diff --git a/bindings/C/adios2/adios2_c_engine.cpp b/bindings/C/adios2/adios2_c_engine.cpp
index d2d0880834b4201288021e4aa8b34529d7df8e44..cbdd0ab0846e4cda143dbdb116850e22b6505aa0 100644
--- a/bindings/C/adios2/adios2_c_engine.cpp
+++ b/bindings/C/adios2/adios2_c_engine.cpp
@@ -156,6 +156,142 @@ void adios2_perform_puts(adios2_Engine *engine)
engineCpp.PerformPuts();
}
+void adios2_get_sync(adios2_Engine *engine, adios2_Variable *variable,
+ void *values)
+{
+ adios2::VariableBase *variableBase =
+ reinterpret_cast<adios2::VariableBase *>(variable);
+ const std::string type(variableBase->m_Type);
+
+ adios2::Engine &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetSync(*dynamic_cast<adios2::Variable<T> *>(variableBase), \
+ reinterpret_cast<T *>(values)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_get_sync_self(adios2_Engine *engine, adios2_Variable *variable)
+{
+ adios2::VariableBase *variableBase =
+ reinterpret_cast<adios2::VariableBase *>(variable);
+ const std::string type(variableBase->m_Type);
+
+ adios2::Engine &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetSync(*dynamic_cast<adios2::Variable<T> *>(variableBase)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_get_sync_by_name(adios2_Engine *engine, const char *variable_name,
+ void *values)
+{
+ auto &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+ const std::string type(
+ engineCpp.GetIO().InquireVariableType(variable_name));
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetSync(variable_name, reinterpret_cast<T *>(values)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_get_deferred(adios2_Engine *engine, adios2_Variable *variable,
+ void *values)
+{
+ adios2::VariableBase *variableBase =
+ reinterpret_cast<adios2::VariableBase *>(variable);
+ const std::string type(variableBase->m_Type);
+
+ adios2::Engine &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetDeferred( \
+ *dynamic_cast<adios2::Variable<T> *>(variableBase), \
+ reinterpret_cast<T *>(values)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_get_deferred_self(adios2_Engine *engine, adios2_Variable *variable)
+{
+ adios2::VariableBase *variableBase =
+ reinterpret_cast<adios2::VariableBase *>(variable);
+ const std::string type(variableBase->m_Type);
+
+ adios2::Engine &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetDeferred( \
+ *dynamic_cast<adios2::Variable<T> *>(variableBase)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_get_deferred_by_name(adios2_Engine *engine,
+ const char *variable_name, void *values)
+{
+ auto &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+ const std::string type(
+ engineCpp.GetIO().InquireVariableType(variable_name));
+
+ if (type == "compound")
+ {
+ // not supported
+ }
+#define declare_template_instantiation(T) \
+ else if (type == adios2::GetType<T>()) \
+ { \
+ engineCpp.GetDeferred(variable_name, reinterpret_cast<T *>(values)); \
+ }
+ ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+}
+
+void adios2_perform_gets(adios2_Engine *engine)
+{
+ auto &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
+ engineCpp.PerformGets();
+}
+
void adios2_end_step(adios2_Engine *engine)
{
auto &engineCpp = *reinterpret_cast<adios2::Engine *>(engine);
diff --git a/bindings/C/adios2/adios2_c_engine.h b/bindings/C/adios2/adios2_c_engine.h
index 178905524681968a70ede719b4dbf2bfd7f2adae..7cb9af4d891dd0b9354ba9d2d0689765228bb04e 100644
--- a/bindings/C/adios2/adios2_c_engine.h
+++ b/bindings/C/adios2/adios2_c_engine.h
@@ -22,6 +22,8 @@ extern "C" {
*/
void adios2_begin_step(adios2_Engine *engine);
+//***************** PUT *****************
+
/**
* Put a variable in IO using a adios2_Variable handler
* @param engine handler for engine executing the write
@@ -33,7 +35,7 @@ void adios2_put_sync(adios2_Engine *engine, adios2_Variable *variable,
void adios2_put_sync_self(adios2_Engine *engine, adios2_Variable *variable);
-void adios2_put_sync_by_name(adios2_Engine *engine, const char *variableName,
+void adios2_put_sync_by_name(adios2_Engine *engine, const char *variable_name,
const void *values);
/**
@@ -48,10 +50,29 @@ void adios2_put_deferred(adios2_Engine *engine, adios2_Variable *variable,
void adios2_put_deferred_self(adios2_Engine *engine, adios2_Variable *variable);
void adios2_put_deferred_by_name(adios2_Engine *engine,
- const char *variableName, const void *values);
+ const char *variable_name, const void *values);
void adios2_perform_puts(adios2_Engine *engine);
+//***************** GET *****************
+void adios2_get_sync(adios2_Engine *engine, adios2_Variable *variable,
+ void *values);
+
+void adios2_get_sync_self(adios2_Engine *engine, adios2_Variable *variable);
+
+void adios2_get_sync_by_name(adios2_Engine *engine, const char *variable_name,
+ void *values);
+
+void adios2_get_deferred(adios2_Engine *engine, adios2_Variable *variable,
+ void *values);
+
+void adios2_get_deferred_self(adios2_Engine *engine, adios2_Variable *variable);
+
+void adios2_get_deferred_by_name(adios2_Engine *engine,
+ const char *variable_name, void *values);
+
+void adios2_perform_gets(adios2_Engine *engine);
+
/**
* terminates interaction with current step
* @param engine handler executing IO tasks
diff --git a/bindings/C/adios2/adios2_c_variable.cpp b/bindings/C/adios2/adios2_c_variable.cpp
index 405a1af082996e6b288e8f7222cc751b2de2f6fe..798dd9784c191705354fe3b814397d9017d33c1a 100644
--- a/bindings/C/adios2/adios2_c_variable.cpp
+++ b/bindings/C/adios2/adios2_c_variable.cpp
@@ -144,7 +144,7 @@ void adios2_set_selection(adios2_Variable *variable, const size_t ndims,
reinterpret_cast<adios2::VariableBase *>(variable);
const adios2::Dims startV(start, start + ndims);
- const adios2::Dims countV(start, start + ndims);
+ const adios2::Dims countV(count, count + ndims);
variableBase->SetSelection({startV, countV});
variableBase->CheckDimensions("in call to adios2_set_selection");
}
diff --git a/bindings/fortran/CMakeLists.txt b/bindings/fortran/CMakeLists.txt
index acc3f72e6a704f1b6935cf72a52db9bd95fc84dd..58a4191a4e6f7002cd119c32037cf516e8ad9914 100644
--- a/bindings/fortran/CMakeLists.txt
+++ b/bindings/fortran/CMakeLists.txt
@@ -25,6 +25,8 @@ set(MODULES
modules/adios2_engine_mod.f90
modules/adios2_engine_write_mod.f90
modules/adios2_engine_iwrite_mod.f90
+ modules/adios2_engine_read_mod.f90
+ modules/adios2_engine_iread_mod.f90
)
add_library(adios2_f ${MODULES} ${F2C})
diff --git a/bindings/fortran/f2c/adios2_f2c_engine.cpp b/bindings/fortran/f2c/adios2_f2c_engine.cpp
index 67cc5cd5bdc17dab4c2ba9e1d066c24878a5bb49..3a9c8108b9547309e490f0be3ac23bac2783663a 100644
--- a/bindings/fortran/f2c/adios2_f2c_engine.cpp
+++ b/bindings/fortran/f2c/adios2_f2c_engine.cpp
@@ -26,6 +26,7 @@ void FC_GLOBAL(adios2_begin_step_f2c,
}
}
+// ******** PUTS */
void FC_GLOBAL(adios2_put_sync_f2c,
ADIOS2_PUT_SYNC_F2C)(adios2_Engine **engine,
adios2_Variable **variable,
@@ -58,6 +59,67 @@ void FC_GLOBAL(adios2_put_deferred_f2c,
}
}
+void FC_GLOBAL(adios2_perform_puts_f2c,
+ ADIOS2_PERFORM_PUTS_F2C)(adios2_Engine **engine, int *ierr)
+{
+ *ierr = 0;
+ try
+ {
+ adios2_perform_puts(*engine);
+ }
+ catch (std::exception &e)
+ {
+ *ierr = 1;
+ }
+}
+
+// ******** GETS */
+void FC_GLOBAL(adios2_get_sync_f2c,
+ ADIOS2_get_SYNC_F2C)(adios2_Engine **engine,
+ adios2_Variable **variable, void *values,
+ int *ierr)
+{
+ *ierr = 0;
+ try
+ {
+ adios2_get_sync(*engine, *variable, values);
+ }
+ catch (std::exception &e)
+ {
+ *ierr = 1;
+ }
+}
+
+void FC_GLOBAL(adios2_get_deferred_f2c,
+ ADIOS2_get_DEFERRED_F2C)(adios2_Engine **engine,
+ adios2_Variable **variable,
+ void *values, int *ierr)
+{
+ *ierr = 0;
+ try
+ {
+ adios2_get_deferred(*engine, *variable, values);
+ }
+ catch (std::exception &e)
+ {
+ *ierr = 1;
+ }
+}
+
+void FC_GLOBAL(adios2_perform_gets_f2c,
+ ADIOS2_PERFORM_GETS_F2C)(adios2_Engine **engine, int *ierr)
+{
+ *ierr = 0;
+ try
+ {
+ adios2_perform_gets(*engine);
+ }
+ catch (std::exception &e)
+ {
+ *ierr = 1;
+ }
+}
+
void FC_GLOBAL(adios2_end_step_f2c, ADIOS2_END_STEP_F2C)(adios2_Engine **engine,
int *ierr)
{
diff --git a/bindings/fortran/f2c/adios2_f2c_engine.h b/bindings/fortran/f2c/adios2_f2c_engine.h
index 0b481dbef034698404225e199d17a6d2d683f28a..bc3ee6250f2bd94f77bd66e1199a7155e9708cf1 100644
--- a/bindings/fortran/f2c/adios2_f2c_engine.h
+++ b/bindings/fortran/f2c/adios2_f2c_engine.h
@@ -22,6 +22,7 @@ extern "C" {
void FC_GLOBAL(adios2_begin_step_f2c,
ADIOS2_BEGIN_STEP_F2C)(adios2_Engine **engine, int *ierr);
+// ************** PUT
void FC_GLOBAL(adios2_put_sync_f2c,
ADIOS2_PUT_SYNC_F2C)(adios2_Engine **engine,
adios2_Variable **variable,
@@ -32,6 +33,23 @@ void FC_GLOBAL(adios2_put_deferred_f2c,
adios2_Variable **variable,
const void *values, int *ierr);
+void FC_GLOBAL(adios2_perform_puts_f2c,
+ ADIOS2_PERFORM_PUTS_F2C)(adios2_Engine **engine, int *ierr);
+
+// ************** GET
+void FC_GLOBAL(adios2_get_sync_f2c,
+ ADIOS2_get_SYNC_F2C)(adios2_Engine **engine,
+ adios2_Variable **variable, void *values,
+ int *ierr);
+
+void FC_GLOBAL(adios2_get_deferred_f2c,
+ ADIOS2_get_DEFERRED_F2C)(adios2_Engine **engine,
+ adios2_Variable **variable,
+ void *values, int *ierr);
+
+void FC_GLOBAL(adios2_perform_gets_f2c,
+ ADIOS2_PERFORM_GETS_F2C)(adios2_Engine **engine, int *ierr);
+
void FC_GLOBAL(adios2_end_step_f2c, ADIOS2_END_STEP_F2C)(adios2_Engine **engine,
int *ierr);
diff --git a/bindings/fortran/f2c/adios2_f2c_io.cpp b/bindings/fortran/f2c/adios2_f2c_io.cpp
index 615f2e2a4fb2b1884e6aa2232d2a9d4ff617cbc9..99113da382f5979ec52c035ede19b1248ca03221 100644
--- a/bindings/fortran/f2c/adios2_f2c_io.cpp
+++ b/bindings/fortran/f2c/adios2_f2c_io.cpp
@@ -78,7 +78,8 @@ void FC_GLOBAL(adios2_define_variable_f2c, ADIOS2_DEFINE_VARIABLE_F2C)(
const int *count, const int *constant_dims, int *ierr)
{
auto lf_IntToSizeT = [](const int *dimensions, const int size,
- std::vector<std::size_t> &output) {
+ std::vector<std::size_t> &output,
+ const bool offset) {
if (dimensions == nullptr)
{
@@ -86,18 +87,29 @@ void FC_GLOBAL(adios2_define_variable_f2c, ADIOS2_DEFINE_VARIABLE_F2C)(
}
output.resize(size);
- for (unsigned int d = 0; d < size; ++d)
+
+ if (offset)
+ {
+ for (unsigned int d = 0; d < size; ++d)
+ {
+ output[d] = dimensions[d] - 1;
+ }
+ }
+ else
{
- output[d] = dimensions[d];
+ for (unsigned int d = 0; d < size; ++d)
+ {
+ output[d] = dimensions[d];
+ }
}
};
*ierr = 0;
std::vector<std::size_t> shapeV, startV, countV;
- lf_IntToSizeT(shape, *ndims, shapeV);
- lf_IntToSizeT(start, *ndims, startV);
- lf_IntToSizeT(count, *ndims, countV);
+ lf_IntToSizeT(shape, *ndims, shapeV, false);
+ lf_IntToSizeT(start, *ndims, startV, true);
+ lf_IntToSizeT(count, *ndims, countV, false);
try
{
@@ -112,6 +124,27 @@ void FC_GLOBAL(adios2_define_variable_f2c, ADIOS2_DEFINE_VARIABLE_F2C)(
}
}
+void FC_GLOBAL(adios2_inquire_variable_f2c,
+ ADIOS2_INQUIRE_VARIABLE_F2C)(adios2_Variable **variable,
+ adios2_IO **io,
+ const char *variable_name,
+ int *ierr)
+{
+ *ierr = 0;
+ try
+ {
+ *variable = adios2_inquire_variable(*io, variable_name);
+ if (*variable == nullptr)
+ {
+ *ierr = 2;
+ }
+ }
+ catch (std::exception &e)
+ {
+ *ierr = 1;
+ }
+}
+
void FC_GLOBAL(adios2_open_f2c,
ADIOS2_OPEN_F2C)(adios2_Engine **engine, adios2_IO **io,
const char *name, const int *open_mode,
diff --git a/bindings/fortran/f2c/adios2_f2c_io.h b/bindings/fortran/f2c/adios2_f2c_io.h
index 0e73994df8b3b387e18fd73e994f26dd47bf6ed1..b5aa9b364549c0536fbf49721b5921f3c2c5a2ab 100644
--- a/bindings/fortran/f2c/adios2_f2c_io.h
+++ b/bindings/fortran/f2c/adios2_f2c_io.h
@@ -39,6 +39,12 @@ void FC_GLOBAL(adios2_define_variable_f2c, ADIOS2_DEFINE_VARIABLE_F2C)(
const int *type, const int *ndims, const int *shape, const int *start,
const int *count, const int *constant_dims, int *ierr);
+void FC_GLOBAL(adios2_inquire_variable_f2c,
+ ADIOS2_INQUIRE_VARIABLE_F2C)(adios2_Variable **variable,
+ adios2_IO **io,
+ const char *variable_name,
+ int *ierr);
+
void FC_GLOBAL(adios2_open_f2c,
ADIOS2_OPEN_F2C)(adios2_Engine **engine, adios2_IO **io,
const char *name, const int *open_mode,
diff --git a/bindings/fortran/f2c/adios2_f2c_variable.cpp b/bindings/fortran/f2c/adios2_f2c_variable.cpp
index 97d44bf7915351139016d2d919548f6b594b2bf3..799f6626ad5ada4d86bdbe452d0505e969192e69 100644
--- a/bindings/fortran/f2c/adios2_f2c_variable.cpp
+++ b/bindings/fortran/f2c/adios2_f2c_variable.cpp
@@ -64,6 +64,33 @@ void FC_GLOBAL(adios2_set_selection_f2c,
const int *ndims, const int *start,
const int *count, int *ierr)
{
+ auto lf_IntToSizeT = [](const int *dimensions, const int size,
+ std::vector<std::size_t> &output,
+ const bool offset) {
+
+ if (dimensions == nullptr)
+ {
+ return;
+ }
+
+ output.resize(size);
+
+ if (offset)
+ {
+ for (unsigned int d = 0; d < size; ++d)
+ {
+ output[d] = dimensions[d] - 1;
+ }
+ }
+ else
+ {
+ for (unsigned int d = 0; d < size; ++d)
+ {
+ output[d] = dimensions[d];
+ }
+ }
+ };
+
*ierr = 0;
if (start == nullptr || count == nullptr)
{
@@ -71,8 +98,9 @@ void FC_GLOBAL(adios2_set_selection_f2c,
return;
}
- std::vector<std::size_t> startV(start, start + *ndims);
- std::vector<std::size_t> countV(count, count + *ndims);
+ std::vector<std::size_t> startV, countV;
+ lf_IntToSizeT(start, *ndims, startV, true);
+ lf_IntToSizeT(count, *ndims, countV, false);
try
{
diff --git a/bindings/fortran/modules/adios2_engine_iread_mod.f90 b/bindings/fortran/modules/adios2_engine_iread_mod.f90
new file mode 100644
index 0000000000000000000000000000000000000000..44ac5b5039e961df44e5b146655cdf4f916d458a
--- /dev/null
+++ b/bindings/fortran/modules/adios2_engine_iread_mod.f90
@@ -0,0 +1,660 @@
+!
