From 5fbab031fd479e73e4d4022f115cb644f4b5785e Mon Sep 17 00:00:00 2001
From: Norbert Podhorszki <pnorbert@ornl.gov>
Date: Fri, 1 Dec 2017 19:19:20 -0500
Subject: [PATCH] Refactored heat transfer example. A config file is now
command line argument. Reader's decomposition is also command line argument.
---
examples/heatTransfer/ReadMe.md | 62 +++++++-
examples/heatTransfer/read/CMakeLists.txt | 6 +-
examples/heatTransfer/read/heatRead.cpp | 178 ++++++++++------------
examples/heatTransfer/write/IO_adios2.cpp | 38 ++---
examples/heatTransfer/write/Settings.cpp | 35 ++---
examples/heatTransfer/write/Settings.h | 1 +
examples/heatTransfer/write/main.cpp | 51 ++-----
7 files changed, 177 insertions(+), 194 deletions(-)
diff --git a/examples/heatTransfer/ReadMe.md b/examples/heatTransfer/ReadMe.md
index eabafd502..d7e91df82 100644
--- a/examples/heatTransfer/ReadMe.md
+++ b/examples/heatTransfer/ReadMe.md
@@ -1,21 +1,69 @@
examples/heatTransfer
-Test that solves a 2D Poisson equation for temperature in homogeneous media
+This example solves a 2D Poisson equation for temperature in homogeneous media
using finite differences. This examples shows a straight-forward way to hook
an application to the ADIOS2 library for its IO.
-1. read: illustrates the Read API that allows running the reader either as
-
- * post-mortem to read all output steps
- * in situ to read step by step as the writer outputs them
-
-2. write: illustrates the Write API as well as has implementations of other IO libraries
+1. write: illustrates the Write API as well as has implementations of other IO libraries
* adios 1.x
* hdf5
* phdf5
+2. read: illustrates the Read API that allows running the reader either as
+
+ * post-mortem to read all output steps
+ * in situ to read step by step as the writer outputs them
+ (need to run with a suitable engine)
+
3. read_fileonly: illustrates reading all output steps at once (a single read
statement) into a single contiguous memory block. This approach only works
for post-mortem processing.
+
+
+
+Example
+
+
+1. Produce an output
+
+Writer usage: heatTransfer config output N M nx ny steps iterations
+ config: XML config file to use
+ output: name of output data file/stream
+ N: number of processes in X dimension
+ M: number of processes in Y dimension
+ nx: local array size in X dimension per processor
+ ny: local array size in Y dimension per processor
+ steps: the total number of steps to output
+ iterations: one step consist of this many iterations
+
+$ mpirun -np 12 ./bin/heatTransfer_write_adios2 ../examples/heatTransfer/heat.xml heat 4 3 5 10 10 10
+
+
+2. Read the output step-by-step and print data into text files (data.<rank> per reader process)
+
+Reader Usage: heatRead config input N M
+ config: XML config file to use
+ input: name of input data file/stream
+ N: number of processes in X dimension
+ M: number of processes in Y dimension
+
+
+$ mpirun -np 2 ./bin/heatTransfer_read ../examples/heatTransfer/heat.xml heat 2 1
+
+
+Notes:
+1. Engines for file-based output and post-mortem reading: i
+
+ * BPFileWriter/BPFileReader
+ * HDF5Writer/HDF5Reader
+ * ADIOS1Writer/ADIOS1Reader
+
+2. Engines for in situ execution
+
+ * DataManWriter/DataManReader
+ (Must run writer and reader with the same number of processes and same decomposition)
+
+
+
diff --git a/examples/heatTransfer/read/CMakeLists.txt b/examples/heatTransfer/read/CMakeLists.txt
index e3e143b83..06d36db01 100644
--- a/examples/heatTransfer/read/CMakeLists.txt
+++ b/examples/heatTransfer/read/CMakeLists.txt
@@ -4,7 +4,11 @@
#------------------------------------------------------------------------------#
if(ADIOS2_HAVE_MPI)
- add_executable(heatTransfer_read heatRead.cpp PrintDataStep.h)
