diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 4f27787615b8e4604cdeee78ddd67c510ff981c5..cff55b7612dea88c6033417e74a3e199434fde0a 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -5,4 +5,4 @@
add_subdirectory(hello)
add_subdirectory(heatTransfer)
-add_subdirectory(groupless)
+add_subdirectory(experimental)
diff --git a/examples/groupless/CMakeLists.txt b/examples/experimental/CMakeLists.txt
similarity index 82%
rename from examples/groupless/CMakeLists.txt
rename to examples/experimental/CMakeLists.txt
index 5f37a0bb41ec07985f272f2a6f0b06b85e5eebbb..5d46e776b55df9085089e8cc35a5af4304e33310 100644
--- a/examples/groupless/CMakeLists.txt
+++ b/examples/experimental/CMakeLists.txt
@@ -3,4 +3,6 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_subdirectory(multistep)
+if(ADIOS_USE_ADIOS1)
+ add_subdirectory(multistep)
+endif()
diff --git a/examples/groupless/multistep/CMakeLists.txt b/examples/experimental/multistep/CMakeLists.txt
similarity index 100%
rename from examples/groupless/multistep/CMakeLists.txt
rename to examples/experimental/multistep/CMakeLists.txt
diff --git a/examples/groupless/multistep/reader_allsteps.cpp b/examples/experimental/multistep/reader_allsteps.cpp
similarity index 100%
rename from examples/groupless/multistep/reader_allsteps.cpp
rename to examples/experimental/multistep/reader_allsteps.cpp
diff --git a/examples/groupless/multistep/reader_stepping.cpp b/examples/experimental/multistep/reader_stepping.cpp
similarity index 100%
rename from examples/groupless/multistep/reader_stepping.cpp
rename to examples/experimental/multistep/reader_stepping.cpp
diff --git a/examples/groupless/multistep/writer_multistep.cpp b/examples/experimental/multistep/writer_multistep.cpp
similarity index 100%
rename from examples/groupless/multistep/writer_multistep.cpp
rename to examples/experimental/multistep/writer_multistep.cpp
diff --git a/examples/globalArray/globalArrayNoXML.cpp b/examples/globalArray/globalArrayNoXML.cpp
deleted file mode 100644
index aa4a3d5c652118830efb50f840f9ef4178aad773..0000000000000000000000000000000000000000
--- a/examples/globalArray/globalArrayNoXML.cpp
+++ /dev/null
@@ -1,126 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * globalArrayNoXML.cpp
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <mpi.h>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include "adios2/../../include/ADIOS.h"
-
-int main(int argc, char *argv[])
-{
- int rank, size;
- const int NX = 10;
- double t[NX];
- std::vector<double> p(NX);
- MPI_Comm comm = MPI_COMM_WORLD;
-
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
-
- // set a maximum buffersize that ADIOS can use (for one group).
- // multiple groups may use each such buffersize if they are overlapped
- // or
- // use time-aggregation or use zero-copy staging
-
- // Define Group and its variables
- // The group's transport can be defined at runtime in the input XML file
- adios.CreateGroup("arrays");
-
- // Set the maximum buffersize for this group. This must happen before
- // defining a zero copy variable, which will cause the group's internal
- // buffer
- // allocated (during the variable definition call)
- // adios.SetMaxBuffersize ("arrays", 10000000);
-
- adios.CreateVariable("arrays", "NX", "int"); // scalar variable
- adios.CreateVariable("arrays", "size", "int");
- adios.CreateVariable("arrays", "size", "rank");
-
- // define a 2D array with 1D decomposition
- adios.CreateVariable("arrays", "temperature", "double", "1,NX", "NONE",
- "size,NX", "rank,0");
-
- // // set a variable-level transformation for this variable
- // adios.SetVariableTransform ("arrays", "temperature", "none");
-
- adios.CreateVariable("arrays", "pressure", "std::vector<double>",
- "1,NX", "size,NX", "rank,0");
-
- // set a group-level transport
- adios.SetTransport("arrays",
- "time-aggregate"); // no options passed here
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
-
- adios.Open("arrays", "globalArray.bp", "w", 100000000);
-
- for (int it = 1; it <= 13; it++)
- {
-
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
-
- // if (it==1)
- //
- // else
- // adios.Open("arrays", "globalArray.bp", "a",
- // 100000000 );
-
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
-
- adios.Write("arrays", "NX", &NX);
- adios.Write("arrays", "size", &size);
- adios.Write("arrays", "rank", &rank);
- adios.Write("arrays", "temperature", t);
- adios.Write("arrays", "pressure", &p);
-
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
- }
-
- adios.Close("arrays");
-
- MPI_Barrier(comm);
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << e.what() << "\n";
- }
- }
-
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
-}
diff --git a/examples/globalArray/globalArrayNoXML.xml b/examples/globalArray/globalArrayNoXML.xml
deleted file mode 100644
index 87cceeab1b8f3e06b107059797a506182f52fe91..0000000000000000000000000000000000000000
--- a/examples/globalArray/globalArrayNoXML.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<adios-config>