+! Distributed under the OSI-approved Apache License, Version 2.0. See
+! accompanying file Copyright.txt for details.
+!
+! adios2_engine_iread_mod.f90 : ADIOS2 Fortran bindings for Engine generic
+! deferred READ (iread) functions
+!
+! Created on: Aug 22, 2017
+! Author: William F Godoy godoywf@ornl.gov
+!
+module adios2_engine_iread
+
+ interface adios2_iread
+
+ ! Single Value
+ module procedure adios2_iread_integer
+ module procedure adios2_iread_real
+ module procedure adios2_iread_dp
+ module procedure adios2_iread_complex
+ module procedure adios2_iread_complex_dp
+ module procedure adios2_iread_integer1
+ module procedure adios2_iread_integer2
+ module procedure adios2_iread_integer8
+
+ ! 1D Array
+ module procedure adios2_iread_integer_1d
+ module procedure adios2_iread_real_1d
+ module procedure adios2_iread_dp_1d
+ module procedure adios2_iread_complex_1d
+ module procedure adios2_iread_complex_dp_1d
+ module procedure adios2_iread_integer1_1d
+ module procedure adios2_iread_integer2_1d
+ module procedure adios2_iread_integer8_1d
+
+ ! 2D Array
+ module procedure adios2_iread_integer_2d
+ module procedure adios2_iread_real_2d
+ module procedure adios2_iread_dp_2d
+ module procedure adios2_iread_complex_2d
+ module procedure adios2_iread_complex_dp_2d
+ module procedure adios2_iread_integer1_2d
+ module procedure adios2_iread_integer2_2d
+ module procedure adios2_iread_integer8_2d
+
+ ! 3D Array
+ module procedure adios2_iread_integer_3d
+ module procedure adios2_iread_real_3d
+ module procedure adios2_iread_dp_3d
+ module procedure adios2_iread_complex_3d
+ module procedure adios2_iread_complex_dp_3d
+ module procedure adios2_iread_integer1_3d
+ module procedure adios2_iread_integer2_3d
+ module procedure adios2_iread_integer8_3d
+
+ ! 4D Array
+ module procedure adios2_iread_integer_4d
+ module procedure adios2_iread_real_4d
+ module procedure adios2_iread_dp_4d
+ module procedure adios2_iread_complex_4d
+ module procedure adios2_iread_complex_dp_4d
+ module procedure adios2_iread_integer1_4d
+ module procedure adios2_iread_integer2_4d
+ module procedure adios2_iread_integer8_4d
+
+ ! 5D Array
+ module procedure adios2_iread_integer_5d
+ module procedure adios2_iread_real_5d
+ module procedure adios2_iread_dp_5d
+ module procedure adios2_iread_complex_5d
+ module procedure adios2_iread_complex_dp_5d
+ module procedure adios2_iread_integer1_5d
+ module procedure adios2_iread_integer2_5d
+ module procedure adios2_iread_integer8_5d
+
+ ! 6D Array
+ module procedure adios2_iread_integer_6d
+ module procedure adios2_iread_real_6d
+ module procedure adios2_iread_dp_6d
+ module procedure adios2_iread_complex_6d
+ module procedure adios2_iread_complex_dp_6d
+ module procedure adios2_iread_integer1_6d
+ module procedure adios2_iread_integer2_6d
+ module procedure adios2_iread_integer8_6d
+
+ end interface
+
+contains
+
+ ! Single Value
+ subroutine adios2_iread_integer( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ subroutine adios2_iread_integer8( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 1D Array
+ subroutine adios2_iread_integer_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 2D Array
+ subroutine adios2_iread_integer_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 3D Array
+ subroutine adios2_iread_integer_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 4D Array
+ subroutine adios2_iread_integer_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 5D Array
+ subroutine adios2_iread_integer_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 6D Array
+ subroutine adios2_iread_integer_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_real_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_dp_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_complex_dp_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer1_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer2_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_iread_integer8_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_deferred_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+end module
diff --git a/bindings/fortran/modules/adios2_engine_mod.f90 b/bindings/fortran/modules/adios2_engine_mod.f90
index 3bda71211d135e5f9722c221ac480d7fe077e0d4..9ff921673598c7718859518270b0b5f4c550c282 100644
--- a/bindings/fortran/modules/adios2_engine_mod.f90
+++ b/bindings/fortran/modules/adios2_engine_mod.f90
@@ -10,10 +10,39 @@
module adios2_engine
use adios2_engine_write
use adios2_engine_iwrite
+ use adios2_engine_read
+ use adios2_engine_iread
implicit none
contains
+ subroutine adios2_begin_step(engine, ierr)
+ integer(kind=8), intent(in) :: engine
+ integer, intent(out) :: ierr
+
+ call adios2_begin_step_f2c(engine, ierr)
+
+ end subroutine
+
+
+ subroutine adios2_perform_puts(engine, ierr)
+ integer(kind=8), intent(in) :: engine
+ integer, intent(out) :: ierr
+
+ call adios2_perform_puts_f2c(engine, ierr)
+
+ end subroutine
+
+
+ subroutine adios2_perform_gets(engine, ierr)
+ integer(kind=8), intent(in) :: engine
+ integer, intent(out) :: ierr
+
+ call adios2_perform_gets_f2c(engine, ierr)
+
+ end subroutine
+
+
subroutine adios2_end_step(engine, ierr)
integer(kind=8), intent(in) :: engine
integer, intent(out) :: ierr
diff --git a/bindings/fortran/modules/adios2_engine_read_mod.f90 b/bindings/fortran/modules/adios2_engine_read_mod.f90
new file mode 100644
index 0000000000000000000000000000000000000000..220937e4fd9e4a39da59bd7c9331e67ff2a83a0c
--- /dev/null
+++ b/bindings/fortran/modules/adios2_engine_read_mod.f90
@@ -0,0 +1,660 @@
+!
+! Distributed under the OSI-approved Apache License, Version 2.0. See
+! accompanying file Copyright.txt for details.
+!
+! adios2_engine_read_mod.f90 : ADIOS2 Fortran bindings for Engine generic
+! Read functions
+!
+! Created on: Aug 22, 2017
+! Author: William F Godoy godoywf@ornl.gov
+!
+module adios2_engine_read
+
+ interface adios2_read
+
+ ! Single Value
+ module procedure adios2_read_integer
+ module procedure adios2_read_real
+ module procedure adios2_read_dp
+ module procedure adios2_read_complex
+ module procedure adios2_read_complex_dp
+ module procedure adios2_read_integer1
+ module procedure adios2_read_integer2
+ module procedure adios2_read_integer8
+
+ ! 1D Array
+ module procedure adios2_read_integer_1d
+ module procedure adios2_read_real_1d
+ module procedure adios2_read_dp_1d
+ module procedure adios2_read_complex_1d
+ module procedure adios2_read_complex_dp_1d
+ module procedure adios2_read_integer1_1d
+ module procedure adios2_read_integer2_1d
+ module procedure adios2_read_integer8_1d
+
+ ! 2D Array
+ module procedure adios2_read_integer_2d
+ module procedure adios2_read_real_2d
+ module procedure adios2_read_dp_2d
+ module procedure adios2_read_complex_2d
+ module procedure adios2_read_complex_dp_2d
+ module procedure adios2_read_integer1_2d
+ module procedure adios2_read_integer2_2d
+ module procedure adios2_read_integer8_2d
+
+ ! 3D Array
+ module procedure adios2_read_integer_3d
+ module procedure adios2_read_real_3d
+ module procedure adios2_read_dp_3d
+ module procedure adios2_read_complex_3d
+ module procedure adios2_read_complex_dp_3d
+ module procedure adios2_read_integer1_3d
+ module procedure adios2_read_integer2_3d
+ module procedure adios2_read_integer8_3d
+
+ ! 4D Array
+ module procedure adios2_read_integer_4d
+ module procedure adios2_read_real_4d
+ module procedure adios2_read_dp_4d
+ module procedure adios2_read_complex_4d
+ module procedure adios2_read_complex_dp_4d
+ module procedure adios2_read_integer1_4d
+ module procedure adios2_read_integer2_4d
+ module procedure adios2_read_integer8_4d
+
+ ! 5D Array
+ module procedure adios2_read_integer_5d
+ module procedure adios2_read_real_5d
+ module procedure adios2_read_dp_5d
+ module procedure adios2_read_complex_5d
+ module procedure adios2_read_complex_dp_5d
+ module procedure adios2_read_integer1_5d
+ module procedure adios2_read_integer2_5d
+ module procedure adios2_read_integer8_5d
+
+ ! 6D Array
+ module procedure adios2_read_integer_6d
+ module procedure adios2_read_real_6d
+ module procedure adios2_read_dp_6d
+ module procedure adios2_read_complex_6d
+ module procedure adios2_read_complex_dp_6d
+ module procedure adios2_read_integer1_6d
+ module procedure adios2_read_integer2_6d
+ module procedure adios2_read_integer8_6d
+
+ end interface
+
+contains
+
+ ! Single Value
+ subroutine adios2_read_integer( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ subroutine adios2_read_integer8( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 1D Array
+ subroutine adios2_read_integer_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_1d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 2D Array
+ subroutine adios2_read_integer_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_2d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ ! 3D Array
+ subroutine adios2_read_integer_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_3d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 4D Array
+ subroutine adios2_read_integer_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_4d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 5D Array
+ subroutine adios2_read_integer_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_5d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+
+ ! 6D Array
+ subroutine adios2_read_integer_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_real_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_dp_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ real(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex, dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_complex_dp_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ complex(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer1_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=1), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer2_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=2), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+ subroutine adios2_read_integer8_6d( engine, variable, values, ierr )
+ integer(kind=8), intent(in):: engine
+ integer(kind=8), intent(in):: variable
+ integer(kind=8), dimension(:,:,:,:,:,:), intent(out):: values
+ integer, intent(out):: ierr
+
+ call adios2_get_sync_f2c(engine, variable, values, ierr)
+
+ end subroutine
+
+end module
diff --git a/bindings/fortran/modules/adios2_io_mod.f90 b/bindings/fortran/modules/adios2_io_mod.f90
index a0a1169fd9714a19e9e092cde2b68be5fbdac5e7..8ac098bd8b04a6100c95ecde7c1d76005ab6fee2 100644
--- a/bindings/fortran/modules/adios2_io_mod.f90
+++ b/bindings/fortran/modules/adios2_io_mod.f90
@@ -80,4 +80,16 @@ contains
end subroutine
+ subroutine adios2_inquire_variable(variable, io, variable_name, ierr)
+ integer(kind=8), intent(out) :: variable
+ integer(kind=8), intent(in) :: io
+ character*(*), intent(in) :: variable_name
+ integer, intent(out) :: ierr
+
+ call adios2_inquire_variable_f2c(variable, io, &
+ & TRIM(ADJUSTL(variable_name))//char(0), ierr)
+
+ end subroutine
+
+
end module
diff --git a/bindings/fortran/modules/adios2_parameters_mod.f90 b/bindings/fortran/modules/adios2_parameters_mod.f90
index 44290156424d23844046e1c0576aadfaf1f1a8cd..997ba65b56fb84c9e6a864bb654151eda0ab833b 100644
--- a/bindings/fortran/modules/adios2_parameters_mod.f90
+++ b/bindings/fortran/modules/adios2_parameters_mod.f90
@@ -35,6 +35,10 @@ module adios2_parameters
logical, parameter :: adios2_constant_dims_true = .true.
logical, parameter :: adios2_constant_dims_false = .false.