+ add_executable(heatTransfer_read
+ heatRead.cpp
+ PrintDataStep.h
+ ReadSettings.cpp
+ )
target_link_libraries(heatTransfer_read adios2 MPI::MPI_C)
target_compile_definitions(heatTransfer_read PRIVATE
-DDEFAULT_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}/../heat.xml)
diff --git a/examples/heatTransfer/read/heatRead.cpp b/examples/heatTransfer/read/heatRead.cpp
index 83bf75b66..1bf2cb0b8 100644
--- a/examples/heatTransfer/read/heatRead.cpp
+++ b/examples/heatTransfer/read/heatRead.cpp
@@ -22,29 +22,26 @@
#include <vector>
#include "PrintDataStep.h"
+#include "ReadSettings.h"
-#define str_helper(X) #X
-#define str(X) str_helper(X)
-#ifndef DEFAULT_CONFIG
-#define DEFAULT_CONFIG "../heat.xml"
-#endif
-#define DEFAULT_CONFIG_STR str(DEFAULT_CONFIG)
+void printUsage()
+{
+ std::cout << "Usage: heatRead config input N M \n"
+ << " config: XML config file to use\n"
+ << " input: name of input data file/stream\n"
+ << " N: number of processes in X dimension\n"
+ << " M: number of processes in Y dimension\n\n";
+}
int main(int argc, char *argv[])
{
MPI_Init(&argc, &argv);
- if (argc < 2)
- {
- std::cout << "Not enough arguments: need an input file\n";
- return 1;
- }
- const char *inputfile = argv[1];
-
- /* World comm spans all applications started with the same aprun command
- on a Cray XK6. So we have to split and create the local
- 'world' communicator for the reader only.
- In normal start-up, the communicator will just equal the MPI_COMM_WORLD.
+ /* When writer and reader is launched together with a single mpirun command,
+ the world comm spans all applications. We have to split and create the
+ local 'world' communicator for the reader only.
+ When writer and reader is launched separately, the mpiReaderComm
+ communicator will just equal the MPI_COMM_WORLD.
*/
int wrank, wnproc;
@@ -60,100 +57,87 @@ int main(int argc, char *argv[])
MPI_Comm_rank(mpiReaderComm, &rank);
MPI_Comm_size(mpiReaderComm, &nproc);
- adios2::ADIOS ad(std::string(DEFAULT_CONFIG_STR), mpiReaderComm,
- adios2::DebugON);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
-
- adios2::IO &bpReaderIO = ad.DeclareIO("reader");
- if (!bpReaderIO.InConfigFile())
+ try
{
- // if not defined by user, we can change the default settings
- // BPFileWriter is the default engine
- bpReaderIO.SetEngine("ADIOS1Reader");
- bpReaderIO.SetParameters({{"num_threads", "2"}});
-
- // ISO-POSIX file output is the default transport (called "File")
- // Passing parameters to the transport
- bpReaderIO.AddTransport("File", {{"verbose", "4"}});
- }
+ ReadSettings settings(argc, argv, rank, nproc);
+ adios2::ADIOS ad(settings.configfile, mpiReaderComm, adios2::DebugON);
- adios2::Engine &bpReader =
- bpReaderIO.Open(inputfile, adios2::Mode::Read, mpiReaderComm);
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
- unsigned int gndx;
- unsigned int gndy;
- double *T;
- adios2::Dims readsize;
- adios2::Dims offset;
- adios2::Variable<double> *vT = nullptr;
- bool firstStep = true;
- int step = 0;
+ adios2::IO &bpReaderIO = ad.DeclareIO("reader");
+ if (!bpReaderIO.InConfigFile())
+ {
+ // if not defined by user, we can change the default settings
+ // BPFileWriter is the default engine
+ bpReaderIO.SetEngine("ADIOS1Reader");
+ bpReaderIO.SetParameters({{"num_threads", "2"}});
+
+ // ISO-POSIX file output is the default transport (called "File")
+ // Passing parameters to the transport
+ bpReaderIO.AddTransport("File", {{"verbose", "4"}});
+ }
- while (true)
- {
- adios2::StepStatus status =
- bpReader.BeginStep(adios2::StepMode::NextAvailable);
- if (status != adios2::StepStatus::OK)
- break;
+ adios2::Engine &bpReader = bpReaderIO.Open(