-
- <method group="arrays" method="MPI">ts_buffersize=32000;verbose=4</method>
- <!--
- <method group="arrays" method="MPI_AGGREGATE">num_aggregators=1;num_ost=1</method>
- -->
-
- <buffer max-size-MB="1"/>
-
-</adios-config>
-
diff --git a/examples/globalArray/globalArrayXML.cpp b/examples/globalArray/globalArrayXML.cpp
deleted file mode 100644
index 9ab2027674e73ec31d8a5a1320fbd889f9317b62..0000000000000000000000000000000000000000
--- a/examples/globalArray/globalArrayXML.cpp
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * globalArrayXML.cpp
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <mpi.h>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include "adios2/../../include/ADIOS.h"
-
-int main(int argc, char *argv[])
-{
- int rank, size;
- const int NX = 10;
- double t[NX];
- std::vector<double> p(NX);
- MPI_Comm comm = MPI_COMM_WORLD;
-
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayXML.xml", comm, true);
-
- adios::ADIOS_OUTPUT &ckptfile =
- adios.Open("globalArray.bp", comm, "a", "POSIX");
-
- adios::ADIOS_OUTPUT ckptfile("globalArray.bp", subcomm, "a", "POSIX");
- // adios::ADIOS_OUTPUT *ckptfile = adios.Open( "globalArray.bp",
- // "POSIX");
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
-
- for (int it = 1; it <= 13; it++)
- {
-
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
-
- // if (it==1)
- // adios.Open("arrays", "globalArray.bp", "w");
- // else
- // adios.Open("arrays", "globalArray.bp", "a");
-
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
-
- ckptfile.Write("NX", &NX);
- ckptfile.Write("pressure", &p);
- // adios.Write ("arrays", "NX", &NX);
- // adios.Write ("arrays", "size", &size);
- // adios.Write ("arrays", "rank", &rank);
- // adios.Write ("arrays", "temperature", t);
- // adios.Write ("arrays", "pressure", &p);
-
- // adios.Close ("arrays");
- ckptfile.PerformIO();
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
- }
- MPI_Barrier(comm);
- ckptfile.Close();
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << e.what() << "\n";
- }
- }
-
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
-}
diff --git a/examples/globalArray/globalArrayXML.xml b/examples/globalArray/globalArrayXML.xml
deleted file mode 100644
index 315ba12963a9d6bbc4574c85bb769f668d1255ef..0000000000000000000000000000000000000000
--- a/examples/globalArray/globalArrayXML.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0"?>
-<adios-config>
- <adios-group name="arrays">
- <var name="NX" type="integer"/>
- <var name="size" type="integer"/>
- <var name="rank" type="integer"/>
-
- <global-bounds dimensions="size,NX" offsets="rank,0">
- <var name="temperature" gwrite="t" type="double" dimensions="1,NX"/>
- <var name="pressure" gwrite="p" type="std::vector<double>" dimensions="1,NX"/>
- </global-bounds>
-
- <attribute name="temperature/description"
- value="Global array written from 'size' processes over several timesteps"
- type="string"/>
- </adios-group>
-
- <method group="arrays" method="MPI">ts_buffersize=32000;verbose=4</method>
- <!--
- <method group="arrays" method="MPI_AGGREGATE">num_aggregators=1;num_ost=1</method>
- -->
-
- <buffer max-size-MB="1"/>
-
-</adios-config>
-
diff --git a/examples/globalArray/globalArrayZeroCopy.cpp b/examples/globalArray/globalArrayZeroCopy.cpp
deleted file mode 100644
index 7b7506eb974f34b1fb41fa9ef66d2f4065667652..0000000000000000000000000000000000000000
--- a/examples/globalArray/globalArrayZeroCopy.cpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * globalArrayZeroCopy.cpp
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <mpi.h>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include "adios2/../../include/ADIOS.h"
-
-int main(int argc, char *argv[])
-{
- int rank, size;
- const int NX = 10;
- MPI_Comm comm = MPI_COMM_WORLD;
-
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
-
- // set a maximum buffersize that ADIOS can use (for one group).
- // multiple groups may use each such buffersize if they are overlapped
- // or
- // use time-aggregation or use zero-copy staging
- adios.SetMaxBuffersize(100000000);
-
- // Define Group and its variables
- // The group's transport can be defined at runtime in the input XML file
- adios.CreateGroup("arrays", adios_stat_default);
-
- // Set the maximum buffersize for this group. This must happen before
- // defining a zero copy variable, which will cause the group's internal
- // buffer
- // allocated (during the variable definition call)
- adios.SetMaxBuffersize("arrays", 10000000);
-
- adios.DefineVariable("arrays", "NX", "int"); // scalar variable
- adios.DefineVariable("arrays", "size", "int");
- adios.DefineVariable("arrays", "size", "rank");
-
- // Define and allocate a 2D array with 1D decomposition and get back a
- // pre-allocated typed pointer.
- // The size of the array must be known at this point, so no scalar
- // variables
- // can
- // be used for its dimensions.