+ ! Found or not found, ierr value
+ integer, parameter :: adios2_found = 0
+ integer, parameter :: adios2_not_found = 2
+
! Mode
integer, parameter :: adios2_mode_undefined = 0
integer, parameter :: adios2_mode_write = 1
diff --git a/bindings/python/EnginePy.cpp b/bindings/python/EnginePy.cpp
index a3e7b11800e13497b14894064af80282e033a6b8..3120be8a4f2445a43aa5112106494056bdc23340 100644
--- a/bindings/python/EnginePy.cpp
+++ b/bindings/python/EnginePy.cpp
@@ -5,7 +5,7 @@
* EnginePy.cpp
*
* Created on: Mar 15, 2017
- * Author: wgodoy
+ * Author: William F Godoy godoywf@ornl.gov
*/
#include "EnginePy.h"
@@ -25,35 +25,12 @@ EnginePy::EnginePy(IO &io, const std::string &name, const Mode openMode,
{
}
+void EnginePy::BeginStep() { m_Engine.BeginStep(); }
+
void EnginePy::PutSync(VariableBase *variable, const pybind11::array &array)
{
- if (variable->m_Type.empty()) // Define in IO
- {
- auto &io = m_Engine.GetIO();
+ DefineInIO(variable, array);
- if (array.is(pybind11::array()))
- {
- if (m_DebugMode)
- {
- throw std::invalid_argument(
- "ERROR: passing an empty numpy array for variable " +
- variable->m_Name + ", in call to PutSync");
- }
- }
-#define declare_type(T) \
- else if (pybind11::isinstance< \
- pybind11::array_t<T, pybind11::array::c_style>>(array)) \
- { \
- variable = &io.DefineVariable<T>(variable->m_Name, variable->m_Shape, \
- variable->m_Start, variable->m_Count, \
- variable->m_ConstantDims); \
- m_VariablesPlaceholder.erase(variable->m_Name); \
- }
- ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)
-#undef declare_type
- }
-
- // PutSync
if (variable->m_Type == "compound")
{
// not supported
@@ -80,10 +57,143 @@ void EnginePy::PutSync(VariableBase *variable, const pybind11::array &array)
void EnginePy::PutSync(VariableBase *variable, const std::string &string)
{
+ DefineInIO(variable, string);
m_Engine.PutSync(*dynamic_cast<adios2::Variable<std::string> *>(variable),
string);
}
+void EnginePy::PutDeferred(VariableBase *variable, const pybind11::array &array)
+{
+ DefineInIO(variable, array);
+
+ if (variable->m_Type == "compound")
+ {
+ // not supported
+ }
+#define declare_type(T) \
+ else if (variable->m_Type == GetType<T>()) \
+ { \
+ m_Engine.PutDeferred(*dynamic_cast<adios2::Variable<T> *>(variable), \
+ reinterpret_cast<const T *>(array.data())); \
+ }
+ ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)
+#undef declare_type
+ else
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument("ERROR: variable " + variable->m_Name +
+ " numpy array type is not supported or "
+ "is not memory contiguous "
+ ", in call to PutDeferred\n");
+ }
+ }
+}
+
+void EnginePy::PutDeferred(VariableBase *variable, const std::string &string)
+{
+ DefineInIO(variable, string);
+ m_Engine.PutDeferred(
+ *dynamic_cast<adios2::Variable<std::string> *>(variable), string);
+}
+
+void EnginePy::PerformPuts() { m_Engine.PerformPuts(); }
+
+void EnginePy::GetSync(VariableBase *variable, pybind11::array &array)
+{
+ if (variable->m_Type == "compound")
+ {
+ // not supported
+ }
+#define declare_type(T) \
+ else if (variable->m_Type == GetType<T>()) \
+ { \
+ m_Engine.GetSync( \
+ *dynamic_cast<adios2::Variable<T> *>(variable), \
+ reinterpret_cast<T *>(const_cast<void *>(array.data()))); \
+ }
+ ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)
+#undef declare_type
+ else
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument(
+ "ERROR: in variable " + variable->m_Name + " of type " +
+ variable->m_Type +
+ ", numpy array type is 1) not supported, 2) a type mismatch or"
+ "3) is not memory contiguous "
+ ", in call to GetSync\n");
+ }
+ }
+}
+
+void EnginePy::GetSync(VariableBase *variable, std::string &string)
+{
+ if (variable->m_Type == GetType<std::string>())
+ {
+ m_Engine.GetSync(
+ *dynamic_cast<adios2::Variable<std::string> *>(variable), string);
+ }
+ else
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument("ERROR: variable " + variable->m_Name +
+ " of type " + variable->m_Type +
+ " is not string, in call to GetSync");
+ }
+ }
+}
+
+void EnginePy::GetDeferred(VariableBase *variable, pybind11::array &array)
+{
+ if (variable->m_Type == "compound")
+ {
+ // not supported
+ }
+#define declare_type(T) \
+ else if (variable->m_Type == GetType<T>()) \
+ { \
+ m_Engine.GetDeferred( \
+ *dynamic_cast<adios2::Variable<T> *>(variable), \
+ reinterpret_cast<T *>(const_cast<void *>(array.data()))); \
+ }
+ ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)
+#undef declare_type
+ else
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument(
+ "ERROR: in variable " + variable->m_Name + " of type " +
+ variable->m_Type +
+ ", numpy array type is 1) not supported, 2) a type mismatch or"
+ "3) is not memory contiguous "
+ ", in call to GetSync\n");
+ }
+ }
+}
+
+void EnginePy::GetDeferred(VariableBase *variable, std::string &string)
+{
+ if (variable->m_Type == GetType<std::string>())
+ {
+ m_Engine.GetDeferred(
+ *dynamic_cast<adios2::Variable<std::string> *>(variable), string);
+ }
+ else
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument(
+ "ERROR: variable " + variable->m_Name + " of type " +
+ variable->m_Type + " is not string, in call to GetDeferred");
+ }
+ }
+}
+void EnginePy::PerformGets() { m_Engine.PerformGets(); }
+
void EnginePy::EndStep() { m_Engine.EndStep(); }
void EnginePy::Close(const int transportIndex)
@@ -91,4 +201,46 @@ void EnginePy::Close(const int transportIndex)
m_Engine.Close(transportIndex);
}
+// PRIVATE
+void EnginePy::DefineInIO(VariableBase *variable, const pybind11::array &array)
+{
+ if (variable->m_Type.empty()) // Define in IO
+ {
+ auto &io = m_Engine.GetIO();
+
+ if (array.is(pybind11::array()))
+ {
+ if (m_DebugMode)
+ {
+ throw std::invalid_argument(
+ "ERROR: passing an empty numpy array for variable " +
+ variable->m_Name + ", in call to Put/Get");
+ }
+ }
+#define declare_type(T) \
+ else if (pybind11::isinstance< \
+ pybind11::array_t<T, pybind11::array::c_style>>(array)) \
+ { \
+ variable = &io.DefineVariable<T>(variable->m_Name, variable->m_Shape, \
+ variable->m_Start, variable->m_Count, \
+ variable->m_ConstantDims); \
+ m_VariablesPlaceholder.erase(variable->m_Name); \
+ }
+ ADIOS2_FOREACH_NUMPY_TYPE_1ARG(declare_type)
+#undef declare_type
+ }
+}
+
+void EnginePy::DefineInIO(VariableBase *variable, const std::string &string)
+{
+ if (variable->m_Type.empty()) // Define in IO
+ {
+ auto &io = m_Engine.GetIO();
+ variable = &io.DefineVariable<std::string>(
+ variable->m_Name, variable->m_Shape, variable->m_Start,
+ variable->m_Count, variable->m_ConstantDims);
+ m_VariablesPlaceholder.erase(variable->m_Name);
+ }
+}
+
} // end namespace adios2
diff --git a/bindings/python/EnginePy.h b/bindings/python/EnginePy.h
index e4b426345c488a559113ed1991178138999c836c..7ef45d27fdcaa1867dd651abdcba9fa4039e4ddf 100644
--- a/bindings/python/EnginePy.h
+++ b/bindings/python/EnginePy.h
@@ -32,9 +32,24 @@ public:
~EnginePy() = default;
+ void BeginStep();
+
void PutSync(VariableBase *variable, const pybind11::array &array);
void PutSync(VariableBase *variable, const std::string &string);
+ void PutDeferred(VariableBase *variable, const pybind11::array &array);
+ void PutDeferred(VariableBase *variable, const std::string &string);
+
+ void PerformPuts();
+
+ void GetSync(VariableBase *variable, pybind11::array &array);
+ void GetSync(VariableBase *variable, std::string &string);
+
+ void GetDeferred(VariableBase *variable, pybind11::array &array);
+ void GetDeferred(VariableBase *variable, std::string &string);
+
+ void PerformGets();
+
void EndStep();
void Close(const int transportIndex = -1);
@@ -43,6 +58,9 @@ private:
Engine &m_Engine;
std::map<std::string, VariableBase> &m_VariablesPlaceholder;
const bool m_DebugMode;
+
+ void DefineInIO(VariableBase *variable, const pybind11::array &array);
+ void DefineInIO(VariableBase *variable, const std::string &string);
};
} // end namespace adios2
diff --git a/bindings/python/gluePyBind11.cpp b/bindings/python/gluePyBind11.cpp
index ec8b28731a4f1ed5d13c291b8fccbbe423a08ef7..374b72a11313a8289d6215a0943a4164186b28cc 100644
--- a/bindings/python/gluePyBind11.cpp
+++ b/bindings/python/gluePyBind11.cpp
@@ -134,7 +134,8 @@ PYBIND11_MODULE(adios2, m)
.def("DeclareIO", &adios2::ADIOSPy::DeclareIO);
pybind11::class_<adios2::VariableBase>(m, "Variable")
- .def("SetSelection", &adios2::VariableBase::SetSelection);
+ .def("SetSelection", &adios2::VariableBase::SetSelection)
+ .def("SelectionSize", &adios2::VariableBase::SelectionSize);
pybind11::class_<adios2::IOPy>(m, "IOPy")
.def("SetEngine", &adios2::IOPy::SetEngine)
@@ -158,12 +159,34 @@ PYBIND11_MODULE(adios2, m)
adios2::IOPy::Open);
pybind11::class_<adios2::EnginePy>(m, "EnginePy")
+ .def("BeginStep", &adios2::EnginePy::BeginStep)
.def("PutSync", (void (adios2::EnginePy::*)(adios2::VariableBase *,
const pybind11::array &)) &
adios2::EnginePy::PutSync)
.def("PutSync", (void (adios2::EnginePy::*)(adios2::VariableBase *,
const std::string &)) &
adios2::EnginePy::PutSync)
+ .def("PutDeferred",
+ (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ const pybind11::array &)) &
+ adios2::EnginePy::PutDeferred)
+ .def("PutDeferred", (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ const std::string &)) &
+ adios2::EnginePy::PutDeferred)
+ .def("PerformPuts", &adios2::EnginePy::PerformPuts)
+ .def("GetSync", (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ pybind11::array &)) &
+ adios2::EnginePy::GetSync)
+ .def("GetSync", (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ std::string &)) &
+ adios2::EnginePy::GetSync)
+ .def("GetDeferred", (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ pybind11::array &)) &
+ adios2::EnginePy::GetDeferred)
+ .def("GetDeferred", (void (adios2::EnginePy::*)(adios2::VariableBase *,
+ std::string &)) &
+ adios2::EnginePy::GetDeferred)
+ .def("PerformGets", &adios2::EnginePy::PerformGets)
.def("EndStep", &adios2::EnginePy::EndStep)
.def("Close", &adios2::EnginePy::Close,
pybind11::arg("transportIndex") = -1);
diff --git a/examples/hello/bpReader/helloBPReaderHeatMap3D.cpp b/examples/hello/bpReader/helloBPReaderHeatMap3D.cpp
index 1085571c40fb0f0b4f5b7e60a88d044bd4a47bb4..d41d039c1a49b42717022192ce3d46db0078c2bc 100644
--- a/examples/hello/bpReader/helloBPReaderHeatMap3D.cpp
+++ b/examples/hello/bpReader/helloBPReaderHeatMap3D.cpp
@@ -2,17 +2,21 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * helloBPReaderHeatMap.cpp : Writes a heat map in a regular 2D mesh,
+ * helloBPReaderHeatMap3D.cpp : Writes a heat map in a regular 3D mesh,
* values grow from 0 in increments of 1
*
- * temperature[gNx, Ny]
+ * temperature[gNx, Ny, Nz]
* where: gNx = MPI_size_x * Nx
*
- * 0 1 2 ... Ny-1
- * Ny Ny+1 Ny+2 ... 2*Ny-1
+ * k Map:
+ * k= Nz-1 . . . .
+ * k=1 . . . .
+ * k=0 . . . .
+ * 0 1 2 ... Nz-1
+ * Nz Nz+1 Nz+2 ... 2*Nz-1
* ...
* ...
