(RecordComponent::SCALAR) == 1);
REQUIRE(s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR].containsAttribute("shape"));
REQUIRE(s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR].getAttribute("shape").get< std::vector< uint64_t > >() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR].containsAttribute("value"));
REQUIRE(s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR].getAttribute("value").get< int >() == -42);
REQUIRE(s.iterations[1].particles["e"]["positionOffset"][RecordComponent::SCALAR].getExtent() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"].count("velocity") == 1);
REQUIRE(s.iterations[1].particles["e"]["velocity"].count("x") == 1);
REQUIRE(s.iterations[1].particles["e"]["velocity"]["x"].containsAttribute("shape"));
REQUIRE(s.iterations[1].particles["e"]["velocity"]["x"].getAttribute("shape").get< std::vector< uint64_t > >() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"]["velocity"]["x"].containsAttribute("value"));
REQUIRE(s.iterations[1].particles["e"]["velocity"]["x"].getAttribute("value").get< short >() == -1);
REQUIRE(s.iterations[1].particles["e"]["velocity"]["x"].getExtent() == Extent{3, 2, 1});
REQUIRE(s.iterations[1].particles["e"]["velocity"].count("y") == 1);
REQUIRE(!s.iterations[1].particles["e"]["velocity"]["y"].containsAttribute("shape"));
REQUIRE(!s.iterations[1].particles["e"]["velocity"]["y"].containsAttribute("value"));
REQUIRE(s.iterations[1].particles["e"]["velocity"]["y"].getExtent() == Extent{3, 2, 1});
Mesh & E_mesh = s.iterations[1].meshes["E"];
REQUIRE( E_mesh.geometry() == geometry );
REQUIRE( E_mesh.geometryParameters() == geometryParameters );
REQUIRE( E_mesh.dataOrder() == dataOrder );
REQUIRE( E_mesh.gridSpacing< double >() == gridSpacing );
REQUIRE( E_mesh.gridGlobalOffset() == gridGlobalOffset );
REQUIRE( E_mesh.gridUnitSI() == gridUnitSI );
REQUIRE( E_mesh.axisLabels() == axisLabels );
// REQUIRE( E_mesh.unitDimension() == unitDimensions );
REQUIRE( E_mesh.timeOffset< double >() == timeOffset );
auto E_x_value = s.iterations[1].meshes["E"]["x"].loadChunk< float >();
s.flush();
for( int idx = 0; idx < 1*2*3; ++idx )
REQUIRE( E_x_value.get()[idx] == static_cast< float >(13.37) );
}
{
Series list{ "../samples/constant_scalar." + file_ending, Access::READ_ONLY };
helper::listSeries( list );
}
}
TEST_CASE( "constant_scalar", "[serial]" )
{
for (auto const & t: testedFileExtensions())
{
constant_scalar( t );
}
}
TEST_CASE( "flush_without_position_positionOffset", "[serial]" )
{
for( auto const & t : testedFileExtensions() )
{
const std::string & file_ending = t;
Series s = Series(
"../samples/flush_without_position_positionOffset." + file_ending,
Access::CREATE );
ParticleSpecies e = s.iterations[ 0 ].particles[ "e" ];
RecordComponent weighting = e[ "weighting" ][ RecordComponent::SCALAR ];
weighting.resetDataset( Dataset( Datatype::FLOAT, Extent{ 2, 2 } ) );
weighting.storeChunk( std::shared_ptr< float >(
new float[ 4 ](),
[]( float const * ptr ) { delete[] ptr; } ),
{ 0, 0 },
{ 2, 2 } );
s.flush();
for( auto const & key : { "position", "positionOffset" } )
{
for( auto const & dim : { "x", "y", "z" } )
{
RecordComponent rc = e[ key ][ dim ];
rc.resetDataset( Dataset( Datatype::FLOAT , Extent{ 2, 2 } ) );
rc.storeChunk( std::shared_ptr< float >(
new float[ 4 ](),
[]( float const * ptr ) { delete[] ptr; } ),
{ 0, 0 },
{ 2, 2 } );
}
}
}
}
inline
void particle_patches( std::string file_ending )
{
constexpr auto SCALAR = openPMD::RecordComponent::SCALAR;
uint64_t const extent = 123u;
uint64_t const num_patches = 2u;
{
// constant scalar
Series s = Series("../samples/particle_patches%T." + file_ending, Access::CREATE);
auto e = s.iterations[42].particles["electrons"];
