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Group api revision #2614

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merged 4 commits into from
Feb 10, 2021
Merged

Group api revision #2614

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710ce0b
Group API revision
dmitry-ganyushin Feb 3, 2021
5ec6b0d
Fix for CI to get it running
dmitry-ganyushin Feb 9, 2021
a380f11
Fixed int type
dmitry-ganyushin Feb 9, 2021
295e008
Group API revision
dmitry-ganyushin Feb 9, 2021
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4 changes: 2 additions & 2 deletions bindings/CXX11/adios2/cxx11/IO.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -109,9 +109,9 @@ Engine IO::Open(const std::string &name, const Mode mode)
"for engine " + name + ", in call to IO::Open");
return Engine(&m_IO->Open(name, mode));
}
Group IO::InquireGroup(const std::string &path, char delimiter)
Group IO::InquireGroup(char delimiter)
{
return Group(&m_IO->CreateGroup(path, delimiter));
return Group(&m_IO->CreateGroup(delimiter));
};
void IO::FlushAll()
{
Expand Down
2 changes: 1 addition & 1 deletion bindings/CXX11/adios2/cxx11/IO.h
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Original file line number Diff line number Diff line change
Expand Up @@ -262,7 +262,7 @@ class IO
* @param a delimiter to separate groups in a string representation
* @return Group object
*/
Group InquireGroup(const std::string &path, char delimiter = '/');
Group InquireGroup(char delimiter = '/');

#if ADIOS2_USE_MPI
/**
Expand Down
46 changes: 29 additions & 17 deletions source/adios2/core/Group.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ std::vector<std::string> split(const std::string &s, char delimiter)
}
return tokens;
}
void Group::setPath(std::string path) { currentPath = path; }
void Group::setPath(std::string path) { currentPath = ADIOS_root + "/" + path; }
void Group::setDelimiter(char delimiter) { groupDelimiter = delimiter; }

Group::Group(std::string path, char delimiter, IO &io)
Expand All @@ -51,10 +51,13 @@ Group::Group(const Group &G)
}
Group *Group::InquireGroup(std::string groupName)
{
Group *g_out = new Group(currentPath + groupDelimiter + groupName,
this->groupDelimiter, this->m_IO);
g_out->mapPtr = this->mapPtr;
return g_out;
if (currentPath.compare("") != 0)
{
groupName = currentPath + groupDelimiter + groupName;
}
m_Gr = std::make_shared<Group>(groupName, this->groupDelimiter, this->m_IO);
m_Gr->mapPtr = this->mapPtr;
return m_Gr.get();
}
void Group::PrintTree()
{
Expand All @@ -74,6 +77,12 @@ void Group::BuildTree()
{
std::vector<std::string> tokens =
split(variablePair.first, groupDelimiter);
// Adding artificial root element
if (tokens[0] == "")
tokens[0] = ADIOS_root;
else
tokens.insert(tokens.begin(), ADIOS_root);
currentPath = ADIOS_root;

if (tokens.size() == 0)
{
Expand All @@ -83,7 +92,7 @@ void Group::BuildTree()
{
// case record = "/group1" or "group/"
}
if (tokens.size() > 1)
else
{
std::string key = tokens[0];
for (int level = 1; level < tokens.size(); level++)
Expand Down Expand Up @@ -140,9 +149,10 @@ std::vector<std::string> Group::AvailableVariables()
mapPtr->treeMap.end())
{
const core::VarMap &variables = m_IO.GetVariables();

if (variables.find(currentPath + groupDelimiter + v) !=
variables.end())
std::string variablePath = currentPath + groupDelimiter + v;
variablePath = variablePath.substr(
ADIOS_root.size() + 1, variablePath.size() - ADIOS_root.size());
if (variables.find(variablePath) != variables.end())
{
available_variables.push_back(v);
}
Expand All @@ -164,8 +174,10 @@ std::vector<std::string> Group::AvailableAttributes()
mapPtr->treeMap.end())
{
const core::AttrMap &attributes = m_IO.GetAttributes();
if (attributes.find(currentPath + groupDelimiter + v) !=
attributes.end())
std::string variablePath = currentPath + groupDelimiter + v;
variablePath = variablePath.substr(
ADIOS_root.size() + 1, variablePath.size() - ADIOS_root.size());
if (attributes.find(variablePath) != attributes.end())
{
available_attributes.push_back(v);
}
Expand All @@ -180,14 +192,14 @@ std::vector<std::string> Group::AvailableGroups()