- * (gNx-1)*Ny ... gNx*Ny-1
+ *(Ny-1)*Nz ... Ny*Nz-1
*
*
* Created on: Nov 1, 2017
@@ -73,7 +77,7 @@ int main(int argc, char *argv[])
// ************************** WRITE
/*** IO class object: settings and factory of Settings: Variables,
* Parameters, Transports, and Execution: Engines */
- adios2::IO &putHeatMap = adios.DeclareIO("HeatMapWriter");
+ adios2::IO &putHeatMap = adios.DeclareIO("HeatMapWrite");
adios2::Variable<unsigned int> &outTemperature =
putHeatMap.DefineVariable<unsigned int>(
@@ -89,7 +93,7 @@ int main(int argc, char *argv[])
// ************************** READ
if (rank == 0)
{
- adios2::IO &getHeatMap = adios.DeclareIO("HeatMapReader");
+ adios2::IO &getHeatMap = adios.DeclareIO("HeatMapRead");
adios2::Engine &bpReader =
getHeatMap.Open("HeatMap3D.bp", adios2::Mode::Read);
@@ -107,7 +111,8 @@ int main(int argc, char *argv[])
bpReader.GetSync(*inTemperature, inTemperatures.data());
- std::cout << "Incoming temperature map:\n";
+ std::cout << "Temperature map selection: ";
+ std::cout << "{ start = [2,2,2], count = [4,4,4] }\n";
for (auto i = 0; i < inTemperatures.size(); ++i)
{
diff --git a/examples/hello/bpReader/helloBPReaderHeatMap3D.f90 b/examples/hello/bpReader/helloBPReaderHeatMap3D.f90
index 1f79e7fcd3aded1d28a89878f0773915b67a2afd..89805866bb9d83d6b2079890d07fa73aec7da020 100644
--- a/examples/hello/bpReader/helloBPReaderHeatMap3D.f90
+++ b/examples/hello/bpReader/helloBPReaderHeatMap3D.f90
@@ -4,11 +4,14 @@ program helloBPReaderHeatMap3D
implicit none
- integer(kind=8) :: adios, io, var_temperatures, engine
- integer, dimension(:,:,:), allocatable :: temperatures
+ integer(kind=8) :: adios
+ integer(kind=8) :: ioPut, var_temperatures, bpWriter
+ integer(kind=8) :: ioGet, var_temperaturesIn, bpReader
+ integer, dimension(:,:,:), allocatable :: temperatures, sel_temperatures
integer, dimension(3) :: ishape, istart, icount
+ integer, dimension(3) :: sel_start, sel_count
integer :: ierr, irank, isize, inx, iny, inz
- integer :: i, j, k, iglobal, value, ilinear
+ integer :: i, j, k, iglobal, value, ilinear, icounter
call MPI_INIT(ierr)
call MPI_COMM_RANK(MPI_COMM_WORLD, irank, ierr)
@@ -18,17 +21,17 @@ program helloBPReaderHeatMap3D
iny = 10
inz = 10
- icount = (/ inx, iny, inz /)
- istart = (/ irank * inx, 1, 1 /)
- ishape = (/ isize * inx, iny, inz /)
+ icount = (/ inx, iny, inz /)
+ istart = (/ irank * inx+1, 1, 1 /)
+ ishape = (/ isize * inx, iny, inz /)
allocate( temperatures( inx, iny, inz ) )
! populate temperature
do k=1, icount(3)
do j=1, icount(2)
do i=1, icount(1)
- iglobal = istart(1) + i
- value = k * ishape(2) * ishape(1) + j * ishape(1) + &
+ iglobal = istart(1) + (i-1)-1
+ value = (k-1) * ishape(1) * ishape(2) + (j-1) * ishape(1) + &
& iglobal
temperatures(i,j,k) = value
end do
@@ -37,23 +40,65 @@ program helloBPReaderHeatMap3D
! Start adios2 Writer
call adios2_init( adios, MPI_COMM_WORLD, adios2_debug_mode_on, ierr )
- call adios2_declare_io( io, adios, "bpFileIO", ierr )
+ call adios2_declare_io( ioPut, adios, 'HeatMapWrite', ierr )
- call adios2_define_variable( var_temperatures, io, "temperatures", &
+ call adios2_define_variable( var_temperatures, ioPut, 'temperatures', &
& adios2_type_integer, 3, ishape, istart, icount, &
& adios2_constant_dims_true, ierr )
- call adios2_open( engine, io, "HeatMap3D_f.bp", adios2_mode_write, ierr )
+ call adios2_open( bpWriter, ioPut, 'HeatMap3D_f.bp', &
+ & adios2_mode_write, ierr )
- call adios2_write( engine, var_temperatures, temperatures, ierr )
+ call adios2_write( bpWriter, var_temperatures, temperatures, ierr )
- call adios2_close( engine, ierr )
+ call adios2_close( bpWriter, ierr )
if( allocated(temperatures) ) deallocate(temperatures)
- ! Start adios2 Reader
+ ! Start adios2 Reader in rank 0
+ if( irank == 0 ) then
+ call adios2_declare_io( ioGet, adios, 'HeatMapRead', ierr )
+ call adios2_open( bpReader, ioGet, 'HeatMap3D_f.bp', &
+ & adios2_mode_read, ierr)
+
+ call adios2_inquire_variable( var_temperaturesIn, ioGet, &
+ & 'temperatures', ierr )
+
+ if( ierr == adios2_found ) then
+
+ sel_start = (/ 3, 3, 3 /)
+ sel_count = (/ 4, 4, 4 /)
+ allocate( sel_temperatures( sel_count(1), sel_count(2), &
+ & sel_count(3) ) )
+
+ call adios2_set_selection( var_temperaturesIn, 3, sel_start, &
+ & sel_count, ierr )
+
+ call adios2_read( bpReader, var_temperaturesIn, sel_temperatures, &
+ & ierr )
+
+ write(*,'(A,3(I1,A),A,3(I1,A),A)') 'Temperature map selection &
+ & [ start = (', (sel_start(i),',',i=1,3) , ') &
+ & count = (', (sel_count(i),',',i=1,3) , ') ]'
+
+
+ do k=1,sel_count(3)
+ do j=1,sel_count(2)
+ do i=1,sel_count(1)
+ write(6,'(I4) ', advance="no") sel_temperatures(i,j,k)
+ end do
+ write(*,*)
+ end do
+ end do
+
+
+ if( allocated(sel_temperatures) ) deallocate(sel_temperatures)
+
+ end if
+
+ end if
end program helloBPReaderHeatMap3D
diff --git a/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp b/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
index 6f485e1606291cec97678a19efa80c14c5c8f8ad..6ab37a388f24beb17266d3828f77a1df4a906028 100644
--- a/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
+++ b/examples/hello/bpTimeWriter/helloBPTimeWriter.cpp
@@ -36,69 +36,109 @@ int main(int argc, char *argv[])
* recommended */
adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
- /*** IO class object: settings and factory of Settings: Variables,
- * Parameters, Transports, and Execution: Engines */
- adios2::IO &bpIO = adios.DeclareIO("BPFile_N2N");
- bpIO.SetParameters({{"Threads", "2"}});
+ /// WRITE
+ {
+ /*** IO class object: settings and factory of Settings: Variables,
+ * Parameters, Transports, and Execution: Engines */
+ adios2::IO &bpIO = adios.DeclareIO("BPFile_N2N");
+ bpIO.SetParameters({{"Threads", "2"}});
- /** global array: name, { shape (total dimensions) }, { start
- * (local) },
- * { count (local) }, all are constant dimensions */
- const unsigned int variablesSize = 1;
- std::vector<adios2::Variable<float> *> bpFloats(variablesSize);
+ /** global array: name, { shape (total dimensions) }, { start
+ * (local) },
+ * { count (local) }, all are constant dimensions */
+ const unsigned int variablesSize = 1;
+ std::vector<adios2::Variable<float> *> bpFloats(variablesSize);
- adios2::Variable<std::string> &bpString =
- bpIO.DefineVariable<std::string>("bpString");
+ adios2::Variable<std::string> &bpString =
+ bpIO.DefineVariable<std::string>("bpString");
- for (unsigned int v = 0; v < variablesSize; ++v)
- {
- std::string namev("bpFloats");
- if (v < 10)
+ for (unsigned int v = 0; v < variablesSize; ++v)
{
- namev += "00";
+ std::string namev("bpFloats");
+ if (v < 10)
+ {
+ namev += "00";
+ }
+ else if (v < 100)
+ {
+ namev += "0";
+ }
+ namev += std::to_string(v);
+
+ bpFloats[v] =
+ &bpIO.DefineVariable<float>(namev, {size * Nx}, {rank * Nx},
+ {Nx}, adios2::ConstantDims);
}
- else if (v < 100)
+
+ /** global single value variable: name */
+ adios2::Variable<unsigned int> &bpTimeStep =
+ bpIO.DefineVariable<unsigned int>("timeStep");
+
+ /** Engine derived class, spawned to start IO operations */
+ adios2::Engine &bpWriter =
+ bpIO.Open("myVector.bp", adios2::Mode::Write);
+
+ for (unsigned int timeStep = 0; timeStep < 3; ++timeStep)
{
- namev += "0";
+ // bpWriter.BeginStep();
+ if (rank == 0) // global single value, only saved by rank 0
+ {
+ bpWriter.PutSync<unsigned int>(bpTimeStep, timeStep);
+ }
+
+ // template type is optional, but recommended
+ for (unsigned int v = 0; v < variablesSize; ++v)
+ {
+ myFloats[0] = static_cast<float>(v + timeStep);
+ bpWriter.PutSync(*bpFloats[v], myFloats.data());
+ }
+ const std::string myString(
+ "Hello from rank: " + std::to_string(rank) +
+ " and timestep: " + std::to_string(timeStep));
+
+ bpWriter.PutSync(bpString, myString);
+
+ bpWriter.EndStep();
}
- namev += std::to_string(v);
- bpFloats[v] = &bpIO.DefineVariable<float>(
- namev, {size * Nx}, {rank * Nx}, {Nx}, adios2::ConstantDims);
+ bpWriter.Close();
}
+ MPI_Barrier(MPI_COMM_WORLD);
- /** global single value variable: name */
- adios2::Variable<unsigned int> &bpTimeStep =
- bpIO.DefineVariable<unsigned int>("timeStep");
+ { /////////////////////READ
+ // if (rank == 0)
+ // {
+ adios2::IO &ioReader = adios.DeclareIO("bpReader");
- /** Engine derived class, spawned to start IO operations */
- adios2::Engine &bpWriter =
- bpIO.Open("myVector.bp", adios2::Mode::Write);
+ adios2::Engine &bpReader =
+ ioReader.Open("myVector.bp", adios2::Mode::Read);
- for (unsigned int timeStep = 0; timeStep < 3; ++timeStep)
- {
- // bpWriter.BeginStep();
- if (rank == 0) // global single value, only saved by rank 0
+ adios2::Variable<float> *bpFloats000 =
+ ioReader.InquireVariable<float>("bpFloats000");
+
+ if (bpFloats000 != nullptr)
{
- bpWriter.PutSync<unsigned int>(bpTimeStep, timeStep);
+ bpFloats000->SetSelection({{rank * Nx}, {Nx}});
+ bpFloats000->SetStepSelection({3, 1});
+
+ std::vector<float> data(bpFloats000->SelectionSize());
+ bpReader.GetSync(*bpFloats000, data.data());
+
+ std::cout << "Data timestep " << bpFloats000->m_StepsStart
+ << " from rank " << rank << "\n";
+ for (const auto datum : data)
+ {
+ std::cout << datum << " ";
+ }
+ std::cout << "\n";
}
-
- // template type is optional, but recommended
- for (unsigned int v = 0; v < variablesSize; ++v)
+ else
{
- myFloats[0] = static_cast<float>(v + timeStep);
- bpWriter.PutSync(*bpFloats[v], myFloats.data());
+ std::cout << "Variable bpFloats000 not found\n";
}
- const std::string myString(
- "Hello from rank: " + std::to_string(rank) + " and timestep: " +
- std::to_string(timeStep));
-
- bpWriter.PutSync(bpString, myString);
-
- bpWriter.EndStep();
+ bpReader.Close();
+ //}
}
-
- bpWriter.Close();
}
catch (std::invalid_argument &e)
{
diff --git a/source/adios2/ADIOSMacros.h b/source/adios2/ADIOSMacros.h
index d95c2fab7c50a05c161641cd119e2e4435510fac..0d002d332d5702a107da96a6d8ef614193adf03c 100644
--- a/source/adios2/ADIOSMacros.h
+++ b/source/adios2/ADIOSMacros.h
@@ -70,6 +70,27 @@
MACRO(std::complex<double>) \
MACRO(std::complex<long double>)
+#define ADIOS2_FOREACH_CHAR_TYPE_1ARG(MACRO) \
+ MACRO(char) \
+ MACRO(signed char) \
+ MACRO(unsigned char)
+
+#define ADIOS2_FOREACH_NUMERIC_TYPE_1ARG(MACRO) \
+ MACRO(short) \
+ MACRO(unsigned short) \
+ MACRO(int) \
+ MACRO(unsigned int) \
+ MACRO(long int) \
+ MACRO(long long int) \
+ MACRO(unsigned long int) \
+ MACRO(unsigned long long int) \
+ MACRO(float) \
+ MACRO(double) \
+ MACRO(long double) \
+ MACRO(std::complex<float>) \
+ MACRO(std::complex<double>) \
+ MACRO(std::complex<long double>)
+
#define ADIOS2_FOREACH_ZFP_TYPE_1ARG(MACRO) \
MACRO(int32_t) \
MACRO(int64_t) \
diff --git a/source/adios2/core/ADIOS.h b/source/adios2/core/ADIOS.h
index 0b00c1da889334b34e0557ee662465fcd81a1795..dc093d31f1696f68d35bfbcde6f239a4f589b59b 100644
--- a/source/adios2/core/ADIOS.h
+++ b/source/adios2/core/ADIOS.h
@@ -2,8 +2,7 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * ADIOS.h : ADIOS library starting point, factory class for IO and
- * (polymorphic) Engines
+ * ADIOS.h : ADIOS library starting point, factory class for IO objects
* Created on: Oct 3, 2016
* Author: William F Godoy godoywf@ornl.gov
*/
@@ -107,11 +106,18 @@ public:
* @param name must be unique for each operator created with DefineOperator
* @param type from derived class
* @param parameters optional parameters
- * @return
+ * @return reference to Operator object
*/
Operator &DefineOperator(const std::string name, const std::string type,
const Params ¶meters = Params());
+ /**
+ * Signature for passing Callback functions as operators
+ * @param name unique operator name
+ * @param function callable function
+ * @param parameters
+ * @return reference to Operator object
+ */
template <class R, class... Args>
Operator &DefineOperator(const std::string name,
const std::function<R(Args...)> &function,
diff --git a/source/adios2/core/IO.cpp b/source/adios2/core/IO.cpp
index f780868b54439aa4e510524fadab13ceb43ce985..b4b0abf4537989875dee1ecc43a1a09b8b79fb8f 100644
--- a/source/adios2/core/IO.cpp
+++ b/source/adios2/core/IO.cpp
@@ -173,6 +173,26 @@ std::map<std::string, Params> IO::GetAvailableVariables() noexcept
if (type == "compound")
{
}
+// TODO : enable string, add dimensions
+#define declare_template_instantiation(C) \
+ else if (type == GetType<C>()) \
+ { \
+ Variable<C> &variable = *InquireVariable<C>(name); \
+ \
+ const int min = static_cast<int>(variable.m_Min); \
+ variablesInfo[name]["Min"] = std::to_string(min); \
+ \
+ const int max = static_cast<int>(variable.m_Max); \
+ variablesInfo[name]["Max"] = std::to_string(max); \
+ \
+ variablesInfo[name]["StepsStart"] = \
+ std::to_string(variable.m_AvailableStepsStart); \
+ variablesInfo[name]["StepsCount"] = \
+ std::to_string(variable.m_AvailableStepsCount); \
+ }
+ ADIOS2_FOREACH_CHAR_TYPE_1ARG(declare_template_instantiation)
+#undef declare_template_instantiation
+
#define declare_template_instantiation(T) \
else if (type == GetType<T>()) \
{ \
@@ -188,10 +208,10 @@ std::map<std::string, Params> IO::GetAvailableVariables() noexcept
variablesInfo[name]["StepsCount"] = \
std::to_string(variable.m_AvailableStepsCount); \
}
- ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
+ ADIOS2_FOREACH_NUMERIC_TYPE_1ARG(declare_template_instantiation)
#undef declare_template_instantiation
}
- // TODO: add dimensions
+
return variablesInfo;
}
diff --git a/source/adios2/engine/bp/BPFileReader.cpp b/source/adios2/engine/bp/BPFileReader.cpp
index 207505d2932e2a10414e62e048c1c45a285cc94e..6900ccd06eda7f8a30d78db3da3b290c4d30401d 100644
--- a/source/adios2/engine/bp/BPFileReader.cpp
+++ b/source/adios2/engine/bp/BPFileReader.cpp
@@ -8,6 +8,8 @@
* Author: William F Godoy godoywf@ornl.gov
*/
+#include <iostream> //TODO will go away
