From a7af19d6eac67eda8a5d30f9e64a8300c3c5a760 Mon Sep 17 00:00:00 2001
From: Norbert Podhorszki <pnorbert@ornl.gov>
Date: Fri, 1 Dec 2017 09:51:19 -0500
Subject: [PATCH] refactor heatTransfer example: read_fileonly/ contains
the file reader examples, read/ contains the streaming version,
writer and reader is using heat.xml config file from the root directory
---
examples/heatTransfer/CMakeLists.txt | 3 +-
examples/heatTransfer/ReadMe.md | 20 ++-
examples/heatTransfer/heat.xml | 84 +++++++++
examples/heatTransfer/read/CMakeLists.txt | 16 +-
examples/heatTransfer/read/PrintDataStep.h | 63 +++++++
examples/heatTransfer/read/heatRead.cpp | 159 ++++++++++++++++++
.../heatTransfer/read_fileonly/CMakeLists.txt | 19 +++
.../{read => read_fileonly}/PrintData.h | 0
.../{read => read_fileonly}/heatRead_a2h5.cpp | 0
.../heatRead_adios1.cpp | 0
.../heatRead_adios2.cpp | 3 +-
11 files changed, 346 insertions(+), 21 deletions(-)
create mode 100644 examples/heatTransfer/heat.xml
create mode 100644 examples/heatTransfer/read/PrintDataStep.h
create mode 100644 examples/heatTransfer/read/heatRead.cpp
create mode 100644 examples/heatTransfer/read_fileonly/CMakeLists.txt
rename examples/heatTransfer/{read => read_fileonly}/PrintData.h (100%)
rename examples/heatTransfer/{read => read_fileonly}/heatRead_a2h5.cpp (100%)
rename examples/heatTransfer/{read => read_fileonly}/heatRead_adios1.cpp (100%)
rename examples/heatTransfer/{read => read_fileonly}/heatRead_adios2.cpp (97%)
diff --git a/examples/heatTransfer/CMakeLists.txt b/examples/heatTransfer/CMakeLists.txt
index f6c932be4..52f9cab1a 100644
--- a/examples/heatTransfer/CMakeLists.txt
+++ b/examples/heatTransfer/CMakeLists.txt
@@ -4,4 +4,5 @@
#------------------------------------------------------------------------------#
add_subdirectory(write)
-add_subdirectory(read)
\ No newline at end of file
+add_subdirectory(read)
+add_subdirectory(read_fileonly)
diff --git a/examples/heatTransfer/ReadMe.md b/examples/heatTransfer/ReadMe.md
index 639eed4e7..eabafd502 100644
--- a/examples/heatTransfer/ReadMe.md
+++ b/examples/heatTransfer/ReadMe.md
@@ -1,15 +1,21 @@
examples/heatTransfer
Test that 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.
+using finite differences. This examples shows a straight-forward way to hook
+an application to the ADIOS2 library for its IO.
-1. read: illustrates an experimental Read API, uses adios1 underneath
+1. read: illustrates the Read API that allows running the reader either as
-2. write: illustrates the Write API, resulting binaries under build/bin require arguments
+ * 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
- * adios1
- * adios2
+ * adios 1.x
* hdf5
- * phdf5
\ No newline at end of file
+ * phdf5
+
+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.