- std::string ldim = "1," + std::to_string(NX); // == "1,10" if NX==10
- std::string gdim = std::to_string(size) + "," + std::to_string(NX);
- std::string offs = std::to_string(rank) + ",0";
-
- double *t = adios.DefineZeroCopyVariable("arrays", "temperature",
- "double", ldim, gdim, offs);
-
- // set a variable-level transformation for this variable
- adios.SetVariableTransform("arrays", "temperature", "none");
-
- std::vector<double> p = adios.DefineZeroCopyVariable(
- "arrays", "pressure", "std::vector<double>", ldim, gdim, offs);
-
- // set a group-level transformation
- adios.SetGroupTransform("arrays", "time-aggregate",
- ""); // no options passed here
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
-
- for (int it = 1; it <= 13; it++)
- {
-
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
-
- if (it == 1)
- adios.Open("arrays", "globalArray.bp", "w");
- else
- adios.Open("arrays", "globalArray.bp", "a");
-
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
-
- adios.Write("arrays", "NX", &NX);
- adios.Write("arrays", "size", &size);
- adios.Write("arrays", "rank", &rank);
- adios.Write("arrays", "temperature", t);
- adios.Write("arrays", "pressure", &p);
-
- adios.Close("arrays");
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
- }
- MPI_Barrier(comm);
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << e.what() << "\n";
- }
- }
-
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
-}
diff --git a/examples/groupless/basic/reader.cpp b/examples/groupless/basic/reader.cpp
deleted file mode 100644
index c65cbe3a31da986f361e1abcb51c731dde146074..0000000000000000000000000000000000000000
--- a/examples/groupless/basic/reader.cpp
+++ /dev/null
@@ -1,197 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * reader.cpp
- *
- * Created on: Feb 13, 2017
- * Author: pnorbert
- */
-
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-#include <mpi.h>
-
-int main(int argc, char *argv[])
-{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> NiceArray;
- std::vector<float> RaggedArray;
- unsigned int Nx;
- int Nparts;
- int Nwriters;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- }
-
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- // All the above is same as default use:
- // auto bpReader = adios.Open( "myNumbers.bp", "r");
-
- if (bpReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to open ADIOS bpReader\n");
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << bpReader->VariableNames
- << "\n";
-
- /* NX */
- bpReader->Read<unsigned int>(
- "NX",
- Nx); // read a Global scalar which has a single value in a step
-
- /* nproc */
- bpReader->Read<int>("nproc", Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We need to read a specific value the same way as reading from any 1D
- // array.
- // Make a single-value selection to describe our rank's position in the
- // 1D array of Nwriters values.
- if (rank < Nwriters)
- {
- std::shared_ptr<adios::Variable> varNparts =
- bpReader.InquiryVariable("Nparts");
- std::unique_ptr<adios::Selection> selNparts =
- adios.SelectionBoundingBox({1}, {rank});
- varNparts->SetSelection(selNparts);
- bpReader->Read<int>(varNparts, Nparts);
- }
- // or we could just read the whole array by every process
- std::vector<int> partsV(Nwriters);
- bpReader->Read<int>("Nparts",
- partsV.data()); // read with string name, no
- // selection => read whole array
-
- std::vector<int> partsV;
- bpReader->Read<int>("Nparts",
- partsV); // read with string name, no selection =>
- // read whole array
- (Nwriters == partsV.size())
-
- /* Nice */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable>
- varNice = bpReader.InquiryVariable("Nice");
-
- if (varNice == nullptr)
- throw std::ios_base::failure("ERROR: failed to find variable "
- "'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- uint64_t gdim = varNice->m_Shape[0]; // ?member var or member func?
- uint64_t ldim = gdim / nproc;
- uint64_t offs = rank * ldim;
- if (rank == nproc - 1)
- {
- ldim = gdim - (ldim * gdim);
- }
-
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable
- // we
- // READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- varNice->SetSelection(bbsel);
- bpReader->Read<double>(varNice, NiceArray.data());
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_Shape[1] != adios::VARYING_DIMENSION)
- {
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
- }
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank <
- varRagged->nblocks[0]) // same as rank < Nwriters in this example
- {
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim =
- varRagged->blockinfo[rank].m_Dimensions[1];
- RaggedArray.resize(ldim);
-
- std::unique_ptr<adios::Selection> wbsel =
- adios.SelectionWriteblock(rank);
- varRagged->SetSelection(wbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- varRagged->SetSelection(rbbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
- }
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // Close file/stream
- bpReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/groupless/basic/writer.cpp b/examples/groupless/basic/writer.cpp
deleted file mode 100644
index fb4e9c76d6dd212c53b8a62a03724ec7b9d9275c..0000000000000000000000000000000000000000
--- a/examples/groupless/basic/writer.cpp
+++ /dev/null
@@ -1,178 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * writer.cpp
- *
- * Created on: Feb 13, 2017
- * Author: pnorbert
- */
-
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-#include <mpi.h>
-
-namespace adios
-{
-typedef enum { VARYING_DIMENSION = -1, LOCAL_VALUE = 0, GLOBAL_VALUE = 1 };
-}
-
-int main(int argc, char *argv[])
-{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- const unsigned int Nx = 10;
- const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
-
- std::vector<double> NiceArray(Nx);
- for (int i = 0; i < Nx; i++)
- {
- NiceArray[i] = rank * Nx + (double)i;
- }
-
- std::vector<float> RaggedArray(Nparts);
- for (int i = 0; i < Nparts; i++)
- {
- RaggedArray[i] = rank * Nx + (float)i;
- }
-
- try
- {
- // Define group and variables with transforms, variables don't have
- // functions, only group can access variables
- adios::Variable<unsigned int> &varNX =
- adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- adios::Variable<int> &varNproc = adios.DefineVariable<int>(
- "nproc", adios::GLOBAL_VALUE); // same def for global value
- adios::Variable<int> &varNparts =
- adios.DefineVariable<int>("Nparts",
- adios::LOCAL_VALUE); // a single-value
- // different on
- // every process
- adios::Variable<double> &varNice = adios.DefineVariable<double>(
- "Nice", {nproc * Nx}); // 1D global array
- adios::Variable<float> &varRagged = adios.DefineVariable<float>(
- "Ragged", {nproc, adios::VARYING_DIMENSION}); // ragged array
-
- // add transform to variable in group...not executed (just testing API)
- adios::Transform bzip2 = adios::transform::BZIP2();
- varNice->AddTransform(bzip2, 1);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = adios.GetMethod("output");
- if (bpWriterSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AddTransport(
- "File",
- "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters(
- "have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters("Aggregation",
- (nproc + 1) /
- 2); // number of aggregators
- }
-
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- // "w" means we overwrite any existing file on disk, but AdvanceStep
- // will
- // append steps later.
- auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to open ADIOS bpWriter\n");
-
- if (rank == 0)
- {
- // Writing a global scalar from only one process
- bpWriter->Write<unsigned int>(varNX, Nx);
- }
- // Writing a local scalar on every process. Will be shown at reading as
- // a 1D
- // array
- bpWriter->Write<int>(varNparts, Nparts);
-
- // Writing a global scalar on every process is useless. Information will
- // be
- // thrown away
- // and only rank 0's data will be in the output
- bpWriter->Write<int>(varNproc, nproc);
-
- // Make a 1D selection to describe the local dimensions of the variable
- // we
- // write and
- // its offsets in the global spaces
- adios::Selection &sel = adios.SelectionBoundingBox(
- {Nx}, {rank * Nx}); // local dims and offsets; both as list
- varNice.SetSelection(sel);
- bpWriter->Write<double>(varNice,
- NiceArray.data()); // Base class Engine own
- // the Write<T> that
- // will call overloaded
- // Write from Derived
-
- adios::Selection &lsel =
- adios.SelectionBoundingBox({1, Nparts}, {rank, 0});
- varRagged.SetSelection(sel);
- bpWriter->Write<float>(varRagged,
- RaggedArray.data()); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
-
- // Indicate we are done for this step
- // N-to-M Aggregation, disk I/O will be performed during this call,
- // unless
- // time aggregation postpones all of that to some later step
- bpWriter->Advance();
- bpWriter->AdvanceAsync(callback_func_to_notify_me);
-
- // Called once: indicate that we are done with this output for the run
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/groupless/compound/reader.cpp b/examples/groupless/compound/reader.cpp
deleted file mode 100644
index aa6ff6d3168ec0d05065f5eb832ced3a908f24b5..0000000000000000000000000000000000000000
--- a/examples/groupless/compound/reader.cpp
+++ /dev/null
@@ -1,221 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * reader.cpp
- *
- * Created on: Feb 21, 2017
- * Author: eisen, modified from basic by pnorbert
- */
-
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-#include <mpi.h>
-
-int main(int argc, char *argv[])
-{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- // GSE === user-defined structure
- //
- // Like HDF5 example, read with a subset of the structure that was written.
- // Easily handled by FFS and HDF5, but ambitious for ADIOS
- typedef struct s2_t
- {
- double c;
- int a;
- };
- unsigned int Nx;
- int Nparts;
- int Nwriters;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- }
-
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- // All the above is same as default use:
- // auto bpReader = adios.Open( "myNumbers.bp", "r");
-
- if (bpReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to open ADIOS bpReader\n");
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << bpReader->VariableNames
- << "\n";
-
- /* NX */
- bpReader->Read<unsigned int>(
- "NX",
- Nx); // read a Global scalar which has a single value in a step
-
- /* nproc */
- bpReader->Read<int>("nproc", Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We need to read a specific value the same way as reading from any 1D
- // array.
- // Make a single-value selection to describe our rank's position in the
- // 1D array of Nwriters values.
- if (rank < Nwriters)
- {
- std::shared_ptr<adios::Variable> varNparts =
- bpReader.InquiryVariable("Nparts");
- std::unique_ptr<adios::Selection> selNparts =
- adios.SelectionBoundingBox({1}, {rank});
- varNparts->SetSelection(selNparts);
- bpReader->Read<int>(varNparts, Nparts);
- }
- // or we could just read the whole array by every process
- std::vector<int> partsV(Nwriters);
- bpReader->Read<int>("Nparts",
- partsV.data()); // read with string name, no
- // selection => read whole array
-
- std::vector<int> partsV;
- bpReader->Read<int>("Nparts",
- partsV); // read with string name, no selection =>
- // read whole array
- (Nwriters == partsV.size())
-
- /* Nice */
- // inquiry about a variable, whose name we know
- /* GSE === compound type declaration borrowed heavily from HDF5
- style */
- adios::CompType mtype(sizeof(s2_t));
- mtype.insertMember("c_name", OFFSET(s2_t, c), PredType::NATIVE_DOUBLE);
- mtype.insertMember("a_name", OFFSET(s2_t, a), PredType::NATIVE_INT);
-
- /*
- * GSE === this is a bit conceptually different. There was no real
- * check in the prior API that the variable in the file was in any way
- * "compatible" with how we planned to read it. This could be done
- * here, by providing the details of the structure that we are
- * prepared to read in the inquiryVariable, or if we had an API that
- * allowed more introspection, we could perhaps support a query on the
- * adios::Variable and a later operation that informed it of the data
- * type that we were prepared to extract from it.
- */
- std::shared_ptr<adios::Variable> varNice =
- bpReader.InquiryVariable("Nice", mtype);
-
- if (varNice == nullptr)
- throw std::ios_base::failure("ERROR: failed to find variable "
- "'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- uint64_t gdim = varNice->m_Shape[0]; // ?member var or member func?
- uint64_t ldim = gdim / nproc;
- uint64_t offs = rank * ldim;
- if (rank == nproc - 1)
- {
- ldim = gdim - (ldim * gdim);
- }
-
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable
- // we
- // READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- varNice->SetSelection(bbsel);
- // GSE === Again, templated here?