std::vector<std::string> available_groups;
std::set<std::string> val = mapPtr->treeMap[currentPath];

for (auto v : val)
{
if (mapPtr->treeMap.find(currentPath + groupDelimiter + v) !=
mapPtr->treeMap.end())
available_groups.push_back(v);
for (auto v : val)
{
if (mapPtr->treeMap.find(currentPath + groupDelimiter + v) !=
mapPtr->treeMap.end())
available_groups.push_back(v);
}
}

return available_groups;
}

Expand Down
4 changes: 4 additions & 0 deletions source/adios2/core/Group.h
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,8 @@ class Group
char groupDelimiter;
/** shared pointer to a map representing the tree structure */
std::shared_ptr<TreeMap> mapPtr = nullptr;
/** root of the tree */
const std::string ADIOS_root = "_ADIOS_ROOT_";

public:
/**
Expand All @@ -50,6 +52,8 @@ class Group
Group(const Group &G);
/** destructor */
~Group();
/** a pointer to a Group Object */
std::shared_ptr<Group> m_Gr;
/**
* @brief Builds map that represents tree structure from m_Variable and
* m_Attributes from IO class
Expand Down
13 changes: 9 additions & 4 deletions source/adios2/core/Group.tcc
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,10 @@ namespace core
template <class T>
Variable<T> *Group::InquireVariable(const std::string &name) noexcept
{
Variable<T> &variable =
*m_IO.InquireVariable<T>(currentPath + groupDelimiter + name);
std::string variablePath = currentPath + groupDelimiter + name;
variablePath = variablePath.substr(ADIOS_root.size() + 1,
variablePath.size() - ADIOS_root.size());
Variable<T> &variable = *m_IO.InquireVariable<T>(variablePath);
return &variable;
}

Expand All @@ -30,8 +32,11 @@ Attribute<T> *Group::InquireAttribute(const std::string &name,
const std::string &variableName,
const std::string separator) noexcept
{
Attribute<T> &attribute = m_IO.InquireAttribute<T>(
currentPath + groupDelimiter + name, variableName, separator);
std::string variablePath = currentPath + groupDelimiter + name;
variablePath = variablePath.substr(ADIOS_root.size() + 1,
variablePath.size() - ADIOS_root.size());
Attribute<T> &attribute =
m_IO.InquireAttribute<T>(variablePath, variableName, separator);
return &attribute;
}
} // end namespace core
Expand Down
5 changes: 2 additions & 3 deletions source/adios2/core/IO.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -655,10 +655,9 @@ Engine &IO::Open(const std::string &name, const Mode mode)
{
return Open(name, mode, m_ADIOS.GetComm().Duplicate());
}
Group &IO::CreateGroup(const std::string &path, char delimiter)
Group &IO::CreateGroup(char delimiter)
{

m_Gr = std::make_shared<Group>(path, delimiter, *this);
m_Gr = std::make_shared<Group>("", delimiter, *this);
m_Gr->BuildTree();
return *m_Gr;
}
Expand Down
2 changes: 1 addition & 1 deletion source/adios2/core/IO.h
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Original file line number Diff line number Diff line change
Expand Up @@ -412,7 +412,7 @@ class IO
*/
void FlushAll();

Group &CreateGroup(const std::string &path, char delimiter);
Group &CreateGroup(char delimiter);

