diff --git a/examples/solidfluid/solidfluid_read.cpp b/examples/solidfluid/solidfluid_read.cpp
index 7d94ad22ff743c0ff0df52322f3aa75526b4332f..38f0e528737fbc8abf36e0577e9f9900961d6ee0 100644
--- a/examples/solidfluid/solidfluid_read.cpp
+++ b/examples/solidfluid/solidfluid_read.cpp
@@ -12,7 +12,7 @@
#include <string>
#include <vector>
-#include "public/ADIOS.h"
+#include "ADIOS.h"
struct MYDATA {
@@ -26,26 +26,27 @@ struct MYDATA solid, fluid;
MPI_Comm comm=MPI_COMM_WORLD;
int rank, size;
-void read_ckpt (struct MYDATA &solid, struct MYDATA &fluid)
+void read_ckpt (adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid)
{
try {
// Open an input which was written with an expected Method
- // The writing transport method is associated with the group in the XML
+ // The write transport is associated with the group in the XML
// ADIOS pairs that with the corresponding read transport
// "r" is required to indicate we are reading
- adios::ADIOS_INPUT ckptfile( comm, "r", "checkpoint");
- ckptfile.Open("ckpt.bp");
+ int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "r", comm);
+ // We can also manually set the read transport
+ //int ckptfile = adios.Open("checkpoint.bp", adios::READ_METHOD_BP, "r", comm);
// Note: we only see a single step in the input but the checkpoint has
// only one step anyway. This makes this code simple
// simple immediate read of a scalar
- ckptfile.ReadScalar ("solid/NX", &solid.NX);
+ adios.ReadScalar (ckptfile, "solid/NX", &solid.NX);
// solid.NX is filled at this point
// scheduled version of read of another scalar
- ckptfile.ScheduleRead ("fluid/NX", &fluid.NX);
- ckptfile.Read(); // perform reading now
+ adios.ScheduleRead (ckptfile, "fluid/NX", &fluid.NX);
+ adios.Read(ckptfile); // perform reading now
// fluid.NX is filled at this point
solid.t = new double(solid.NX);
@@ -55,13 +56,13 @@ void read_ckpt (struct MYDATA &solid, struct MYDATA &fluid)
fluid.p = std::vector<double>(fluid.NX);
adios::ADIOS_SELECTION_WRITEBLOCK sel(rank);
- ckptfile.ScheduleRead (sel, "solid/temperature", solid.t);
- ckptfile.ScheduleRead (sel, "solid/pressure", solid.p);
- ckptfile.ScheduleRead (sel, "fluid/temperature", fluid.t);
+ adios.ScheduleRead (ckptfile, sel, "solid/temperature", solid.t);
+ adios.ScheduleRead (ckptfile, sel, "solid/pressure", solid.p);
+ adios.ScheduleRead (ckptfile, sel, "fluid/temperature", fluid.t);
// force checking if the allocated space equals to the size of the selection:
- ckptfile.ScheduleRead (sel, "fluid/pressure", fluid.p, fluid.NX*sizeof(double));
- ckptfile.Read(true); // true: blocking read
- ckptfile.Close(); // Should this do Read() if user misses or should we complain?
+ adios.ScheduleRead (ckptfile, sel, "fluid/pressure", fluid.p, fluid.NX*sizeof(double));
+ adios.Read(ckptfile, true); // true: blocking read, which is also default
+ adios.Close(ckptfile); // Should this do Read() if user misses or should we complain?