- bpReader->Read<s2_t>(varNice, NiceArray.data());
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_Shape[1] != adios::VARYING_DIMENSION)
- {
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
- }
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank <
- varRagged->nblocks[0]) // same as rank < Nwriters in this example
- {
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim =
- varRagged->blockinfo[rank].m_Dimensions[1];
- RaggedArray.resize(ldim);
-
- std::unique_ptr<adios::Selection> wbsel =
- adios.SelectionWriteblock(rank);
- varRagged->SetSelection(wbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- varRagged->SetSelection(rbbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
- }
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // Close file/stream
- bpReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/groupless/compound/writer.cpp b/examples/groupless/compound/writer.cpp
deleted file mode 100644
index 9c49ddf1e528344dd6a7206b898c1b69013d65db..0000000000000000000000000000000000000000
--- a/examples/groupless/compound/writer.cpp
+++ /dev/null
@@ -1,179 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * writer.cpp
- *
- * Created on: Feb 13, 2017
- * Author: pnorbert
- */
-
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-#include <mpi.h>
-
-namespace adios
-{
-typedef enum { VARYING_DIMENSION = -1, LOCAL_VALUE = 0, GLOBAL_VALUE = 1 };
-}
-
-int main(int argc, char *argv[])
-{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- const unsigned int Nx = 10;
- // GSE === user-defined structure
- typedef struct s1_t
- {
- int a;
- float b;
- double c;
- };
- const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
-
- std::vector<s1_t> NiceArray(Nx);
- for (int i = 0; i < Nx; i++)
- {
- NiceArray.push_back(ss1_t());
- NiceArray[i].a = rank * Nx + (double)i;
- NiceArray[i].b = 100.0 * rank * Nx + 100.0 * (double)i;
- NiceArray[i].c = 10000.0 * rank * Nx + 10000.0 * (double)i;
- }
-
- try
- {
- /* GSE === compound type declaration borrowed heavily from HDF5 style */
- adios::CompType mtype(sizeof(s1_t));
- mtype.insertMember("a_name", OFFSET(s1_t, a), PredType::NATIVE_INT);
- mtype.insertMember("c_name", OFFSET(s1_t, c), PredType::NATIVE_DOUBLE);
- mtype.insertMember("b_name", OFFSET(s1_t, b), PredType::NATIVE_FLOAT);
-
- // Define group and variables with transforms, variables don't have
- // functions, only group can access variables
- adios::Variable<unsigned int> &varNX =
- adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- adios::Variable<int> &varNproc = adios.DefineVariable<int>(
- "nproc", adios::GLOBAL_VALUE); // same def for global value
- adios::Variable<int> &varNparts =
- adios.DefineVariable<int>("Nparts",
- adios::LOCAL_VALUE); // a single-value
- // different on
- // every process
-
- // GSE === template necessary or useful here? Extra argument for
- // previously-built compound type information */
- adios::Variable<s1_t> &varNice = adios.DefineVariable<s1_t>(
- "Nice", {nproc * Nx}, mtype); // 1D global array
-
- // add transform to variable in group...not executed (just testing API)
- adios::Transform bzip2 = adios::transform::BZIP2();
- varNice->AddTransform(bzip2, 1);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = adios.GetMethod("output");
- if (bpWriterSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AddTransport(
- "File",
- "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters(
- "have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters("Aggregation",
- (nproc + 1) /
- 2); // number of aggregators
- }
-
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- // "w" means we overwrite any existing file on disk, but AdvanceStep
- // will
- // append steps later.
- auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to open ADIOS bpWriter\n");
-
- if (rank == 0)
- {
- // Writing a global scalar from only one process
- bpWriter->Write<unsigned int>(varNX, Nx);
- }
- // Writing a local scalar on every process. Will be shown at reading as
- // a 1D
- // array
- bpWriter->Write<int>(varNparts, Nparts);
-
- // Writing a global scalar on every process is useless. Information will
- // be
- // thrown away
- // and only rank 0's data will be in the output
- bpWriter->Write<int>(varNproc, nproc);
-
- // Make a 1D selection to describe the local dimensions of the variable
- // we
- // write and
- // its offsets in the global spaces
- adios::Selection &sel = adios.SelectionBoundingBox(
- {Nx}, {rank * Nx}); // local dims and offsets; both as list
- varNice.SetSelection(sel);
-
- // GSE === Template useful or necessary here? We have to treat this as
- // a
- // void* inside ADIOS...