+
#include "BPFileReader.h"
#include "BPFileReader.tcc"
@@ -27,8 +29,9 @@ BPFileReader::BPFileReader(IO &io, const std::string &name, const Mode mode,
void BPFileReader::PerformGets()
{
- const auto variablesSubFileInfo =
+ const std::map<std::string, SubFileInfoMap> variablesSubfileInfo =
m_BP3Deserializer.PerformGetsVariablesSubFileInfo(m_IO);
+ ReadVariables(m_IO, variablesSubfileInfo);
}
void BPFileReader::Close(const int transportIndex)
@@ -89,8 +92,7 @@ void BPFileReader::InitBuffer()
fileSize);
}
// broadcast buffer to all ranks from zero
- m_BP3Deserializer.m_Metadata.m_Buffer =
- BroadcastVector(m_BP3Deserializer.m_Metadata.m_Buffer, m_MPIComm);
+ BroadcastVector(m_BP3Deserializer.m_Metadata.m_Buffer, m_MPIComm);
// fills IO with Variables and Attributes
m_BP3Deserializer.ParseMetadata(m_IO);
@@ -127,13 +129,14 @@ void BPFileReader::ReadVariables(
for (const auto &subFileIndexPair : variableNamePair.second)
{
const size_t subFileIndex = subFileIndexPair.first;
- const std::string subFile(
- m_BP3Deserializer.GetBPSubFileName(m_Name, subFileIndex));
if (m_SubFileManager.m_Transports.count(subFileIndex) == 0)
{
- m_SubFileManager.OpenFiles({subFile}, adios2::Mode::Read,
- {{{"transport", "File"}}}, profile);
+ const std::string subFile(
+ m_BP3Deserializer.GetBPSubFileName(m_Name, subFileIndex));
+
+ m_SubFileManager.OpenFileID(subFile, subFileIndex, Mode::Read,
+ {{"transport", "File"}}, profile);
}
for (const auto &stepPair : subFileIndexPair.second) // step
diff --git a/source/adios2/helper/adiosMPIFunctions.h b/source/adios2/helper/adiosMPIFunctions.h
index 0e4ebe68b7905707e190bcf33e82d5cd94f7b194..81a5562f6b42d6f050acdfdc0008056b838695b4 100644
--- a/source/adios2/helper/adiosMPIFunctions.h
+++ b/source/adios2/helper/adiosMPIFunctions.h
@@ -25,8 +25,8 @@ template <class T>
T BroadcastValue(const T &input, MPI_Comm mpiComm, const int rankSource = 0);
template <class T>
-std::vector<T> BroadcastVector(const std::vector<T> &input, MPI_Comm mpiComm,
- const int rankSource = 0);
+void BroadcastVector(std::vector<T> &vector, MPI_Comm mpiComm,
+ const int rankSource = 0);
template <class T>
T ReduceValues(const T source, MPI_Comm mpiComm, MPI_Op operation = MPI_SUM,
diff --git a/source/adios2/helper/adiosMPIFunctions.tcc b/source/adios2/helper/adiosMPIFunctions.tcc
index a312d13335e80ec7267475bc5342e4eda9cc01ae..6bbf28df0886e482f01915d35d57fab9ea276a1a 100644
--- a/source/adios2/helper/adiosMPIFunctions.tcc
+++ b/source/adios2/helper/adiosMPIFunctions.tcc
@@ -105,56 +105,29 @@ unsigned long long int ReduceValues(const unsigned long long int source,
// BroadcastVector specializations
template <>
-std::vector<char> BroadcastVector(const std::vector<char> &input,
- MPI_Comm mpiComm, const int rankSource)
+void BroadcastVector(std::vector<char> &vector, MPI_Comm mpiComm,
+ const int rankSource)
{
- // First Broadcast the size, then the contents
- size_t inputSize = BroadcastValue(input.size(), mpiComm, rankSource);
- int rank;
- MPI_Comm_rank(mpiComm, &rank);
- std::vector<char> output;
+ int size;
+ MPI_Comm_size(mpiComm, &size);
- if (rank == rankSource)
+ if (size == 1)
{
- MPI_Bcast(const_cast<char *>(input.data()), static_cast<int>(inputSize),
- MPI_CHAR, rankSource, mpiComm);
- return input; // no copy
- }
- else
- {
- output.resize(inputSize);
- MPI_Bcast(output.data(), static_cast<int>(inputSize), MPI_CHAR,
- rankSource, mpiComm);
+ return;
}
- return output;
-}
-
-template <>
-std::vector<size_t> BroadcastVector(const std::vector<size_t> &input,
- MPI_Comm mpiComm, const int rankSource)
-{
// First Broadcast the size, then the contents
- size_t inputSize = BroadcastValue(input.size(), mpiComm, rankSource);
+ size_t inputSize = BroadcastValue(vector.size(), mpiComm, rankSource);
int rank;
MPI_Comm_rank(mpiComm, &rank);
- std::vector<size_t> output;
- if (rank == rankSource)
+ if (rank != rankSource)
{
- MPI_Bcast(const_cast<size_t *>(input.data()),
- static_cast<int>(inputSize), ADIOS2_MPI_SIZE_T, rankSource,
- mpiComm);
- return input; // no copy in rankSource
- }
- else
- {
- output.resize(inputSize);
- MPI_Bcast(output.data(), static_cast<int>(inputSize), ADIOS2_MPI_SIZE_T,
- rankSource, mpiComm);
+ vector.resize(inputSize);
}
- return output;
+ MPI_Bcast(vector.data(), static_cast<int>(inputSize), MPI_CHAR, rankSource,
+ mpiComm);
}
// GatherArrays specializations
diff --git a/source/adios2/helper/adiosMath.cpp b/source/adios2/helper/adiosMath.cpp
index 5ee06cd03ec323d8c26e2273faf260409e055e5e..79c3a2bdbc5b9e7aa84d008764c95dc0bca37aba 100644
--- a/source/adios2/helper/adiosMath.cpp
+++ b/source/adios2/helper/adiosMath.cpp
@@ -135,10 +135,10 @@ Box<Dims> IntersectionBox(const Box<Dims> &box1, const Box<Dims> &box2) noexcept
}
size_t LinearIndex(const Box<Dims> &localBox, const Dims &point,
- const bool isRowMajor, const bool isZeroIndex) noexcept
+ const bool isRowMajor) noexcept
{
- auto lf_RowZero = [](const Dims &count,
- const Dims &normalizedPoint) -> size_t {
+ auto lf_RowMajor = [](const Dims &count,
+ const Dims &normalizedPoint) -> size_t {
const size_t countSize = count.size();
size_t linearIndex = 0;
@@ -154,8 +154,8 @@ size_t LinearIndex(const Box<Dims> &localBox, const Dims &point,
return linearIndex;
};
- auto lf_ColumnOne = [](const Dims &count,
- const Dims &normalizedPoint) -> size_t {
+ auto lf_ColumnMajor = [](const Dims &count,
+ const Dims &normalizedPoint) -> size_t {
const size_t countSize = count.size();
size_t linearIndex = 0;
@@ -164,10 +164,10 @@ size_t LinearIndex(const Box<Dims> &localBox, const Dims &point,
for (size_t p = 1; p < countSize; ++p)
{
- linearIndex += (normalizedPoint[countSize - p] - 1) * product;
+ linearIndex += (normalizedPoint[countSize - p]) * product;
product /= count[countSize - p];
}
- linearIndex += (normalizedPoint[0] - 1); // fastest
+ linearIndex += normalizedPoint[0]; // fastest
return linearIndex;
};
@@ -190,13 +190,13 @@ size_t LinearIndex(const Box<Dims> &localBox, const Dims &point,
size_t linearIndex = MaxSizeT - 1;
- if (isRowMajor && isZeroIndex)
+ if (isRowMajor)
{
- linearIndex = lf_RowZero(count, normalizedPoint);
+ linearIndex = lf_RowMajor(count, normalizedPoint);
}
- else if (!isRowMajor && !isZeroIndex)
+ else
{
- linearIndex = lf_ColumnOne(count, normalizedPoint);
+ linearIndex = lf_ColumnMajor(count, normalizedPoint);
}
return linearIndex;
diff --git a/source/adios2/helper/adiosMath.h b/source/adios2/helper/adiosMath.h
index d8dd481fc6498e0bfe55db8f411273caf4d71395..f5ab4bf9d2f2158606ac3a0e2123bbdcaa7d1d5d 100644
--- a/source/adios2/helper/adiosMath.h
+++ b/source/adios2/helper/adiosMath.h
@@ -128,7 +128,7 @@ Box<Dims> IntersectionBox(const Box<Dims> &box1,
* @return linear index for contiguous memory
*/
size_t LinearIndex(const Box<Dims> &localBox, const Dims &point,
- const bool isRowMajor, const bool isZeroIndex) noexcept;
+ const bool isRowMajor) noexcept;
} // end namespace adios2
diff --git a/source/adios2/toolkit/format/bp3/BP3Base.h b/source/adios2/toolkit/format/bp3/BP3Base.h
index a5d5d0c72d91f81df53237432972b87cffc798b0..45bf3174e62fa95f2ce23eaf8e1052ce0fd1086a 100644
--- a/source/adios2/toolkit/format/bp3/BP3Base.h
+++ b/source/adios2/toolkit/format/bp3/BP3Base.h
@@ -208,9 +208,7 @@ protected:
const bool m_DebugMode = false;
/** from host language in data information */
- bool m_IsRowMajor = true; // C, C++ defaults
- /** from host language in data information */
- bool m_IsZeroIndex = true; // C, C++
+ bool m_IsRowMajor = true;
/** method type for file I/O */
enum IO_METHOD
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp b/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
index eae06acfce6613456a578a10ec237559ccc739cf..47f680981fb3dc73a1964f1808f15bdcc30c18e9 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.cpp
@@ -117,14 +117,14 @@ void BP3Deserializer::ParsePGIndex()
position = m_Minifooter.PGIndexStart;
m_MetadataSet.DataPGCount = ReadValue<uint64_t>(buffer, position);
- position += 10; // skipping lengths
- position += 2 + ReadValue<uint16_t>(buffer, position); // skipping name
+ position += 10; // skipping lengths
+ const uint16_t nameLength = ReadValue<uint16_t>(buffer, position);
+ position += static_cast<size_t>(nameLength); // skipping name
const char isFortran = ReadValue<char>(buffer, position);
if (isFortran == 'y')
{
m_IsRowMajor = false;
- m_IsZeroIndex = false;
}
}
@@ -141,7 +141,7 @@ void BP3Deserializer::ParseVariablesIndex(IO &io)
case (type_byte):
{
- DefineVariableInIO<char>(header, io, buffer, position);
+ DefineVariableInIO<signed char>(header, io, buffer, position);
break;
}
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.h b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
index 01f829dcbd53d30a875d831b988f9ecff5a8c50f..b81107c04ce05ef9b01775ce086b9d8c86511e5a 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.h
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.h
@@ -99,7 +99,7 @@ private:
* @param intersectionBox
*/
template <class T>
- void ClipContiguousMemoryCommonRowZero(
+ void ClipContiguousMemoryCommonRow(
Variable<T> &variable, const std::vector<char> &contiguousMemory,
const Box<Dims> &blockBox, const Box<Dims> &intersectionBox) const;
@@ -111,7 +111,7 @@ private:
* @param intersectionBox
*/
template <class T>
- void ClipContiguousMemoryCommonColumnOne(
+ void ClipContiguousMemoryCommonColumn(
Variable<T> &variable, const std::vector<char> &contiguousMemory,
const Box<Dims> &blockBox, const Box<Dims> &intersectionBox) const;
};
diff --git a/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc b/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
index 8e90253eef67ff1ceaae5495ca08caf74dd0aa9b..31600629260a90b5c282f11364499d77d28b13cc 100644
--- a/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
+++ b/source/adios2/toolkit/format/bp3/BP3Deserializer.tcc
@@ -84,10 +84,7 @@ void BP3Deserializer::DefineVariableInIO(const ElementIndexHeader &header,
position = initialPosition;
- size_t currentStep = 1;
-
- std::vector<size_t> subsetPositions; // per step
- subsetPositions.reserve(1); // expecting one subset per step
+ size_t currentStep = 0; // Starts at 1 in bp file
while (position < endPosition)
{
@@ -100,14 +97,6 @@ void BP3Deserializer::DefineVariableInIO(const ElementIndexHeader &header,
buffer, position, static_cast<DataTypes>(header.DataType),
false);
- if (subsetCharacteristics.Statistics.Step > currentStep)
- {
- currentStep = subsetCharacteristics.Statistics.Step;
- variable->m_IndexStepBlockStarts[currentStep] = subsetPositions;
- ++variable->m_AvailableStepsCount;
- subsetPositions.clear();
- }
-
if (subsetCharacteristics.Statistics.Min < variable->m_Min)
{
variable->m_Min = subsetCharacteristics.Statistics.Min;
@@ -118,14 +107,14 @@ void BP3Deserializer::DefineVariableInIO(const ElementIndexHeader &header,
variable->m_Max = subsetCharacteristics.Statistics.Max;
}
- subsetPositions.push_back(subsetPosition);
- position = subsetPosition + subsetCharacteristics.EntryLength + 5;
-
- if (position == endPosition) // check if last one
+ if (subsetCharacteristics.Statistics.Step > currentStep)
{
- variable->m_IndexStepBlockStarts[currentStep] = subsetPositions;
- break;
+ currentStep = subsetCharacteristics.Statistics.Step;
+ variable->m_AvailableStepsCount =
+ subsetCharacteristics.Statistics.Step;
}
+ variable->m_IndexStepBlockStarts[currentStep].push_back(subsetPosition);
+ position = subsetPosition + subsetCharacteristics.EntryLength + 5;
}
}
@@ -178,13 +167,13 @@ BP3Deserializer::GetSubFileInfo(const Variable<T> &variable) const
info.Seeks.first =
blockCharacteristics.Statistics.PayloadOffset +
LinearIndex(info.BlockBox, info.IntersectionBox.first,
- m_IsRowMajor, m_IsZeroIndex) *
+ m_IsRowMajor) *
sizeof(T);
info.Seeks.second =
blockCharacteristics.Statistics.PayloadOffset +
(LinearIndex(info.BlockBox, info.IntersectionBox.second,
- m_IsRowMajor, m_IsZeroIndex) +
+ m_IsRowMajor) +
1) *
sizeof(T);
@@ -217,20 +206,20 @@ void BP3Deserializer::ClipContiguousMemoryCommon(
return;
}
- if (m_IsRowMajor && m_IsZeroIndex) // C, C++, Python
+ if (m_IsRowMajor) // stored with C, C++, Python
{
- ClipContiguousMemoryCommonRowZero(variable, contiguousMemory, blockBox,
- intersectionBox);
+ ClipContiguousMemoryCommonRow(variable, contiguousMemory, blockBox,
+ intersectionBox);
}
- else if (!m_IsRowMajor && !m_IsZeroIndex) // Fortran, R
+ else // stored with Fortran, R
{
- ClipContiguousMemoryCommonColumnOne(variable, contiguousMemory,
- blockBox, intersectionBox);
+ ClipContiguousMemoryCommonColumn(variable, contiguousMemory, blockBox,
+ intersectionBox);
}
}
template <class T>
-void BP3Deserializer::ClipContiguousMemoryCommonRowZero(
+void BP3Deserializer::ClipContiguousMemoryCommonRow(
Variable<T> &variable, const std::vector<char> &contiguousMemory,
const Box<Dims> &blockBox, const Box<Dims> &intersectionBox) const
{
@@ -247,17 +236,17 @@ void BP3Deserializer::ClipContiguousMemoryCommonRowZero(
bool run = true;
const size_t intersectionStart =
- LinearIndex(blockBox, intersectionBox.first, true, true) * sizeof(T);
+ LinearIndex(blockBox, intersectionBox.first, true) * sizeof(T);
while (run)
{
// here copy current linear memory between currentPoint and end
const size_t contiguousStart =
- LinearIndex(blockBox, currentPoint, true, true) * sizeof(T) -
+ LinearIndex(blockBox, currentPoint, true) * sizeof(T) -
intersectionStart;
const size_t variableStart =
- LinearIndex(selectionBox, currentPoint, true, true) * sizeof(T);
+ LinearIndex(selectionBox, currentPoint, true) * sizeof(T);
char *rawVariableData = reinterpret_cast<char *>(variable.GetData());
@@ -272,7 +261,7 @@ void BP3Deserializer::ClipContiguousMemoryCommonRowZero(
while (true)
{
++currentPoint[p];