}
catch ( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
@@ -72,21 +73,20 @@ void read_ckpt (struct MYDATA &solid, struct MYDATA &fluid)
}
}
-void read_solid (struct MYDATA &solid)
+void read_solid (adios::ADIOS adios, struct MYDATA &solid)
{
float timeout_sec = 1.0;
int retval = 0;
- // Open a file for input, no group defined
- // A reading transport should be defined if not file based
- // "r" is required to indicate we are reading
- adios::ADIOS_INPUT solidfile( comm, "r");
try {
- solidfile.Open("solid.bp"); //, ADIOS_LOCKMODE_NONE, timeout_sec);
-
+ // Open a file for input, no group defined
+ // A reading transport should be defined if not file based
+ // "r" is required to indicate we are reading
+ int solidfile = adios.Open("solid.bp", "r", comm); //, ADIOS_LOCKMODE_NONE, timeout_sec);
+ //int solidfile = adios.Open("solid.bp", adios::READ_METHOD_BP, "r", comm);
/* process file here... */
- const adios::ADIOS_VARINFO &v = solidfile.InqVar ("temperature");
+ const adios::ADIOS_VARINFO &v = adios.InqVar (solidfile, "temperature");
v.GetBlockInfo();
printf ("ndim = %d\n", v.ndim);
@@ -103,7 +103,7 @@ void read_solid (struct MYDATA &solid)
start[1] = 0;
count[1] = v.dims[1];
- data = malloc (slice_size * v.dims[1] * 8);
+ auto data = std::make_unique<double[]>(slice_size * v.dims[1] * 8);
adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
@@ -161,7 +161,7 @@ void read_solid (struct MYDATA &solid)
}
}
-void read_fluid (struct MYDATA &fluid)
+void read_fluid (adios::ADIOS adios, struct MYDATA &fluid)
{
float timeout_sec = 1.0;
int retval = 0;
@@ -273,11 +273,11 @@ int main (int argc, char ** argv)
// ADIOS manager object creation. MPI must be initialized
adios::ADIOS adios( "globalArrayXML.xml", comm, true );
- read_ckpt(solid, fluid);
+ read_ckpt(adios, solid, fluid);
- read_solid(solid);
+ read_solid(adios, solid);
- read_fluid(fluid);
+ read_fluid(adios, fluid);
}
catch( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
diff --git a/examples/solidfluid/solidfluid_write.cpp b/examples/solidfluid/solidfluid_write.cpp
index 915061b0f294ba4ec66673ddb06aa5d4d271a414..bf38af63321fbf024c19003b0e36d23e2c9c3a7a 100644
--- a/examples/solidfluid/solidfluid_write.cpp
+++ b/examples/solidfluid/solidfluid_write.cpp
@@ -12,7 +12,7 @@
#include <string>
#include <vector>
-#include "public/ADIOS.h"
+#include "ADIOS.h"
struct MYDATA {
@@ -27,7 +27,7 @@ MPI_Comm comm=MPI_COMM_WORLD;
int rank, size;
-void write_data (adios::ADIOS adios, struct MYDATA &data, ADIOS_OUTPUT &outfile)
+void write_data (adios::ADIOS adios, struct MYDATA &data, unsigned int outfile)
{
adios.Write (outfile, "NX", &data.NX);
adios.Write (outfile, "rank", &rank);
@@ -38,27 +38,27 @@ void write_data (adios::ADIOS adios, struct MYDATA &data, ADIOS_OUTPUT &outfile)
adios.Write (outfile);
}
-void write_ckpt (struct MYDATA &solid, struct MYDATA &fluid, adios::ADIOS_OUTPUT &ckptfile)
+void write_checkpoint (adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid)
{
try {
// Open an output for a Group
// a transport or an engine should be associated with the group
- ckptfile.Open("ckpt.bp");
-
- ckptfile.ScheduleWrite ("solid/NX", &solid.NX);
- ckptfile.ScheduleWrite ("solid/rank", &rank);
- ckptfile.ScheduleWrite ("solid/size", &size);
- ckptfile.ScheduleWrite ("solid/temperature", solid.t);
- ckptfile.ScheduleWrite ("solid/pressure", solid.p);
-
- ckptfile.ScheduleWrite ("fluid/NX", &fluid.NX);
- ckptfile.ScheduleWrite ("fluid/rank", &rank);
- ckptfile.ScheduleWrite ("fluid/size", &size);
- ckptfile.ScheduleWrite ("fluid/temperature", fluid.t);
- ckptfile.ScheduleWrite ("fluid/pressure", fluid.p);
-
- ckptfile.Write();
- ckptfile.Close(); // Should this do Write() if user misses or should we complain?