- bpWriter->Write<sl_t>(varNice, NiceArray.data());
-
- // Indicate we are done for this step
- // N-to-M Aggregation, disk I/O will be performed during this call,
- // unless
- // time aggregation postpones all of that to some later step
- bpWriter->Advance();
- bpWriter->AdvanceAsync(callback_func_to_notify_me);
-
- // Called once: indicate that we are done with this output for the run
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/hello/C/fstream.xml b/examples/hello/C/fstream.xml
deleted file mode 100644
index f43942fb1e13329c05a43c714ee3f8e2c6807ac5..0000000000000000000000000000000000000000
--- a/examples/hello/C/fstream.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0"?>
-<adios-config host-language="C">
- <adios-group name="Types">
- <var name="NumbersSize" type="int"/>
- <var name="Numbers" type="double"/>
- <attribute name="description" value="1 to 10"/>
-
- </adios-group>
-
- <transport group="Types" method="FStream">verbose=3</transport>
-
- <!-- <buffer size-MB="40" allocate-time="now"/> -->
-
-</adios-config>
diff --git a/examples/hello/C/helloFStream.c b/examples/hello/C/helloFStream.c
deleted file mode 100644
index 58cca1452e86c5dc2ffb22451b47f7bd0122fdd2..0000000000000000000000000000000000000000
--- a/examples/hello/C/helloFStream.c
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * helloFStream.c Test for C API version of helloFStream
- * Created on: Nov 2, 2016
- * Author: wfg
- */
-
-#include "../../../include/ADIOS_C.h"
-
-void main(int argc, char *argv[])
-{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-
- // populate values
- double *myNumbers;
- myNumbers = (double *)malloc(10 * sizeof(double));
-
- int i;
- for (i = 0; i < 10; ++i)
- myNumbers[i] = i + 1;
-
- // start ADIOS
- ADIOS *adiosC, adiosC2;
- const char group[] = "Types";
- const char group2[] = "Types2";
-
- adiosC2 = adios_init_debug("fstream.xml", MPI_COMM_WORLD); // debug mode
-
- adios_create_group(adiosC, "groupCFD");
- adios_create_variable(adiosC, "groupCFD", "temperature");
- adios_create_group(adiosC2, "groupFEM", "temperature");
- ///
- adios_open(adiosC, group, "helloVector.txt", "w"); // open group Types
- // associated with file
- // "helloVector.txt" for
- // writing
- adios_open(adiosC, group2, "Vector.txt", "w"); // open group Types associated
- // with file "helloVector.txt"
- // for writing
- adios_write(adiosC, group, "Types", myNumbers);
- adios_close(adiosC, group);
-
- free(myNumbers);
-}
diff --git a/examples/hello/README b/examples/hello/README
deleted file mode 100644
index 5966d87b721fe4e925ca70c1d3e959c382b7a6d2..0000000000000000000000000000000000000000
--- a/examples/hello/README
+++ /dev/null
@@ -1,10 +0,0 @@
-Test if ADIOS MPI and noMPI code can be separated at compilation stage
-Single Makefile handles different binaries
-
-make mpi -> for MPI code, links ../../lib/libadios.a
-make nompi -> for noMPI code links ../../lib/libadios_nompi.a
-
-Choose different BASE_NAMES
-
-make nompi BASE_NAME=helloFStream
-make nompi BASE_NAME=helloADIOS
\ No newline at end of file
diff --git a/examples/hello/README.md b/examples/hello/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..0c780bd6b2830759ef4f16846646dd326d3e0404
--- /dev/null
+++ b/examples/hello/README.md
@@ -0,0 +1,19 @@
+examples/hello
+
+Provides tests and illustrates how to use very basic functionality for a new component in adios2
+
+
+* adios1Writer (ADIOS_USE_ADIOS1=ON)
+ 1. Write BP format files using adios1 library through adios2 interface
+
+* bpWriter
+ 1. Write BP format files
+
+* datamanReader (to be deprecated, ADIOS_USE_DataMan=ON)
+ 1. Read real-time WAN streams using dataman
+
+* datamanWriter
+ 1. Write real-time WAN streams using dataman
+
+* hdf5Writer (ADIOS_USE_HDF5=ON)
+ 1. Write HDF5 files using interoperability through the adios2 interface
\ No newline at end of file
diff --git a/examples/hello/bpReader/helloBPReader.cpp b/examples/hello/bpReader/helloBPReader.cpp
deleted file mode 100644
index e83a66c3f7e4a88714334ef4e9843862415dc2f7..0000000000000000000000000000000000000000
--- a/examples/hello/bpReader/helloBPReader.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * helloWriter.cpp
- *
- * Created on: Feb 16, 2017
- * Author: wfg
- */
-
-#include <iostream>
-#include <vector>
-
-#include <mpi.h>
-
-#include <adios2.h>
-
-int main(int argc, char *argv[])
-{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpReaderSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter
- bpReaderSettings.AddTransport("File"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpReader = adios.Open("myDoubles_nompi.bp", "r", bpReaderSettings);
-
- if (bpReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: couldn't create bpReader at Open\n");
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/hello/bpReader/helloBPReader_nompi.cpp b/examples/hello/bpReader/helloBPReader_nompi.cpp
deleted file mode 100644
index fff9b96d42106b5975789771dcd1ad1569520084..0000000000000000000000000000000000000000
--- a/examples/hello/bpReader/helloBPReader_nompi.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * helloADIOSNoXML_OOP.cpp
- *
- * Created on: Jan 9, 2017
- * Author: wfg
- */
-
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-
-int main(int argc, char *argv[])
-{
- const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
-
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpReaderSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter/BPReader
- bpReaderSettings.AddTransport("File"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpReader = adios.Open("myDoubles.bp", "r", bpReaderSettings);
-
- if (bpReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: couldn't create bpReader at Open\n");
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
-
- return 0;
-}
diff --git a/examples/hello/compound/helloCompound.cpp b/examples/hello/compound/helloCompound.cpp
deleted file mode 100644
index 50fed574af830c509dfc6c7a27ef230f312cf583..0000000000000000000000000000000000000000
--- a/examples/hello/compound/helloCompound.cpp
+++ /dev/null
@@ -1,115 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * helloCompound.cpp
- *
- * Created on: Feb 20, 2017
- * Author: wfg
- */
-
-#include <cstddef> // offsetof
-#include <iostream>
-#include <vector>
-
-#include <mpi.h>
-
-#include <adios2.h>
-
-struct Particle
-{
- char Type[10]; ///< alpha, beta, gamma, etc.