+ settings.inputfile, adios2::Mode::Read, mpiReaderComm);
- if (firstStep)
- {
- adios2::Variable<unsigned int> *vgndx =
- bpReaderIO.InquireVariable<unsigned int>("gndx");
- gndx = vgndx->m_Value;
- // bpReader.GetSync<unsigned int>("gndx", gndx);
+ double *T;
+ adios2::Variable<double> *vT = nullptr;
+ bool firstStep = true;
+ int step = 0;
- adios2::Variable<unsigned int> *vgndy =
- bpReaderIO.InquireVariable<unsigned int>("gndy");
- gndy = vgndy->m_Value;
- // bpReader.GetSync<unsigned int>("gndy", gndy);
+ while (true)
+ {
+ adios2::StepStatus status =
+ bpReader.BeginStep(adios2::StepMode::NextAvailable);
+ if (status != adios2::StepStatus::OK)
+ break;
- if (rank == 0)
+ if (firstStep)
{
- std::cout << "gndx = " << gndx << std::endl;
- std::cout << "gndy = " << gndy << std::endl;
+ vT = bpReaderIO.InquireVariable<double>("T");
+ unsigned int gndx = vT->m_Shape[0];
+ unsigned int gndy = vT->m_Shape[1];
+
+ if (rank == 0)
+ {
+ std::cout << "gndx = " << gndx << std::endl;
+ std::cout << "gndy = " << gndy << std::endl;
+ }
+
+ settings.DecomposeArray(gndx, gndy);
+ T = new double[settings.readsize[0] * settings.readsize[1]];
+
+ // Create a 2D selection for the subset
+ vT->SetSelection(adios2::Box<adios2::Dims>(settings.offset,
+ settings.readsize));
+ firstStep = false;
+ MPI_Barrier(mpiReaderComm); // sync processes just for stdout
}
- // 1D decomposition of the columns, which is inefficient for
- // reading!
- readsize.push_back(gndx);
- readsize.push_back(gndy / nproc);
- offset.push_back(0LL);
- offset.push_back(rank * readsize[1]);
- if (rank == nproc - 1)
+ if (!rank)
{
- // last process should read all the rest of columns
- readsize[1] = gndy - readsize[1] * (nproc - 1);
+ std::cout << "Processing step " << step << std::endl;
}
-
- std::cout << "rank " << rank << " reads " << readsize[1]
- << " columns from offset " << offset[1] << std::endl;
-
- vT = bpReaderIO.InquireVariable<double>("T");
- T = new double[readsize[0] * readsize[1]];
-
- // Create a 2D selection for the subset
- vT->SetSelection(adios2::Box<adios2::Dims>(offset, readsize));
- firstStep = false;
+ // Arrays are read by scheduling one or more of them
+ // and performing the reads at once
+ bpReader.GetDeferred<double>(*vT, T);
+ bpReader.PerformGets();
+
+ printDataStep(T, settings.readsize.data(), settings.offset.data(),
+ rank, step);
+ bpReader.EndStep();
+ step++;
}
-
- if (!rank)
- {
- std::cout << "Processing step " << step << std::endl;
- }
- // Arrays are read by scheduling one or more of them
- // and performing the reads at once
- bpReader.GetDeferred<double>(*vT, T);
- bpReader.PerformGets();
-
- printDataStep(T, readsize.data(), offset.data(), rank, step);
- bpReader.EndStep();
- step++;
+ bpReader.Close();
+ delete[] T;
}
- bpReader.Close();
- delete[] T;
+ catch (std::invalid_argument &e) // command-line argument errors
+ {
+ std::cout << e.what() << std::endl;
+ printUsage();
+ }
+
MPI_Finalize();
return 0;
}
diff --git a/examples/heatTransfer/write/IO_adios2.cpp b/examples/heatTransfer/write/IO_adios2.cpp
index c0c943c95..e7b877f49 100644
--- a/examples/heatTransfer/write/IO_adios2.cpp
+++ b/examples/heatTransfer/write/IO_adios2.cpp
@@ -34,7 +34,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
// Define method for engine creation
- adios2::IO &bpio = *ad->InquireIO("output");
+ adios2::IO &bpio = ad->DeclareIO("output");
if (!bpio.InConfigFile())
{
// if not defined by user, we can change the default settings
@@ -75,8 +75,6 @@ IO::~IO()
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
-#if 1
-
bpWriter->BeginStep();
/* This selection is redundant and not required, since we defined
* the selection already in DefineVariable(). It is here just as an example.