diff --git a/examples/heatTransfer/heat.xml b/examples/heatTransfer/heat.xml
new file mode 100644
index 000000000..56cd16dbb
--- /dev/null
+++ b/examples/heatTransfer/heat.xml
@@ -0,0 +1,84 @@
+<?xml version="1.0"?>
+<!-- Config XML file fo the
+ - heatTransfer_write_adios2
+ - heatTransfer_read
+ executables in build/bin -->
+
+<adios-config>
+
+ <!--====================================
+ Configuration for the Writer
+ ====================================-->
+
+ <io name="writer">
+ <engine type="BPFileWriter">
+
+ <!-- for vectorized memory operations, make sure your system
+ enables threads-->
+ <parameter key="Threads" value="2"/>
+
+ <!-- Microseconds (default), Milliseconds, Seconds,
+ Minutes, Hours -->
+ <parameter key="ProfileUnits" value="Microseconds"/>
+
+ <!-- XXKb, XXMb, or XXXGb supported, default=16Kb
+ (applications might choose an optimal value) -->
+ <parameter key="InitialBufferSize" value="16Kb"/>
+
+ <!-- XXKb, XXMb, or XXXGb supported, default=Unlimited (until
+ fails), maximum at each time step
+ (applications might choose an optimal value) -->
+ <!-- <parameter key="MaxBufferSize" value="2Gb"/> -->
+
+ <!-- exponential growth factor > 1, default = 1.05
+ 1.05 is good for a few large variables, for many small
+ variables increase the value to 1.5 to 2
+ (optimal value is application dependent)-->
+ <!-- <parameter key="BufferGrowthFactor" value="1.05"/> -->
+
+ </engine>
+
+ <transport type="File">
+
+ <!-- POSIX, stdio (C FILE*), fstream (C++) -->
+ <parameter key="Library" value="POSIX"/>
+
+ <!-- For read/write, Microseconds (default), Milliseconds, Seconds,
+ Minutes, Hours. open/close always in Microseconds -->
+ <parameter key="ProfileUnits" value="Microseconds"/>
+
+ </transport>
+
+ </io>
+
+
+ <!--====================================
+ Configuration for the Reader
+ ====================================-->
+
+ <io name="reader">
+ <engine type="BPFileReader">
+
+ <!-- for vectorized memory operations, make sure your system
+ enables threads-->
+ <parameter key="Threads" value="2"/>
+
+ <!-- Microseconds (default), Milliseconds, Seconds,
+ Minutes, Hours -->
+ <parameter key="ProfileUnits" value="Microseconds"/>
+
+ </engine>
+
+ <transport type="File">
+
+ <!-- POSIX, stdio (C FILE*), fstream (C++) -->
+ <parameter key="Library" value="POSIX"/>
+
+ <!-- For read/write, Microseconds (default), Milliseconds, Seconds,
+ Minutes, Hours. open/close always in Microseconds -->
+ <parameter key="ProfileUnits" value="Microseconds"/>
+
+ </transport>
+
+ </io>
+</adios-config>
diff --git a/examples/heatTransfer/read/CMakeLists.txt b/examples/heatTransfer/read/CMakeLists.txt
index 2a4ff60f7..e3e143b83 100644
--- a/examples/heatTransfer/read/CMakeLists.txt
+++ b/examples/heatTransfer/read/CMakeLists.txt
@@ -4,16 +4,8 @@
#------------------------------------------------------------------------------#
if(ADIOS2_HAVE_MPI)
- add_executable(heatTransfer_read_adios2 heatRead_adios2.cpp PrintData.h)
- target_link_libraries(heatTransfer_read_adios2 adios2 MPI::MPI_C)
-
- if(ADIOS2_HAVE_HDF5)
- add_executable(heatTransfer_read_a2h5 heatRead_a2h5.cpp PrintData.h)
- target_link_libraries(heatTransfer_read_a2h5 adios2 MPI::MPI_C)
- endif()
-
- if(ADIOS2_HAVE_ADIOS1)
- add_executable(heatTransfer_read_adios1 heatRead_adios1.cpp PrintData.h)
- target_link_libraries(heatTransfer_read_adios1 adios1::adios MPI::MPI_C)
- endif()
+ add_executable(heatTransfer_read heatRead.cpp PrintDataStep.h)
+ target_link_libraries(heatTransfer_read adios2 MPI::MPI_C)
+ target_compile_definitions(heatTransfer_read PRIVATE
+ -DDEFAULT_CONFIG=${CMAKE_CURRENT_SOURCE_DIR}/../heat.xml)
endif()
diff --git a/examples/heatTransfer/read/PrintDataStep.h b/examples/heatTransfer/read/PrintDataStep.h
new file mode 100644
index 000000000..17a6a737d
--- /dev/null
+++ b/examples/heatTransfer/read/PrintDataStep.h
@@ -0,0 +1,63 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * PrintData.h
+ *
+ * Created on: Apr 2017
+ * Author: Norbert Podhorszki
+ */
+
+#ifndef PRINTDATASTEP_H_
+#define PRINTDATASTEP_H_
+
+#include <cstdint>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <string>
+
+template <class T>
+void printDataStep(double *xy, T *size, T *offset, int rank, int step)
+{
+ std::ofstream myfile;
+ std::string filename = "data." + std::to_string(rank);
+ if (step == 0)
+ {
+ myfile.open(filename);
+ }
+ else
+ {
+ myfile.open(filename, std::ios::app);
+ }
+ double *data = xy;
+ uint64_t nelems = size[0] * size[1];
+ myfile << "rank=" << rank << " size=" << size[0] << "x" << size[1]
+ << " offsets=" << offset[0] << ":" << offset[1] << " step=" << step
+ << std::endl;
+
+ myfile << " time row columns " << offset[1] << "..."