- double Position[3]; ///< x, y, z
- double Velocity[3]; ///< Vx, Vy, Vz
-};
-
-int main(int argc, char *argv[])
-{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
-
- Particle myParticle;
- sprintf(myParticle.Type, "%s", "photon");
- myParticle.Position[0] = 0;
- myParticle.Position[1] = 1;
- myParticle.Position[2] = 2;
-
- myParticle.Velocity[0] = 10;
- myParticle.Velocity[1] = 11;
- myParticle.Velocity[2] = 12;
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
-
- adios::VariableCompound &ioMyParticle =
- adios.DefineVariableCompound<Particle>("myParticle",
- adios::Dims{1});
- ioMyParticle.InsertMember<std::string>("Type",
- offsetof(Particle, Type));
- ioMyParticle.InsertMember<std::vector<double>>(
- "Position", offsetof(Particle, Position));
- ioMyParticle.InsertMember<std::vector<double>>(
- "Velocity", offsetof(Particle, Velocity));
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter
- bpWriterSettings.AddTransport(
- "File", "have_metadata_file=yes"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: couldn't create bpWriter at Open\n");
-
- bpWriter->Write(ioMyDoubles,
- myDoubles.data()); // Base class Engine own the
- // Write<T> that will call
- // overloaded Write from
- // Derived
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
-
- return 0;
-}
diff --git a/examples/hello/compound/helloCompound_nompi.cpp b/examples/hello/compound/helloCompound_nompi.cpp
deleted file mode 100644
index e14995a6d025483fa002cb97d54fcb296d7c350c..0000000000000000000000000000000000000000
--- a/examples/hello/compound/helloCompound_nompi.cpp
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * helloCompound.cpp
- *
- * Created on: Feb 20, 2017
- * Author: wfg
- */
-
-#include <cstddef> // offsetof
-#include <cstdio>
-#include <iostream>
-#include <vector>
-
-#include <adios2.h>
-
-struct Particle
-{
- char Type[10]; ///< alpha, beta, gamma, etc.
- double Position[3]; ///< x, y, z
- double Velocity[3]; ///< Vx, Vy, Vz
-};
-
-int main(int argc, char *argv[])
-{
- const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
-
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
-
- Particle myParticle;
- sprintf(myParticle.Type, "%s", "photon");
- myParticle.Position[0] = 0;
- myParticle.Position[1] = 1;
- myParticle.Position[2] = 2;
-
- myParticle.Velocity[0] = 10;
- myParticle.Velocity[1] = 11;
- myParticle.Velocity[2] = 12;
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
-
- adios::VariableCompound &ioMyParticle =
- adios.DefineVariableCompound<Particle>("myParticle");
- ioMyParticle.InsertMember<char>("Type", offsetof(Particle, Type));
- ioMyParticle.InsertMember<double>("Position",
- offsetof(Particle, Position));
- ioMyParticle.InsertMember<double>("Velocity",
- offsetof(Particle, Velocity));
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter
- bpWriterSettings.AddTransport(
- "File", "have_metadata_file=yes"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: couldn't create bpWriter at Open\n");
-
- bpWriter->Write(ioMyDoubles,
- myDoubles.data()); // Base class Engine own the
- // Write<T> that will call
- // overloaded Write from
- // Derived
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
-
- return 0;
-}
diff --git a/examples/hello/fstream.xml b/examples/hello/fstream.xml
deleted file mode 100644
index e46437445a1af49d4a8ee0465ea5a8762cfd430e..0000000000000000000000000000000000000000
--- a/examples/hello/fstream.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<adios-config host-language="C++">
- <adios-group name="Vector">
- <var name="size" type="unsigned int"/>
- <var name="numbers" type="int" dimension="size"/>
- <attribute name="description" value="1 to 10"/>
- </adios-group>
-
-
- <transform type="bzip2" >
- </transform>
-
- <!-- transport group="Types" method="FStream">verbose=3</transport> -->
-
- <method name="SingleFile" profile_units="mus" max_buffer_size="10000">
- <transport type="File" have_metadata_file="no" aggregators="10" profile_units="mus"/>
- </method>
-
- <!-- <buffer size-MB="40" allocate-time="now"/> -->
-
-</adios-config>
diff --git a/examples/hello/writer.xml b/examples/hello/writer.xml
deleted file mode 100644
index 3a467ddc39c54a042e4e8e18e037d7dbb0ca43dc..0000000000000000000000000000000000000000
--- a/examples/hello/writer.xml
+++ /dev/null
@@ -1,44 +0,0 @@
-<?xml version="1.0"?>
-<adios-config host-language="Fortran">
- <adios-group name="writer2D">
-
- <var name="nproc" path="/info" type="integer"/>
- <attribute name="description" path="/info/nproc" value="Number of writers"/>
- <var name="npx" path="/info" type="integer"/>
- <attribute name="description" path="/info/npx" value="Number of processors in x dimension"/>
- <var name="npy" path="/info" type="integer"/>
- <attribute name="description" path="/info/npy" value="Number of processors in y dimension"/>
-
- <var name="gdx" type="integer"/>
- <attribute name="description" path="/gdx" value="Global array size in x dimension"/>
- <var name="gdy" type="integer"/>
- <attribute name="description" path="/gdy" value="Global array size in y dimension"/>
-
- <!-- Auxiliary variables for global array indexing written (overwritten) by each process -->