@@ -87,29 +85,17 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
varT->SetSelection(
adios2::Box<adios2::Dims>({s.offsx, s.offsy}, {s.ndx, s.ndy}));
- /* Select the area that we want to write from the data pointer we pass to
- the
- writer.
- Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
- Engine will copy this bounding box from the data pointer into the output
- buffer.
- Size of the bounding box should match the "space" selection which was
- given
- above.
- Default memspace is always the full selection.
- */
- varT->SetMemorySelection(adios2::Box<adios2::Dims>({1, 1}, {s.ndx, s.ndy}));
-
- bpWriter->PutSync<unsigned int>(*varGndx, s.gndx);
- bpWriter->PutSync<unsigned int>("gndy", s.gndy);
- bpWriter->PutSync<double>(*varT, ht.data_noghost().data());
-
- bpWriter->EndStep();
-
-#else
-
+ if (!step)
+ {
+ int rank;
+ MPI_Comm_rank(comm, &rank);
+ if (!rank)
+ {
+ bpWriter->PutSync<unsigned int>(*varGndx, s.gndx);
+ bpWriter->PutSync<unsigned int>("gndy", s.gndy);
+ }
+ }
bpWriter->PutSync<double>(*varT, ht.data_noghost().data());
+ // bpWriter->PerformPuts();
bpWriter->EndStep();
-
-#endif
}
diff --git a/examples/heatTransfer/write/Settings.cpp b/examples/heatTransfer/write/Settings.cpp
index 616bd2193..fd36fff97 100644
--- a/examples/heatTransfer/write/Settings.cpp
+++ b/examples/heatTransfer/write/Settings.cpp
@@ -35,37 +35,20 @@ static unsigned int convertToUint(std::string varName, char *arg)
Settings::Settings(int argc, char *argv[], int rank, int nproc) : rank{rank}
{
- if (argc < 8)
+ if (argc < 9)
{
throw std::invalid_argument("Not enough arguments");
}
this->nproc = (unsigned int)nproc;
- outputfile = argv[1];
- npx = convertToUint("N", argv[2]);
- npy = convertToUint("M", argv[3]);
- ndx = convertToUint("nx", argv[4]);
- ndy = convertToUint("ny", argv[5]);
- steps = convertToUint("steps", argv[6]);
- iterations = convertToUint("iterations", argv[7]);
-
- if (argc == 9)
- {
- const std::string asyncArg(argv[8]);
- if (asyncArg == "ON" || asyncArg == "on")
- {
- async = true;
- }
- else if (asyncArg == "OFF" || asyncArg == "off")
- {
- // nothing off is default
- }
- else
- {
- throw std::invalid_argument("ERROR: wrong async argument " +
- asyncArg + " must be on or off\n");
- }
- }
+ configfile = argv[1];
+ outputfile = argv[2];
+ npx = convertToUint("N", argv[3]);
+ npy = convertToUint("M", argv[4]);
+ ndx = convertToUint("nx", argv[5]);
+ ndy = convertToUint("ny", argv[6]);
+ steps = convertToUint("steps", argv[7]);
+ iterations = convertToUint("iterations", argv[8]);
if (npx * npy != this->nproc)
{
diff --git a/examples/heatTransfer/write/Settings.h b/examples/heatTransfer/write/Settings.h
index afb30fd29..b32c35bf0 100644
--- a/examples/heatTransfer/write/Settings.h
+++ b/examples/heatTransfer/write/Settings.h
@@ -18,6 +18,7 @@ class Settings
public:
// user arguments
+ std::string configfile;
std::string outputfile;
unsigned int npx; // Number of processes in X (slow) dimension