// READ FUNCTIONS, not yet implemented:
/**
Expand Down
68 changes: 60 additions & 8 deletions testing/adios2/hierarchy/TestHierarchicalReading.cpp
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Expand Up @@ -24,11 +24,16 @@ TEST_F(ADIOSHierarchicalReadVariableTest, Read)
std::string filename = "ADIOSHierarchicalReadVariable.bp";

// Number of steps
const std::size_t NSteps = 1;
const std::size_t NSteps = 2;

long unsigned int rank, size;

#if ADIOS2_USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
#else
rank = 0;
size = 1;
#endif

// Write test data using BP
Expand All @@ -43,9 +48,10 @@ TEST_F(ADIOSHierarchicalReadVariableTest, Read)

io.AddTransport("file");
adios2::Engine engine = io.Open(filename, adios2::Mode::Write);
const adios2::Dims shape = {10};
const adios2::Dims start = {0};
const adios2::Dims count = {10};
const std::size_t Nx = 10;
const adios2::Dims shape = {size * Nx};
const adios2::Dims start = {rank * Nx};
const adios2::Dims count = {Nx};

auto var1 = io.DefineVariable<int32_t>(
"group1/group2/group3/group4/variable1", shape, start, count);
Expand All @@ -57,7 +63,10 @@ TEST_F(ADIOSHierarchicalReadVariableTest, Read)
"group1/group2/group3/group4/variable4", shape, start, count);
auto var5 = io.DefineVariable<int32_t>(
"group1/group2/group3/group4/variable5", shape, start, count);
auto var6 =
io.DefineVariable<int32_t>("variable6", shape, start, count);
std::vector<int32_t> Ints = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};

for (size_t step = 0; step < NSteps; ++step)
{
engine.BeginStep();
Expand All @@ -67,16 +76,21 @@ TEST_F(ADIOSHierarchicalReadVariableTest, Read)
engine.Put(var3, Ints.data());
engine.Put(var4, Ints.data());
engine.Put(var5, Ints.data());
engine.Put(var6, Ints.data());

engine.EndStep();
}
engine.Close();

engine = io.Open(filename, adios2::Mode::Read);
for (int step = 0; step < NSteps; step++)
{
engine.BeginStep();
auto g = io.InquireGroup("group1", '/');
auto g = io.InquireGroup('/');
auto res = g.AvailableGroups();
EXPECT_EQ(res[0], "group2");
EXPECT_EQ(res[0], "group1");
res = g.AvailableVariables();
EXPECT_EQ(res[0], "variable6");
g.setPath("group1/group2");
res = g.AvailableGroups();
EXPECT_EQ(res[0], "group3");
Expand All @@ -92,6 +106,44 @@ TEST_F(ADIOSHierarchicalReadVariableTest, Read)
EXPECT_EQ(res.size(), 0);
engine.EndStep();
}
for (int step = 0; step < NSteps; step++)
{
engine.BeginStep();
auto g = io.InquireGroup('/');
auto res = g.AvailableGroups();
EXPECT_EQ(res[0], "group1");
res = g.AvailableVariables();
EXPECT_EQ(res[0], "variable6");
engine.EndStep();
}
for (int step = 0; step < NSteps; step++)
{
auto g = io.InquireGroup('/');
auto var = g.InquireVariable<int32_t>("variable6");
EXPECT_TRUE(var);
if (var)
{
std::vector<int32_t> myInts;
var.SetSelection({{Nx * rank}, {Nx}});
engine.Get<int32_t>(var, myInts, adios2::Mode::Sync);
EXPECT_EQ(Ints, myInts);
}
}
for (int step = 0; step < NSteps; step++)
{
auto g = io.InquireGroup('/');
g.setPath("group1/group2/group3/group4");
auto var = g.InquireVariable<int32_t>("variable1");
EXPECT_TRUE(var);
if (var)
{
std::vector<int32_t> myInts;
var.SetSelection({{Nx * rank}, {Nx}});
engine.Get<int32_t>(var, myInts, adios2::Mode::Sync);

EXPECT_EQ(Ints, myInts);
}
}
engine.Close();
}
}
Expand Down