- if (currentPoint[p] > end[p]) // TODO: check end condition
+ if (currentPoint[p] > end[p])
{
if (p == 0)
{
@@ -294,7 +283,7 @@ void BP3Deserializer::ClipContiguousMemoryCommonRowZero(
}
template <class T>
-void BP3Deserializer::ClipContiguousMemoryCommonColumnOne(
+void BP3Deserializer::ClipContiguousMemoryCommonColumn(
Variable<T> &variable, const std::vector<char> &contiguousMemory,
const Box<Dims> &blockBox, const Box<Dims> &intersectionBox) const
{
@@ -311,17 +300,17 @@ void BP3Deserializer::ClipContiguousMemoryCommonColumnOne(
bool run = true;
const size_t intersectionStart =
- LinearIndex(blockBox, intersectionBox.first, false, false) * sizeof(T);
+ LinearIndex(blockBox, intersectionBox.first, false) * sizeof(T);
while (run)
{
// here copy current linear memory between currentPoint and end
const size_t contiguousStart =
- LinearIndex(blockBox, currentPoint, false, false) * sizeof(T) -
+ LinearIndex(blockBox, currentPoint, false) * sizeof(T) -
intersectionStart;
const size_t variableStart =
- LinearIndex(selectionBox, currentPoint, false, false) * sizeof(T);
+ LinearIndex(selectionBox, currentPoint, false) * sizeof(T);
char *rawVariableData = reinterpret_cast<char *>(variable.GetData());
@@ -336,7 +325,7 @@ void BP3Deserializer::ClipContiguousMemoryCommonColumnOne(
while (true)
{
++currentPoint[p];
- if (currentPoint[p] > end[p]) // TODO: check end condition
+ if (currentPoint[p] > end[p])
{
if (p == dimensions - 1)
{
diff --git a/source/adios2/toolkit/transport/file/FileFStream.cpp b/source/adios2/toolkit/transport/file/FileFStream.cpp
index e119c15967a873272dd5bda1c235ee006d20ab93..4f33cd22930067a7a57f39c67e501667f50fff90 100644
--- a/source/adios2/toolkit/transport/file/FileFStream.cpp
+++ b/source/adios2/toolkit/transport/file/FileFStream.cpp
@@ -34,7 +34,8 @@ void FileFStream::Open(const std::string &name, const Mode openMode)
case (Mode::Write):
ProfilerStart("open");
MkDir(m_Name);
- m_FileStream.open(name, std::fstream::out | std::fstream::binary);
+ m_FileStream.open(name, std::fstream::out | std::fstream::binary |
+ std::fstream::trunc);
ProfilerStop("open");
break;
diff --git a/source/adios2/toolkit/transport/file/FilePOSIX.cpp b/source/adios2/toolkit/transport/file/FilePOSIX.cpp
index 903c82992abb595fe8c6963826d43a33a076e3a1..c11b56824f89485aae66830b22912a10139f1230 100644
--- a/source/adios2/toolkit/transport/file/FilePOSIX.cpp
+++ b/source/adios2/toolkit/transport/file/FilePOSIX.cpp
@@ -49,7 +49,8 @@ void FilePOSIX::Open(const std::string &name, const Mode openMode)
case (Mode::Write):
ProfilerStart("open");
MkDir(m_Name);
- m_FileDescriptor = open(m_Name.c_str(), O_WRONLY | O_CREAT, 0777);
+ m_FileDescriptor =
+ open(m_Name.c_str(), O_WRONLY | O_CREAT | O_TRUNC, 0777);
ProfilerStop("open");
break;
diff --git a/source/adios2/toolkit/transportman/TransportMan.cpp b/source/adios2/toolkit/transportman/TransportMan.cpp
index 21ed6773e81bb507543011f4b4bc9db6bf807843..4505a3b28d73fee972b689d3a3750e53bdc62542 100644
--- a/source/adios2/toolkit/transportman/TransportMan.cpp
+++ b/source/adios2/toolkit/transportman/TransportMan.cpp
@@ -54,12 +54,12 @@ void TransportMan::OpenFiles(const std::vector<std::string> &fileNames,
}
}
-void TransportMan::OpenFileID(const std::string &name, const unsigned int id,
- const Mode openMode, const Params ¶meters,
+void TransportMan::OpenFileID(const std::string &name, const size_t id,
+ const Mode mode, const Params ¶meters,
const bool profile)
{
std::shared_ptr<Transport> file =
- OpenFileTransport(name, openMode, parameters, profile);
+ OpenFileTransport(name, mode, parameters, profile);
m_Transports.insert({id, file});
}
diff --git a/source/adios2/toolkit/transportman/TransportMan.h b/source/adios2/toolkit/transportman/TransportMan.h
index a305236a7191576159dc55904bd9edf26ef54173..2b7f51f7269a3f8db02581966a06ac266c7c2b91 100644
--- a/source/adios2/toolkit/transportman/TransportMan.h
+++ b/source/adios2/toolkit/transportman/TransportMan.h
@@ -61,9 +61,16 @@ public:
const std::vector<Params> ¶metersVector,
const bool profile);
- void OpenFileID(const std::string &name, const unsigned int id,
- const Mode openMode, const Params ¶meters,
- const bool profile);
+ /**
+ * Used for sub-files defined by index
+ * @param name
+ * @param id
+ * @param openMode
+ * @param parameters
+ * @param profile
+ */
+ void OpenFileID(const std::string &name, const size_t id, const Mode mode,
+ const Params ¶meters, const bool profile);
/**
* Gets each transport base name from either baseName at Open or name
diff --git a/source/utils/bpls2/BPLS2.cpp b/source/utils/bpls2/BPLS2.cpp
index 335444646db3a139ebd28f2018ad9e588fe8e732..3efc634435dbaea05c35eada09423f5ca00b0ea1 100644
--- a/source/utils/bpls2/BPLS2.cpp
+++ b/source/utils/bpls2/BPLS2.cpp
@@ -238,8 +238,8 @@ void BPLS2::ProcessTransport() const
for (const auto &variablePair : variablesMap)
{
const std::string name(variablePair.first);
- const Params ¶meters = variablePair.second;
- const std::string type(parameters.at("Type"));
+ const Params &variableParameters = variablePair.second;
+ const std::string type(variableParameters.at("Type"));
std::cout << " ";
std::cout << std::left << std::setw(maxTypeSize) << type << " ";
@@ -248,8 +248,8 @@ void BPLS2::ProcessTransport() const
// print min max
if (m_Parameters.count("long") == 1)
{
- std::cout << parameters.at("Min") << " / "
- << parameters.at("Max");
+ std::cout << variableParameters.at("Min") << " / "
+ << variableParameters.at("Max");
}
std::cout << "\n";
}
diff --git a/testing/adios2/engine/bp/CMakeLists.txt b/testing/adios2/engine/bp/CMakeLists.txt
index b70bace799f079f933093208d248d8d9009f17a8..55e8f14ea28d71667e82b61b9d4a7409be11afed 100644
--- a/testing/adios2/engine/bp/CMakeLists.txt
+++ b/testing/adios2/engine/bp/CMakeLists.txt
@@ -3,8 +3,16 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-# MPI versions of the test are not properly implemented at the moment
+add_executable(TestBPWriteReadADIOS2 TestBPWriteReadADIOS2.cpp)
+target_link_libraries(TestBPWriteReadADIOS2 adios2 gtest gtest_main)
+if(ADIOS2_HAVE_MPI)
+ target_link_libraries(TestBPWriteReadADIOS2 MPI::MPI_C)
+ set(extra_test_args EXEC_WRAPPER ${MPIEXEC_COMMAND})
+endif()
+
+gtest_add_tests(TARGET TestBPWriteReadADIOS2 ${extra_test_args})
+
if (ADIOS2_HAVE_ADIOS1)
add_executable(TestBPWriteRead TestBPWriteRead.cpp)
target_link_libraries(TestBPWriteRead adios2 gtest adios1::adios)
@@ -29,8 +37,6 @@ if (ADIOS2_HAVE_ADIOS1)
target_link_libraries(TestBPWriteReadstdio MPI::MPI_C)
target_link_libraries(TestBPWriteReadfstream MPI::MPI_C)
target_link_libraries(TestBPWriteProfilingJSON MPI::MPI_C)
-
- set(extra_test_args EXEC_WRAPPER ${MPIEXEC_COMMAND})
endif()
gtest_add_tests(TARGET TestBPWriteRead ${extra_test_args})
diff --git a/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp b/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1515c2702bb80025c6c436f99bd30ae4ff2135ef
--- /dev/null
+++ b/testing/adios2/engine/bp/TestBPWriteReadADIOS2.cpp
@@ -0,0 +1,912 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ */
+#include <cstdint>
+#include <cstring>
+
+#include <iostream>
+#include <stdexcept>
+
+#include <adios2.h>
+
+#include <gtest/gtest.h>
+
+#include "../SmallTestData.h"
+
+class BPWriteReadTestADIOS2 : public ::testing::Test
+{
+public:
+ BPWriteReadTestADIOS2() = default;
+
+ SmallTestData m_TestData;
+};
+
+//******************************************************************************
+// 1D 1x8 test data
+//******************************************************************************
+
+// ADIOS2 BP write, native ADIOS1 read
+TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead1D8)
+{
+ // Each process would write a 1x8 array and all processes would
+ // form a mpiSize * Nx 1D array
+ const std::string fname("ADIOS2BPWriteRead1D8.bp");
+
+ int mpiRank = 0, mpiSize = 1;
+ // Number of rows
+ const size_t Nx = 8;
+
+ // Number of steps
+ const size_t NSteps = 3;
+
+#ifdef ADIOS2_HAVE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+#endif
+
+// Write test data using BP
+
+#ifdef ADIOS2_HAVE_MPI
+ adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
+#else
+ adios2::ADIOS adios(true);
+#endif
+ {
+ adios2::IO &io = adios.DeclareIO("TestIO");
+
+ // Declare 1D variables (NumOfProcesses * Nx)
+ // The local process' part (start, count) can be defined now or later
+ // before Write().
+ {
+ const adios2::Dims shape{static_cast<size_t>(Nx * mpiSize)};
+ const adios2::Dims start{static_cast<size_t>(Nx * mpiRank)};
+ const adios2::Dims count{Nx};
+
+ auto &var_iString = io.DefineVariable<std::string>("iString");
+ auto &var_i8 = io.DefineVariable<int8_t>("i8", shape, start, count);
+ auto &var_i16 =
+ io.DefineVariable<int16_t>("i16", shape, start, count);
+ auto &var_i32 =
+ io.DefineVariable<int32_t>("i32", shape, start, count);
+ auto &var_i64 =
+ io.DefineVariable<int64_t>("i64", shape, start, count);
+ auto &var_u8 =
+ io.DefineVariable<uint8_t>("u8", shape, start, count);
+ auto &var_u16 =
+ io.DefineVariable<uint16_t>("u16", shape, start, count);
+ auto &var_u32 =
+ io.DefineVariable<uint32_t>("u32", shape, start, count);
+ auto &var_u64 =
+ io.DefineVariable<uint64_t>("u64", shape, start, count);
+ auto &var_r32 =
+ io.DefineVariable<float>("r32", shape, start, count);
+ auto &var_r64 =
+ io.DefineVariable<double>("r64", shape, start, count);
+ }
+
+ // Create the BP Engine
+ io.SetEngine("BPFileWriter");
+
+ io.AddTransport("file");
+
+ // QUESTION: It seems that BPFilterWriter cannot overwrite existing
+ // files
+ // Ex. if you tune Nx and NSteps, the test would fail. But if you clear
+ // the cache in
+ // ${adios2Build}/testing/adios2/engine/bp/ADIOS2BPWriteADIOS1Read1D8.bp.dir,
+ // then it works
+ adios2::Engine &bpWriter = io.Open(fname, adios2::Mode::Write);
+
+ for (size_t step = 0; step < NSteps; ++step)
+ {
+ // Generate test data for each process uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, step, mpiRank, mpiSize);
+
+ // Retrieve the variables that previously went out of scope
+ auto &var_iString = *io.InquireVariable<std::string>("iString");
+ auto &var_i8 = *io.InquireVariable<int8_t>("i8");
+ auto &var_i16 = *io.InquireVariable<int16_t>("i16");
+ auto &var_i32 = *io.InquireVariable<int32_t>("i32");
+ auto &var_i64 = *io.InquireVariable<int64_t>("i64");
+ auto &var_u8 = *io.InquireVariable<uint8_t>("u8");
+ auto &var_u16 = *io.InquireVariable<uint16_t>("u16");
+ auto &var_u32 = *io.InquireVariable<uint32_t>("u32");
+ auto &var_u64 = *io.InquireVariable<uint64_t>("u64");
+ auto &var_r32 = *io.InquireVariable<float>("r32");
+ auto &var_r64 = *io.InquireVariable<double>("r64");
+
+ // Make a 1D selection to describe the local dimensions of the
+ // variable we write and its offsets in the global spaces
+ adios2::Box<adios2::Dims> sel({mpiRank * Nx}, {Nx});
+
+ EXPECT_THROW(var_iString.SetSelection(sel), std::invalid_argument);
+ var_i8.SetSelection(sel);
+ var_i16.SetSelection(sel);
+ var_i32.SetSelection(sel);
+ var_i64.SetSelection(sel);
+ var_u8.SetSelection(sel);
+ var_u16.SetSelection(sel);
+ var_u32.SetSelection(sel);
+ var_u64.SetSelection(sel);
+ var_r32.SetSelection(sel);
+ var_r64.SetSelection(sel);
+
+ // Write each one
+ // fill in the variable with values from starting index to
+ // starting index + count
+ bpWriter.BeginStep();
+ bpWriter.PutSync(var_iString, currentTestData.S1);
+ bpWriter.PutSync(var_i8, currentTestData.I8.data());
+ bpWriter.PutSync(var_i16, currentTestData.I16.data());
+ bpWriter.PutSync(var_i32, currentTestData.I32.data());
+ bpWriter.PutSync(var_i64, currentTestData.I64.data());
+ bpWriter.PutSync(var_u8, currentTestData.U8.data());
+ bpWriter.PutSync(var_u16, currentTestData.U16.data());
+ bpWriter.PutSync(var_u32, currentTestData.U32.data());
+ bpWriter.PutSync(var_u64, currentTestData.U64.data());
+ bpWriter.PutSync(var_r32, currentTestData.R32.data());
+ bpWriter.PutSync(var_r64, currentTestData.R64.data());
+ bpWriter.EndStep();
+ }
+
+ // Close the file
+ bpWriter.Close();
+ }
+
+ {
+ adios2::IO &io = adios.DeclareIO("ReadIO");
+
+ adios2::Engine &bpReader = io.Open(fname, adios2::Mode::Read);
+
+ // auto var_iString = io.InquireVariable<std::string>("iString");
+ // ASSERT_NE(var_iString, nullptr);
+ // ASSERT_EQ(var_iString->m_Shape.size(), 0);
+ // ASSERT_EQ(var_iString->m_AvailableStepsCount, NSteps);
+
+ auto var_i8 = io.InquireVariable<int8_t>("i8");
+ ASSERT_NE(var_i8, nullptr);
+ ASSERT_EQ(var_i8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i8->m_Shape[0], mpiSize * Nx);
+
+ auto var_i16 = io.InquireVariable<int16_t>("i16");
+ ASSERT_NE(var_i16, nullptr);
+ ASSERT_EQ(var_i16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i16->m_Shape[0], mpiSize * Nx);
+
+ auto var_i32 = io.InquireVariable<int32_t>("i32");
+ ASSERT_NE(var_i32, nullptr);
+ ASSERT_EQ(var_i32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i32->m_Shape[0], mpiSize * Nx);
+
+ auto var_i64 = io.InquireVariable<int64_t>("i64");
+ ASSERT_NE(var_i64, nullptr);
+ ASSERT_EQ(var_i64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i64->m_Shape[0], mpiSize * Nx);
+
+ auto var_u8 = io.InquireVariable<uint8_t>("u8");
+ ASSERT_NE(var_u8, nullptr);
+ ASSERT_EQ(var_u8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u8->m_Shape[0], mpiSize * Nx);
+
+ auto var_u16 = io.InquireVariable<uint16_t>("u16");
+ ASSERT_NE(var_u16, nullptr);
+ ASSERT_EQ(var_u16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u16->m_Shape[0], mpiSize * Nx);
+
+ auto var_u32 = io.InquireVariable<uint32_t>("u32");
+ ASSERT_NE(var_u32, nullptr);
+ ASSERT_EQ(var_u32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u32->m_Shape[0], mpiSize * Nx);
+
+ auto var_u64 = io.InquireVariable<uint64_t>("u64");