unsigned int npy; // Number of processes in Y (fast) dimension
diff --git a/examples/heatTransfer/write/main.cpp b/examples/heatTransfer/write/main.cpp
index 826ec2311..030f5d5e4 100644
--- a/examples/heatTransfer/write/main.cpp
+++ b/examples/heatTransfer/write/main.cpp
@@ -12,7 +12,6 @@
*/
#include <mpi.h>
-#include <future> //std::future, std::async
#include <iostream>
#include <memory>
#include <stdexcept>
@@ -24,26 +23,28 @@
void printUsage()
{
- std::cout << "Usage: heatTransfer output N M nx ny steps "
- "iterations async\n"
- << " output: name of output file\n"
+ std::cout << "Usage: heatTransfer config output N M nx ny steps "
+ "iterations\n"
+ << " config: XML config file to use\n"
+ << " output: name of output data file/stream\n"
<< " N: number of processes in X dimension\n"
<< " M: number of processes in Y dimension\n"
<< " nx: local array size in X dimension per processor\n"
<< " ny: local array size in Y dimension per processor\n"
<< " steps: the total number of steps to output\n"
- << " iterations: one step consist of this many iterations\n"
- << " async: on or off (default) \n\n";
+ << " iterations: one step consist of this many iterations\n\n";
}
int main(int argc, char *argv[])
{
MPI_Init(&argc, &argv);
- /* World comm spans all applications started with the same aprun command
- on a Cray XK6. So we have to split and create the local
- 'world' communicator for heat_transfer only.
- In normal start-up, the communicator will just equal the MPI_COMM_WORLD.
- */
+
+ /* When writer and reader is launched together with a single mpirun command,
+ the world comm spans all applications. We have to split and create the
+ local 'world' communicator mpiHeatTransferComm for the writer only.
+ When writer and reader is launched separately, the mpiHeatTransferComm
+ communicator will just equal the MPI_COMM_WORLD.
+ */
int wrank, wnproc;
MPI_Comm_rank(MPI_COMM_WORLD, &wrank);
@@ -71,17 +72,7 @@ int main(int argc, char *argv[])
ht.exchange(mpiHeatTransferComm);
// ht.printT("Heated T:", mpiHeatTransferComm);
- std::future<void> futureWrite;
- if (settings.async)
- {
- futureWrite =
- std::async(std::launch::async, &IO::write, &io, 0, std::ref(ht),
- std::ref(settings), mpiHeatTransferComm);
- }
- else
- {
- io.write(0, ht, settings, mpiHeatTransferComm);
- }
+ io.write(0, ht, settings, mpiHeatTransferComm);
for (unsigned int t = 1; t <= settings.steps; ++t)
{
@@ -94,21 +85,7 @@ int main(int argc, char *argv[])
ht.heatEdges();
}
- if (settings.async)
- {
- futureWrite.get();
- futureWrite = std::async(std::launch::async, &IO::write, &io, t,
- std::ref(ht), std::ref(settings),
- mpiHeatTransferComm);
- }
- else
- {
- io.write(t, ht, settings, mpiHeatTransferComm);
- }
- }
- if (settings.async)
- {
- futureWrite.get();
+ io.write(t, ht, settings, mpiHeatTransferComm);
}
MPI_Barrier(mpiHeatTransferComm);
--
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