+ int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
+
+ adios.Write (ckptfile, "solid/NX", &solid.NX);
+ adios.Write (ckptfile, "solid/rank", &rank);
+ adios.Write (ckptfile, "solid/size", &size);
+ adios.Write (ckptfile, "solid/temperature", solid.t);
+ adios.Write (ckptfile, "solid/pressure", solid.p);
+
+ adios.Write (ckptfile, "fluid/NX", &fluid.NX);
+ adios.Write (ckptfile, "fluid/rank", &rank);
+ adios.Write (ckptfile, "fluid/size", &size);
+ adios.Write (ckptfile, "fluid/temperature", fluid.t);
+ adios.Write (ckptfile, "fluid/pressure", fluid.p);
+
+ adios.Write(ckptfile);
+ adios.Close(ckptfile); // Should this do Write() if user misses or should we complain?
}
catch ( std::exception& e ) //need to think carefully how to handle C++ exceptions with MPI to avoid deadlocking
{
@@ -69,7 +69,7 @@ void write_ckpt (struct MYDATA &solid, struct MYDATA &fluid, adios::ADIOS_OUTPUT
}
}
-void write_viz (struct MYDATA &solid, struct MYDATA &fluid, ADIOS_OUTPUT &vizstream)
+void write_viz (adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid, unsigned int vizstream)
{
// This stream is not associated with a group, so we must say for each write which group to use
// The output variable is re-defined inside as <groupname>/<varname>, unless given as third string argument
@@ -87,11 +87,11 @@ void write_viz (struct MYDATA &solid, struct MYDATA &fluid, ADIOS_OUTPUT &vizstr
adios.Write (vizstream, "fluid", "temperature", "temperature", fluid.t);
- vizstream.Write();
+ adios.Write(vizstream); // flushes all data to disk; required operation
vizstream.AdvanceStep();
}
-void compute (struct MYDATA &solid, struct MYDATA &fluid)
+void compute (int it, struct MYDATA &solid, struct MYDATA &fluid)
{
for (int i = 0; i < solid.NX; i++)
{
@@ -129,7 +129,7 @@ int main( int argc, char* argv [] )
// Multiple writes to the same file work as append in this application run
// FIXME: how do we support Update to same step?
- int solidfile = adios.Open("solid", "solid.bp", "a", comm); // "solid" is a method but incidentally also a group
+ int solidfile = adios.Open("solid.bp", "solid", "a", comm); // "solid" is a method but incidentally also a group
// Constructor only creates an object and what is needed there but does not open a stream/file
// It can be used to initialize a staging connection if not declared before
// FIXME: which argument can be post-poned into Open() instead of constructor?
@@ -141,15 +141,14 @@ int main( int argc, char* argv [] )
// "a" will append to an already existing file, "w" would create a new file
// Multiple writes to the same file work as append in this application run
// FIXME: how do we support Update to same step?
- int fluidfile = adios.Open("fluid.bp", "fluid",
- adios::ACCESS_MODE::APPEND, comm);
+ int fluidfile = adios.Open("fluid.bp", "fluid", "a", comm);
- int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
+ //int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
// we do not open this here, but every time when needed in a function
// Another output not associated with a single group, so that we can mix variables to it
//adios:handle vizstream = adios.Open( "stream.bp", comm, "w", "STAGING", "options to staging method");
- adios::handle vizstream = adios.Open( "stream.bp", comm, "w", "groupless");
+ int vizstream = adios.Open( "stream.bp", comm, "w", "groupless");
// This creates an empty group inside, and we can write all kinds of variables to it
@@ -159,16 +158,16 @@ int main( int argc, char* argv [] )
for (int it = 1; it <= 100; it++)
{
- compute (solid, fluid);
+ compute (it, solid, fluid);
- write_data(solid, solidfile);
- write_data(fluid, fluidfile);
+ write_data(adios, solid, solidfile);
+ write_data(adios, fluid, fluidfile);
if (it%10 == 0) {
- write_checkpoint (solid, fluid);
+ write_checkpoint (adios, solid, fluid);
}
- write_viz(solid, fluid, vizstream);
+ write_viz(adios, solid, fluid, vizstream);
MPI_Barrier (comm);
if (rank==0) printf("Timestep %d written\n", it);