+ ASSERT_NE(var_u64, nullptr);
+ ASSERT_EQ(var_u64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u64->m_Shape[0], mpiSize * Nx);
+
+ auto var_r32 = io.InquireVariable<float>("r32");
+ ASSERT_NE(var_r32, nullptr);
+ ASSERT_EQ(var_r32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r32->m_Shape[0], mpiSize * Nx);
+
+ auto var_r64 = io.InquireVariable<double>("r64");
+ ASSERT_NE(var_r64, nullptr);
+ ASSERT_EQ(var_r64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r64->m_Shape[0], mpiSize * Nx);
+
+ // TODO: other types
+
+ SmallTestData testData;
+ std::vector<char> IString(testData.S1.size());
+ std::array<int8_t, Nx> I8;
+ std::array<int16_t, Nx> I16;
+ std::array<int32_t, Nx> I32;
+ std::array<int64_t, Nx> I64;
+ std::array<uint8_t, Nx> U8;
+ std::array<uint16_t, Nx> U16;
+ std::array<uint32_t, Nx> U32;
+ std::array<uint64_t, Nx> U64;
+ std::array<float, Nx> R32;
+ std::array<double, Nx> R64;
+
+ const adios2::Dims start{mpiRank * Nx};
+ const adios2::Dims count{Nx};
+
+ const adios2::Box<adios2::Dims> sel(start, count);
+
+ var_i8->SetSelection(sel);
+ var_i16->SetSelection(sel);
+ var_i32->SetSelection(sel);
+ var_i64->SetSelection(sel);
+
+ var_u8->SetSelection(sel);
+ var_u16->SetSelection(sel);
+ var_u32->SetSelection(sel);
+ var_u64->SetSelection(sel);
+
+ var_r32->SetSelection(sel);
+ var_r64->SetSelection(sel);
+
+ for (size_t t = 0; t < NSteps; ++t)
+ {
+ var_i8->SetStepSelection({t + 1, 1});
+ var_i16->SetStepSelection({t + 1, 1});
+ var_i32->SetStepSelection({t + 1, 1});
+ var_i64->SetStepSelection({t + 1, 1});
+
+ var_u8->SetStepSelection({t + 1, 1});
+ var_u16->SetStepSelection({t + 1, 1});
+ var_u32->SetStepSelection({t + 1, 1});
+ var_u64->SetStepSelection({t + 1, 1});
+
+ var_r32->SetStepSelection({t + 1, 1});
+ var_r64->SetStepSelection({t + 1, 1});
+
+ // Generate test data for each rank uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, t, mpiRank, mpiSize);
+
+ bpReader.GetDeferred(*var_i8, I8.data());
+ bpReader.GetDeferred(*var_i16, I16.data());
+ bpReader.GetDeferred(*var_i32, I32.data());
+ bpReader.GetDeferred(*var_i64, I64.data());
+
+ bpReader.GetDeferred(*var_u8, U8.data());
+ bpReader.GetDeferred(*var_u16, U16.data());
+ bpReader.GetDeferred(*var_u32, U32.data());
+ bpReader.GetDeferred(*var_u64, U64.data());
+
+ bpReader.GetDeferred(*var_r32, R32.data());
+ bpReader.GetDeferred(*var_r64, R64.data());
+
+ bpReader.PerformGets();
+
+ for (size_t i = 0; i < Nx; ++i)
+ {
+ std::stringstream ss;
+ ss << "t=" << t << " i=" << i << " rank=" << mpiRank;
+ std::string msg = ss.str();
+
+ EXPECT_EQ(I8[i], currentTestData.I8[i]) << msg;
+ EXPECT_EQ(I16[i], currentTestData.I16[i]) << msg;
+ EXPECT_EQ(I32[i], currentTestData.I32[i]) << msg;
+ EXPECT_EQ(I64[i], currentTestData.I64[i]) << msg;
+ EXPECT_EQ(U8[i], currentTestData.U8[i]) << msg;
+ EXPECT_EQ(U16[i], currentTestData.U16[i]) << msg;
+ EXPECT_EQ(U32[i], currentTestData.U32[i]) << msg;
+ EXPECT_EQ(U64[i], currentTestData.U64[i]) << msg;
+ EXPECT_EQ(R32[i], currentTestData.R32[i]) << msg;
+ EXPECT_EQ(R64[i], currentTestData.R64[i]) << msg;
+ }
+ }
+ bpReader.Close();
+ }
+}
+
+//******************************************************************************
+// 2D 2x4 test data
+//******************************************************************************
+
+// ADIOS2 BP write, native ADIOS1 read
+TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead2D2x4)
+{
+ // Each process would write a 2x4 array and all processes would
+ // form a 2D 2 * (numberOfProcess*Nx) matrix where Nx is 4 here
+ const std::string fname("ADIOS2BPWriteRead2D2x4Test.bp");
+
+ int mpiRank = 0, mpiSize = 1;
+ // Number of rows
+ const std::size_t Nx = 4;
+
+ // Number of rows
+ const std::size_t Ny = 2;
+
+ // Number of steps
+ const std::size_t NSteps = 3;
+
+#ifdef ADIOS2_HAVE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+#endif
+
+// Write test data using ADIOS2
+
+#ifdef ADIOS2_HAVE_MPI
+ adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
+#else
+ adios2::ADIOS adios(true);
+#endif
+ {
+ adios2::IO &io = adios.DeclareIO("TestIO");
+
+ // Declare 2D variables (Ny * (NumOfProcesses * Nx))
+ // The local process' part (start, count) can be defined now or later
+ // before Write().
+ {
+ const adios2::Dims shape{Ny, static_cast<size_t>(Nx * mpiSize)};
+ const adios2::Dims start{0, static_cast<size_t>(mpiRank * Nx)};
+ const adios2::Dims count{Ny, Nx};
+
+ auto &var_i8 = io.DefineVariable<int8_t>("i8", shape, start, count);
+ auto &var_i16 =
+ io.DefineVariable<int16_t>("i16", shape, start, count);
+ auto &var_i32 =
+ io.DefineVariable<int32_t>("i32", shape, start, count);
+ auto &var_i64 =
+ io.DefineVariable<int64_t>("i64", shape, start, count);
+ auto &var_u8 =
+ io.DefineVariable<uint8_t>("u8", shape, start, count);
+ auto &var_u16 =
+ io.DefineVariable<uint16_t>("u16", shape, start, count);
+ auto &var_u32 =
+ io.DefineVariable<uint32_t>("u32", shape, start, count);
+ auto &var_u64 =
+ io.DefineVariable<uint64_t>("u64", shape, start, count);
+ auto &var_r32 =
+ io.DefineVariable<float>("r32", shape, start, count);
+ auto &var_r64 =
+ io.DefineVariable<double>("r64", shape, start, count);
+ }
+
+ // Create the BP Engine
+ io.SetEngine("BPFileWriter");
+ io.AddTransport("file");
+
+ adios2::Engine &bpWriter = io.Open(fname, adios2::Mode::Write);
+
+ for (size_t step = 0; step < NSteps; ++step)
+ {
+ // Generate test data for each process uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, step, mpiRank, mpiSize);
+
+ // Retrieve the variables that previously went out of scope
+ auto &var_i8 = *io.InquireVariable<int8_t>("i8");
+ auto &var_i16 = *io.InquireVariable<int16_t>("i16");
+ auto &var_i32 = *io.InquireVariable<int32_t>("i32");
+ auto &var_i64 = *io.InquireVariable<int64_t>("i64");
+ auto &var_u8 = *io.InquireVariable<uint8_t>("u8");
+ auto &var_u16 = *io.InquireVariable<uint16_t>("u16");
+ auto &var_u32 = *io.InquireVariable<uint32_t>("u32");
+ auto &var_u64 = *io.InquireVariable<uint64_t>("u64");
+ auto &var_r32 = *io.InquireVariable<float>("r32");
+ auto &var_r64 = *io.InquireVariable<double>("r64");
+
+ // Make a 2D selection to describe the local dimensions of the
+ // variable we write and its offsets in the global spaces
+ adios2::Box<adios2::Dims> sel(
+ {0, static_cast<size_t>(mpiRank * Nx)}, {Ny, Nx});
+ var_i8.SetSelection(sel);
+ var_i16.SetSelection(sel);
+ var_i32.SetSelection(sel);
+ var_i64.SetSelection(sel);
+ var_u8.SetSelection(sel);
+ var_u16.SetSelection(sel);
+ var_u32.SetSelection(sel);
+ var_u64.SetSelection(sel);
+ var_r32.SetSelection(sel);
+ var_r64.SetSelection(sel);
+
+ // Write each one
+ // fill in the variable with values from starting index to
+ // starting index + count
+ bpWriter.BeginStep();
+ bpWriter.PutSync(var_i8, currentTestData.I8.data());
+ bpWriter.PutSync(var_i16, currentTestData.I16.data());
+ bpWriter.PutSync(var_i32, currentTestData.I32.data());
+ bpWriter.PutSync(var_i64, currentTestData.I64.data());
+ bpWriter.PutSync(var_u8, currentTestData.U8.data());
+ bpWriter.PutSync(var_u16, currentTestData.U16.data());
+ bpWriter.PutSync(var_u32, currentTestData.U32.data());
+ bpWriter.PutSync(var_u64, currentTestData.U64.data());
+ bpWriter.PutSync(var_r32, currentTestData.R32.data());
+ bpWriter.PutSync(var_r64, currentTestData.R64.data());
+ bpWriter.EndStep();
+ }
+
+ // Close the file
+ bpWriter.Close();
+ }
+
+ {
+ adios2::IO &io = adios.DeclareIO("ReadIO");
+
+ adios2::Engine &bpReader = io.Open(fname, adios2::Mode::Read);
+
+ auto var_i8 = io.InquireVariable<int8_t>("i8");
+ ASSERT_NE(var_i8, nullptr);
+ ASSERT_EQ(var_i8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i8->m_Shape[0], Ny);
+ ASSERT_EQ(var_i8->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i16 = io.InquireVariable<int16_t>("i16");
+ ASSERT_NE(var_i16, nullptr);
+ ASSERT_EQ(var_i16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i16->m_Shape[0], Ny);
+ ASSERT_EQ(var_i16->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i32 = io.InquireVariable<int32_t>("i32");
+ ASSERT_NE(var_i32, nullptr);
+ ASSERT_EQ(var_i32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i32->m_Shape[0], Ny);
+ ASSERT_EQ(var_i32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i64 = io.InquireVariable<int64_t>("i64");
+ ASSERT_NE(var_i64, nullptr);
+ ASSERT_EQ(var_i64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i64->m_Shape[0], Ny);
+ ASSERT_EQ(var_i64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u8 = io.InquireVariable<uint8_t>("u8");
+ ASSERT_NE(var_u8, nullptr);
+ ASSERT_EQ(var_u8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u8->m_Shape[0], Ny);
+ ASSERT_EQ(var_u8->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u16 = io.InquireVariable<uint16_t>("u16");
+ ASSERT_NE(var_u16, nullptr);
+ ASSERT_EQ(var_u16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u16->m_Shape[0], Ny);
+ ASSERT_EQ(var_u16->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u32 = io.InquireVariable<uint32_t>("u32");
+ ASSERT_NE(var_u32, nullptr);
+ ASSERT_EQ(var_u32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u32->m_Shape[0], Ny);
+ ASSERT_EQ(var_u32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u64 = io.InquireVariable<uint64_t>("u64");
+ ASSERT_NE(var_u64, nullptr);
+ ASSERT_EQ(var_u64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u64->m_Shape[0], Ny);
+ ASSERT_EQ(var_u64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_r32 = io.InquireVariable<float>("r32");
+ ASSERT_NE(var_r32, nullptr);
+ ASSERT_EQ(var_r32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r32->m_Shape[0], Ny);
+ ASSERT_EQ(var_r32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_r64 = io.InquireVariable<double>("r64");
+ ASSERT_NE(var_r64, nullptr);
+ ASSERT_EQ(var_r64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r64->m_Shape[0], Ny);
+ ASSERT_EQ(var_r64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ // If the size of the array is smaller than the data
+ // the result is weird... double and uint64_t would get
+ // completely garbage data
+ std::array<int8_t, Nx * Ny> I8;
+ std::array<int16_t, Nx * Ny> I16;
+ std::array<int32_t, Nx * Ny> I32;
+ std::array<int64_t, Nx * Ny> I64;
+ std::array<uint8_t, Nx * Ny> U8;
+ std::array<uint16_t, Nx * Ny> U16;
+ std::array<uint32_t, Nx * Ny> U32;
+ std::array<uint64_t, Nx * Ny> U64;
+ std::array<float, Nx * Ny> R32;
+ std::array<double, Nx * Ny> R64;
+
+ const adios2::Dims start{0, static_cast<size_t>(mpiRank * Nx)};
+ const adios2::Dims count{Ny, Nx};
+
+ const adios2::Box<adios2::Dims> sel(start, count);
+
+ var_i8->SetSelection(sel);
+ var_i16->SetSelection(sel);
+ var_i32->SetSelection(sel);
+ var_i64->SetSelection(sel);
+
+ var_u8->SetSelection(sel);
+ var_u16->SetSelection(sel);
+ var_u32->SetSelection(sel);
+ var_u64->SetSelection(sel);
+
+ var_r32->SetSelection(sel);
+ var_r64->SetSelection(sel);
+
+ for (size_t t = 0; t < NSteps; ++t)
+ {
+ var_i8->SetStepSelection({t + 1, 1});
+ var_i16->SetStepSelection({t + 1, 1});
+ var_i32->SetStepSelection({t + 1, 1});
+ var_i64->SetStepSelection({t + 1, 1});
+
+ var_u8->SetStepSelection({t + 1, 1});
+ var_u16->SetStepSelection({t + 1, 1});
+ var_u32->SetStepSelection({t + 1, 1});
+ var_u64->SetStepSelection({t + 1, 1});
+
+ var_r32->SetStepSelection({t + 1, 1});
+ var_r64->SetStepSelection({t + 1, 1});
+
+ bpReader.GetDeferred(*var_i8, I8.data());
+ bpReader.GetDeferred(*var_i16, I16.data());
+ bpReader.GetDeferred(*var_i32, I32.data());
+ bpReader.GetDeferred(*var_i64, I64.data());
+
+ bpReader.GetDeferred(*var_u8, U8.data());
+ bpReader.GetDeferred(*var_u16, U16.data());
+ bpReader.GetDeferred(*var_u32, U32.data());
+ bpReader.GetDeferred(*var_u64, U64.data());
+
+ bpReader.GetDeferred(*var_r32, R32.data());
+ bpReader.GetDeferred(*var_r64, R64.data());
+
+ bpReader.PerformGets();
+
+ // Generate test data for each rank uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, t, mpiRank, mpiSize);
+
+ for (size_t i = 0; i < Nx * Ny; ++i)
+ {
+ std::stringstream ss;
+ ss << "t=" << t << " i=" << i << " rank=" << mpiRank;
+ std::string msg = ss.str();
+
+ EXPECT_EQ(I8[i], currentTestData.I8[i]) << msg;
+ EXPECT_EQ(I16[i], currentTestData.I16[i]) << msg;
+ EXPECT_EQ(I32[i], currentTestData.I32[i]) << msg;
+ EXPECT_EQ(I64[i], currentTestData.I64[i]) << msg;
+ EXPECT_EQ(U8[i], currentTestData.U8[i]) << msg;
+ EXPECT_EQ(U16[i], currentTestData.U16[i]) << msg;
+ EXPECT_EQ(U32[i], currentTestData.U32[i]) << msg;
+ EXPECT_EQ(U64[i], currentTestData.U64[i]) << msg;
+ EXPECT_EQ(R32[i], currentTestData.R32[i]) << msg;
+ EXPECT_EQ(R64[i], currentTestData.R64[i]) << msg;
+ }
+ }
+ bpReader.Close();
+ }
+}
+
+//******************************************************************************
+// 2D 4x2 test data
+//******************************************************************************
+
+TEST_F(BPWriteReadTestADIOS2, ADIOS2BPWriteRead2D4x2)
+{
+ // Each process would write a 4x2 array and all processes would
+ // form a 2D 4 * (NumberOfProcess * Nx) matrix where Nx is 2 here
+ const std::string fname("ADIOS2BPWriteRead2D4x2Test.bp");
+
+ int mpiRank = 0, mpiSize = 1;
+ // Number of rows
+ const std::size_t Nx = 2;
+ // Number of cols
+ const std::size_t Ny = 4;
+
+ // Number of steps
+ const std::size_t NSteps = 3;
+
+#ifdef ADIOS2_HAVE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
+#endif
+
+// Write test data using ADIOS2
+
+#ifdef ADIOS2_HAVE_MPI
+ adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
+#else
+ adios2::ADIOS adios(true);
+#endif
+ {
+ adios2::IO &io = adios.DeclareIO("TestIO");
+
+ // Declare 2D variables (4 * (NumberOfProcess * Nx))
+ // The local process' part (start, count) can be defined now or later
+ // before Write().