+ << offset[1] + size[1] - 1 << std::endl;
+ myfile << " ";
+ for (int j = 0; j < size[1]; j++)
+ {
+ myfile << std::setw(9) << offset[1] + j;
+ }
+ myfile << std::endl;
+ myfile << "------------------------------------------------------------"
+ "--\n";
+ for (int i = 0; i < size[0]; i++)
+ {
+ myfile << std::setw(5) << step << std::setw(5) << offset[0] + i;
+ for (int j = 0; j < size[1]; j++)
+ {
+ myfile << std::setw(9) << std::setprecision(2)
+ << data[i * size[1] + j];
+ }
+ myfile << std::endl;
+ }
+ data += nelems;
+ myfile.close();
+}
+
+#endif /* PRINTDATASTEP_H_ */
diff --git a/examples/heatTransfer/read/heatRead.cpp b/examples/heatTransfer/read/heatRead.cpp
new file mode 100644
index 000000000..83bf75b66
--- /dev/null
+++ b/examples/heatTransfer/read/heatRead.cpp
@@ -0,0 +1,159 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * IO_ADIOS2.cpp
+ *
+ * Created on: Nov 2017
+ * Author: Norbert Podhorszki
+ *
+ */
+#include <mpi.h>
+
+#include "adios2.h"
+
+#include <cstdint>
+#include <iomanip>
+#include <iostream>
+#include <math.h>
+#include <memory>
+#include <stdexcept>
+#include <string>
+#include <vector>
+
+#include "PrintDataStep.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)
+
+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.
+ */
+
+ int wrank, wnproc;
+ MPI_Comm_rank(MPI_COMM_WORLD, &wrank);
+ MPI_Comm_size(MPI_COMM_WORLD, &wnproc);
+ MPI_Barrier(MPI_COMM_WORLD);
+
+ const unsigned int color = 2;
+ MPI_Comm mpiReaderComm;
+ MPI_Comm_split(MPI_COMM_WORLD, color, wrank, &mpiReaderComm);
+
+ int rank, nproc;
+ 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())
+ {
+ // 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"}});
+ }
+
+ adios2::Engine &bpReader =
+ bpReaderIO.Open(inputfile, adios2::Mode::Read, mpiReaderComm);
+
+ 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;
+
+ while (true)
+ {
+ adios2::StepStatus status =
+ bpReader.BeginStep(adios2::StepMode::NextAvailable);
+ if (status != adios2::StepStatus::OK)
+ break;
+
+ if (firstStep)
+ {
+ adios2::Variable<unsigned int> *vgndx =
+ bpReaderIO.InquireVariable<unsigned int>("gndx");
+ gndx = vgndx->m_Value;
+ // bpReader.GetSync<unsigned int>("gndx", gndx);
+
+ adios2::Variable<unsigned int> *vgndy =
+ bpReaderIO.InquireVariable<unsigned int>("gndy");
+ gndy = vgndy->m_Value;
+ // bpReader.GetSync<unsigned int>("gndy", gndy);
+
+ if (rank == 0)
+ {
+ std::cout << "gndx = " << gndx << std::endl;
+ std::cout << "gndy = " << gndy << std::endl;
+ }
+
+ // 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)
+ {
+ // last process should read all the rest of columns
+ readsize[1] = gndy - readsize[1] * (nproc - 1);
+ }
+
+ 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;
+ }
+
+ 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;