for( auto r : {"x", "y"} )
{
auto x = e["position"][r];
x.resetDataset(Dataset(determineDatatype<float>(), {extent}));
std::vector<float> xd( extent );
std::iota(xd.begin(), xd.end(), 0);
x.storeChunk(xd);
auto o = e["positionOffset"][r];
o.resetDataset(Dataset(determineDatatype<uint64_t>(), {extent}));
std::vector<uint64_t> od( extent );
std::iota(od.begin(), od.end(), 0);
o.storeChunk(od);
s.flush();
}
auto const dset_n = Dataset(determineDatatype<uint64_t>(), {num_patches, });
e.particlePatches["numParticles"][SCALAR].resetDataset(dset_n);
e.particlePatches["numParticlesOffset"][SCALAR].resetDataset(dset_n);
auto const dset_f = Dataset(determineDatatype<float>(), {num_patches, });
e.particlePatches["offset"]["x"].resetDataset(dset_f);
e.particlePatches["offset"]["y"].resetDataset(dset_f);
e.particlePatches["extent"]["x"].resetDataset(dset_f);
e.particlePatches["extent"]["y"].resetDataset(dset_f);
// patch 0 (decomposed in x)
e.particlePatches["numParticles"][SCALAR].store(0, uint64_t(10u));
e.particlePatches["numParticlesOffset"][SCALAR].store(0, uint64_t(0u));
e.particlePatches["offset"]["x"].store(0, float(0.));
e.particlePatches["offset"]["y"].store(0, float(0.));
e.particlePatches["extent"]["x"].store(0, float(10.));
e.particlePatches["extent"]["y"].store(0, float(123.));
// patch 1 (decomposed in x)
e.particlePatches["numParticles"][SCALAR].store(1, uint64_t(113u));
e.particlePatches["numParticlesOffset"][SCALAR].store(1, uint64_t(10u));
e.particlePatches["offset"]["x"].store(1, float(10.));
e.particlePatches["offset"]["y"].store(1, float(0.));
e.particlePatches["extent"]["x"].store(1, float(113));
e.particlePatches["extent"]["y"].store(1, float(123.));
}
{
Series s = Series("../samples/particle_patches%T." + file_ending, Access::READ_ONLY);
auto e = s.iterations[42].particles["electrons"];
auto numParticles = e.particlePatches["numParticles"][SCALAR].template load< uint64_t >();
auto numParticlesOffset = e.particlePatches["numParticlesOffset"][SCALAR].template load< uint64_t >();
auto extent_x = e.particlePatches["extent"]["x"].template load< float >();
auto extent_y = e.particlePatches["extent"]["y"].template load< float >();
auto offset_x = e.particlePatches["offset"]["x"].template load< float >();
auto offset_y = e.particlePatches["offset"]["y"].template load< float >();
s.flush();
REQUIRE(numParticles.get()[0] == 10);
REQUIRE(numParticles.get()[1] == 113);
REQUIRE(numParticlesOffset.get()[0] == 0);
REQUIRE(numParticlesOffset.get()[1] == 10);
REQUIRE(extent_x.get()[0] == 10.);
REQUIRE(extent_x.get()[1] == 113.);
REQUIRE(extent_y.get()[0] == 123.);
REQUIRE(extent_y.get()[1] == 123.);
REQUIRE(offset_x.get()[0] == 0.);
REQUIRE(offset_x.get()[1] == 10.);
REQUIRE(offset_y.get()[0] == 0.);
REQUIRE(offset_y.get()[1] == 0.);
}
}
TEST_CASE( "particle_patches", "[serial]" )
{
for (auto const & t: testedFileExtensions())
{
particle_patches( t );
}
}
inline
void dtype_test( const std::string & backend )
{
bool test_long_double = (backend != "json") || sizeof (long double) <= 8;
bool test_long_long = (backend != "json") || sizeof (long long) <= 8;
{
Series s = Series("../samples/dtype_test." + backend, Access::CREATE);
char c = 'c';
s.setAttribute("char", c);
unsigned char uc = 'u';
s.setAttribute("uchar", uc);
int16_t i16 = 16;
s.setAttribute("int16", i16);
int32_t i32 = 32;
s.setAttribute("int32", i32);
int64_t i64 = 64;
s.setAttribute("int64", i64);
uint16_t u16 = 16u;
s.setAttribute("uint16", u16);
uint32_t u32 = 32u;
s.setAttribute("uint32", u32);
uint64_t u64 = 64u;
s.setAttribute("uint64", u64);
float f = 16.e10f;
s.setAttribute("float", f);
double d = 1.e64;
s.setAttribute("double", d);
if (test_long_double)