+ {
+ adios2::Dims shape{static_cast<unsigned int>(Ny),
+ static_cast<unsigned int>(mpiSize * Nx)};
+ adios2::Dims start{static_cast<unsigned int>(0),
+ static_cast<unsigned int>(mpiRank * Nx)};
+ adios2::Dims count{static_cast<unsigned int>(Ny),
+ static_cast<unsigned int>(Nx)};
+ auto &var_i8 = io.DefineVariable<int8_t>("i8", shape, start, count);
+ auto &var_i16 =
+ io.DefineVariable<int16_t>("i16", shape, start, count);
+ auto &var_i32 =
+ io.DefineVariable<int32_t>("i32", shape, start, count);
+ auto &var_i64 =
+ io.DefineVariable<int64_t>("i64", shape, start, count);
+ auto &var_u8 =
+ io.DefineVariable<uint8_t>("u8", shape, start, count);
+ auto &var_u16 =
+ io.DefineVariable<uint16_t>("u16", shape, start, count);
+ auto &var_u32 =
+ io.DefineVariable<uint32_t>("u32", shape, start, count);
+ auto &var_u64 =
+ io.DefineVariable<uint64_t>("u64", shape, start, count);
+ auto &var_r32 =
+ io.DefineVariable<float>("r32", shape, start, count);
+ auto &var_r64 =
+ io.DefineVariable<double>("r64", shape, start, count);
+ }
+
+ // Create the BP Engine
+ io.SetEngine("BPFileWriter");
+
+ io.AddTransport("file");
+
+ adios2::Engine &bpWriter = io.Open(fname, adios2::Mode::Write);
+
+ for (size_t step = 0; step < NSteps; ++step)
+ {
+ // Generate test data for each process uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, step, mpiRank, mpiSize);
+
+ // Retrieve the variables that previously went out of scope
+ auto &var_i8 = *io.InquireVariable<int8_t>("i8");
+ auto &var_i16 = *io.InquireVariable<int16_t>("i16");
+ auto &var_i32 = *io.InquireVariable<int32_t>("i32");
+ auto &var_i64 = *io.InquireVariable<int64_t>("i64");
+ auto &var_u8 = *io.InquireVariable<uint8_t>("u8");
+ auto &var_u16 = *io.InquireVariable<uint16_t>("u16");
+ auto &var_u32 = *io.InquireVariable<uint32_t>("u32");
+ auto &var_u64 = *io.InquireVariable<uint64_t>("u64");
+ auto &var_r32 = *io.InquireVariable<float>("r32");
+ auto &var_r64 = *io.InquireVariable<double>("r64");
+
+ // Make a 2D selection to describe the local dimensions of the
+ // variable we write and its offsets in the global spaces
+ adios2::Box<adios2::Dims> sel(
+ {0, static_cast<unsigned int>(mpiRank * Nx)}, {Ny, Nx});
+ var_i8.SetSelection(sel);
+ var_i16.SetSelection(sel);
+ var_i32.SetSelection(sel);
+ var_i64.SetSelection(sel);
+ var_u8.SetSelection(sel);
+ var_u16.SetSelection(sel);
+ var_u32.SetSelection(sel);
+ var_u64.SetSelection(sel);
+ var_r32.SetSelection(sel);
+ var_r64.SetSelection(sel);
+
+ // Write each one
+ // fill in the variable with values from starting index to
+ // starting index + count
+ bpWriter.BeginStep();
+ bpWriter.PutSync(var_i8, currentTestData.I8.data());
+ bpWriter.PutSync(var_i16, currentTestData.I16.data());
+ bpWriter.PutSync(var_i32, currentTestData.I32.data());
+ bpWriter.PutSync(var_i64, currentTestData.I64.data());
+ bpWriter.PutSync(var_u8, currentTestData.U8.data());
+ bpWriter.PutSync(var_u16, currentTestData.U16.data());
+ bpWriter.PutSync(var_u32, currentTestData.U32.data());
+ bpWriter.PutSync(var_u64, currentTestData.U64.data());
+ bpWriter.PutSync(var_r32, currentTestData.R32.data());
+ bpWriter.PutSync(var_r64, currentTestData.R64.data());
+ bpWriter.EndStep();
+ }
+
+ // Close the file
+ bpWriter.Close();
+ }
+
+ {
+ adios2::IO &io = adios.DeclareIO("ReadIO");
+
+ adios2::Engine &bpReader = io.Open(fname, adios2::Mode::Read);
+
+ auto var_i8 = io.InquireVariable<int8_t>("i8");
+ ASSERT_NE(var_i8, nullptr);
+ ASSERT_EQ(var_i8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i8->m_Shape[0], Ny);
+ ASSERT_EQ(var_i8->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i16 = io.InquireVariable<int16_t>("i16");
+ ASSERT_NE(var_i16, nullptr);
+ ASSERT_EQ(var_i16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i16->m_Shape[0], Ny);
+ ASSERT_EQ(var_i16->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i32 = io.InquireVariable<int32_t>("i32");
+ ASSERT_NE(var_i32, nullptr);
+ ASSERT_EQ(var_i32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i32->m_Shape[0], Ny);
+ ASSERT_EQ(var_i32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_i64 = io.InquireVariable<int64_t>("i64");
+ ASSERT_NE(var_i64, nullptr);
+ ASSERT_EQ(var_i64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_i64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_i64->m_Shape[0], Ny);
+ ASSERT_EQ(var_i64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u8 = io.InquireVariable<uint8_t>("u8");
+ ASSERT_NE(var_u8, nullptr);
+ ASSERT_EQ(var_u8->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u8->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u8->m_Shape[0], Ny);
+ ASSERT_EQ(var_u8->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u16 = io.InquireVariable<uint16_t>("u16");
+ ASSERT_NE(var_u16, nullptr);
+ ASSERT_EQ(var_u16->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u16->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u16->m_Shape[0], Ny);
+ ASSERT_EQ(var_u16->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u32 = io.InquireVariable<uint32_t>("u32");
+ ASSERT_NE(var_u32, nullptr);
+ ASSERT_EQ(var_u32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u32->m_Shape[0], Ny);
+ ASSERT_EQ(var_u32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_u64 = io.InquireVariable<uint64_t>("u64");
+ ASSERT_NE(var_u64, nullptr);
+ ASSERT_EQ(var_u64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_u64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_u64->m_Shape[0], Ny);
+ ASSERT_EQ(var_u64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_r32 = io.InquireVariable<float>("r32");
+ ASSERT_NE(var_r32, nullptr);
+ ASSERT_EQ(var_r32->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r32->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r32->m_Shape[0], Ny);
+ ASSERT_EQ(var_r32->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ auto var_r64 = io.InquireVariable<double>("r64");
+ ASSERT_NE(var_r64, nullptr);
+ ASSERT_EQ(var_r64->m_ShapeID, adios2::ShapeID::GlobalArray);
+ ASSERT_EQ(var_r64->m_AvailableStepsCount, NSteps);
+ ASSERT_EQ(var_r64->m_Shape[0], Ny);
+ ASSERT_EQ(var_r64->m_Shape[1], static_cast<size_t>(mpiSize * Nx));
+
+ // If the size of the array is smaller than the data
+ // the result is weird... double and uint64_t would get
+ // completely garbage data
+ std::array<int8_t, Nx * Ny> I8;
+ std::array<int16_t, Nx * Ny> I16;
+ std::array<int32_t, Nx * Ny> I32;
+ std::array<int64_t, Nx * Ny> I64;
+ std::array<uint8_t, Nx * Ny> U8;
+ std::array<uint16_t, Nx * Ny> U16;
+ std::array<uint32_t, Nx * Ny> U32;
+ std::array<uint64_t, Nx * Ny> U64;
+ std::array<float, Nx * Ny> R32;
+ std::array<double, Nx * Ny> R64;
+
+ const adios2::Dims start{0, static_cast<size_t>(mpiRank * Nx)};
+ const adios2::Dims count{Ny, Nx};
+
+ const adios2::Box<adios2::Dims> sel(start, count);
+
+ var_i8->SetSelection(sel);
+ var_i16->SetSelection(sel);
+ var_i32->SetSelection(sel);
+ var_i64->SetSelection(sel);
+
+ var_u8->SetSelection(sel);
+ var_u16->SetSelection(sel);
+ var_u32->SetSelection(sel);
+ var_u64->SetSelection(sel);
+
+ var_r32->SetSelection(sel);
+ var_r64->SetSelection(sel);
+
+ for (size_t t = 0; t < NSteps; ++t)
+ {
+ var_i8->SetStepSelection({t + 1, 1});
+ var_i16->SetStepSelection({t + 1, 1});
+ var_i32->SetStepSelection({t + 1, 1});
+ var_i64->SetStepSelection({t + 1, 1});
+
+ var_u8->SetStepSelection({t + 1, 1});
+ var_u16->SetStepSelection({t + 1, 1});
+ var_u32->SetStepSelection({t + 1, 1});
+ var_u64->SetStepSelection({t + 1, 1});
+
+ var_r32->SetStepSelection({t + 1, 1});
+ var_r64->SetStepSelection({t + 1, 1});
+
+ bpReader.GetDeferred(*var_i8, I8.data());
+ bpReader.GetDeferred(*var_i16, I16.data());
+ bpReader.GetDeferred(*var_i32, I32.data());
+ bpReader.GetDeferred(*var_i64, I64.data());
+
+ bpReader.GetDeferred(*var_u8, U8.data());
+ bpReader.GetDeferred(*var_u16, U16.data());
+ bpReader.GetDeferred(*var_u32, U32.data());
+ bpReader.GetDeferred(*var_u64, U64.data());
+
+ bpReader.GetDeferred(*var_r32, R32.data());
+ bpReader.GetDeferred(*var_r64, R64.data());
+
+ bpReader.PerformGets();
+
+ // Generate test data for each rank uniquely
+ SmallTestData currentTestData =
+ generateNewSmallTestData(m_TestData, t, mpiRank, mpiSize);
+
+ for (size_t i = 0; i < Nx * Ny; ++i)
+ {
+ std::stringstream ss;
+ ss << "t=" << t << " i=" << i << " rank=" << mpiRank;
+ std::string msg = ss.str();
+
+ EXPECT_EQ(I8[i], currentTestData.I8[i]) << msg;
+ EXPECT_EQ(I16[i], currentTestData.I16[i]) << msg;
+ EXPECT_EQ(I32[i], currentTestData.I32[i]) << msg;
+ EXPECT_EQ(I64[i], currentTestData.I64[i]) << msg;
+ EXPECT_EQ(U8[i], currentTestData.U8[i]) << msg;
+ EXPECT_EQ(U16[i], currentTestData.U16[i]) << msg;
+ EXPECT_EQ(U32[i], currentTestData.U32[i]) << msg;
+ EXPECT_EQ(U64[i], currentTestData.U64[i]) << msg;
+ EXPECT_EQ(R32[i], currentTestData.R32[i]) << msg;
+ EXPECT_EQ(R64[i], currentTestData.R64[i]) << msg;
+ }
+ }
+ bpReader.Close();
+ }
+}
+
+//******************************************************************************
+// main
+//******************************************************************************
+
+int main(int argc, char **argv)
+{
+#ifdef ADIOS2_HAVE_MPI
+ MPI_Init(nullptr, nullptr);
+#endif
+
+ ::testing::InitGoogleTest(&argc, argv);
+ int result = RUN_ALL_TESTS();
+
+#ifdef ADIOS2_HAVE_MPI
+ MPI_Finalize();
+#endif
+
+ return result;
+}