+ MPI_Finalize();
+ return 0;
+}
diff --git a/examples/heatTransfer/read_fileonly/CMakeLists.txt b/examples/heatTransfer/read_fileonly/CMakeLists.txt
new file mode 100644
index 000000000..46c5a1e35
--- /dev/null
+++ b/examples/heatTransfer/read_fileonly/CMakeLists.txt
@@ -0,0 +1,19 @@
+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+if(ADIOS2_HAVE_MPI)
+ add_executable(heatTransfer_read_fileonly_adios2 heatRead_adios2.cpp PrintData.h)
+ target_link_libraries(heatTransfer_read_fileonly_adios2 adios2 MPI::MPI_C)
+
+ if(ADIOS2_HAVE_HDF5)
+ add_executable(heatTransfer_read_fileonly_a2h5 heatRead_a2h5.cpp PrintData.h)
+ target_link_libraries(heatTransfer_read_fileonly_a2h5 adios2 MPI::MPI_C)
+ endif()
+
+ if(ADIOS2_HAVE_ADIOS1)
+ add_executable(heatTransfer_read_fileonly_adios1 heatRead_adios1.cpp PrintData.h)
+ target_link_libraries(heatTransfer_read_fileonly_adios1 adios1::adios MPI::MPI_C)
+ endif()
+endif()
diff --git a/examples/heatTransfer/read/PrintData.h b/examples/heatTransfer/read_fileonly/PrintData.h
similarity index 100%
rename from examples/heatTransfer/read/PrintData.h
rename to examples/heatTransfer/read_fileonly/PrintData.h
diff --git a/examples/heatTransfer/read/heatRead_a2h5.cpp b/examples/heatTransfer/read_fileonly/heatRead_a2h5.cpp
similarity index 100%
rename from examples/heatTransfer/read/heatRead_a2h5.cpp
rename to examples/heatTransfer/read_fileonly/heatRead_a2h5.cpp
diff --git a/examples/heatTransfer/read/heatRead_adios1.cpp b/examples/heatTransfer/read_fileonly/heatRead_adios1.cpp
similarity index 100%
rename from examples/heatTransfer/read/heatRead_adios1.cpp
rename to examples/heatTransfer/read_fileonly/heatRead_adios1.cpp
diff --git a/examples/heatTransfer/read/heatRead_adios2.cpp b/examples/heatTransfer/read_fileonly/heatRead_adios2.cpp
similarity index 97%
rename from examples/heatTransfer/read/heatRead_adios2.cpp
rename to examples/heatTransfer/read_fileonly/heatRead_adios2.cpp
index f4a595572..a0833fa10 100644
--- a/examples/heatTransfer/read/heatRead_adios2.cpp
+++ b/examples/heatTransfer/read_fileonly/heatRead_adios2.cpp
@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
MPI_Comm_rank(mpiReaderComm, &rank);
MPI_Comm_size(mpiReaderComm, &nproc);
- adios2::ADIOS ad("adios2.xml", mpiReaderComm, adios2::DebugON);
+ adios2::ADIOS ad(mpiReaderComm, adios2::DebugON);
// Define method for engine creation
// 1. Get method def from config file or define new one
@@ -56,6 +56,7 @@ int main(int argc, char *argv[])
// BPFileWriter is the default engine
bpReaderIO.SetEngine("ADIOS1Reader");
bpReaderIO.SetParameters({{"num_threads", "2"}});
+ bpReaderIO.SetParameter("OpenAsFile", "true");
// ISO-POSIX file is the default transport
// Passing parameters to the transport
--
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