- <var name="ox" type="integer"/>
- <var name="oy" type="integer"/>
- <var name="ldx" type="integer"/>
- <var name="ldy" type="integer"/>
-
- <!-- 2D array to write with block,block decomposition -->
- <global-bounds dimensions="gdx,gdy" offsets="ox,oy">
- <var name="xy" type="double" dimensions="ldx,ldy"/>
- </global-bounds>
- <attribute name="description" path="/xy"
- value="2D array with 2D decomposition"/>
-
- </adios-group>
-
- <!-- Use transport method
- DATASPACES for staging data in memory coupling or
- FLEXPATH for socket based staging between applications
- MPI for file-based coupling
- -->
- <!--transport group="writer2D" method="MPI">verbose=2</transport-->
- <!--transport group="writer2D" method="DATASPACES">verbose=3</transport-->
- <transport group="writer2D" method="DIMES">verbose=3</transport>
- <!--transport group="writer2D" method="FLEXPATH">QUEUE_SIZE=10;verbose=3</transport-->
-
- <buffer size-MB="40" allocate-time="now"/>
-
-</adios-config>
diff --git a/examples/hello/writer2Groups.xml b/examples/hello/writer2Groups.xml
deleted file mode 100644
index d019bdfdc3699c4f91e5c2c3963127e671b5d582..0000000000000000000000000000000000000000
--- a/examples/hello/writer2Groups.xml
+++ /dev/null
@@ -1,72 +0,0 @@
-<?xml version="1.0"?>
-<adios-config host-language="Fortran">
- <adios-group name="writer2D">
-
- <var name="nproc" path="/info" type="integer"/>
- <attribute name="description" path="/info/nproc" value="Number of writers"/>
- <var name="npx" path="/info" type="integer"/>
- <attribute name="description" path="/info/npx" value="Number of processors in x dimension"/>
- <var name="npy" path="/info" type="integer"/>
- <attribute name="description" path="/info/npy" value="Number of processors in y dimension"/>
-
- <var name="gdx" type="integer"/>
- <attribute name="description" path="/gdx" value="Global array size in x dimension"/>
- <var name="gdy" type="integer"/>
- <attribute name="description" path="/gdy" value="Global array size in y dimension"/>
-
- <!-- Auxiliary variables for global array indexing written (overwritten) by each process -->
- <var name="ox" type="integer"/>
- <var name="oy" type="integer"/>
- <var name="ldx" type="integer"/>
- <var name="ldy" type="integer"/>
-
- <!-- 2D array to write with block,block decomposition -->
- <global-bounds dimensions="gdx,gdy" offsets="ox,oy">
- <var name="xy" type="double" dimensions="ldx,ldy"/>
- </global-bounds>
- <attribute name="description" path="/xy"
- value="2D array with 2D decomposition"/>
-
- </adios-group>
-
- <!-- Use transport method
- DATASPACES for staging data in memory coupling or
- FLEXPATH for socket based staging between applications
- MPI for file-based coupling
- -->
- <!--transport group="writer2D" method="MPI">verbose=2</transport-->
- <!--transport group="writer2D" method="DATASPACES">verbose=3</transport-->
- <transport group="writer2D" method="DIMES">verbose=3</transport>
- <!--transport group="writer2D" method="FLEXPATH">QUEUE_SIZE=10;verbose=3</transport-->
- <adios-group name="writer3D">
-
- <var name="nproc" path="/info" type="integer"/>
- <attribute name="description" path="/info/nproc" value="Number of writers"/>
- <var name="npx" path="/info" type="integer"/>
- <attribute name="description" path="/info/npx" value="Number of processors in x dimension"/>
- <var name="npy" path="/info" type="integer"/>
- <attribute name="description" path="/info/npy" value="Number of processors in y dimension"/>
-
- <var name="gdx" type="integer"/>
- <attribute name="description" path="/gdx" value="Global array size in x dimension"/>
- <var name="gdy" type="integer"/>
- <attribute name="description" path="/gdy" value="Global array size in y dimension"/>
-
- <!-- Auxiliary variables for global array indexing written (overwritten) by each process -->
- <var name="ox" type="integer"/>
- <var name="oy" type="integer"/>
- <var name="ldx" type="integer"/>
- <var name="ldy" type="integer"/>
-
- <!-- 2D array to write with block,block decomposition -->
- <global-bounds dimensions="gdx,gdy" offsets="ox,oy">
- <var name="xy" type="double" dimensions="ldx,ldy"/>
- </global-bounds>
- <attribute name="description" path="/xy"
- value="2D array with 2D decomposition"/>
-
- </adios-group>
-
- <buffer size-MB="40" allocate-time="now"/>
-
-</adios-config>
diff --git a/examples/solidfluid/solidfluid.xml b/examples/solidfluid/solidfluid.xml
deleted file mode 100644
index 84cb101326dffce082b2a2870e23e48a9657d7ad..0000000000000000000000000000000000000000
--- a/examples/solidfluid/solidfluid.xml
+++ /dev/null
@@ -1,128 +0,0 @@
-<?xml version="1.0"?>
-<adios-config host-language="C">
-
- <!-- Changes to ADIOS-1 XML
- Accommodate for the following extensions and flexiblity:
- - Multiple engines e.g. SIRIUS can have it's own
- - Do not bind one transport to a group, i.e. we can reuse a group in multiple I/O
- with different transports
- - Do not bind one group to each output file, i.e., we can write variables from
- different groups into a single file at the same step
- -->
-
- <!-- Execution Engines: default-engine, sirius, dataman, hdf5
- -->
-
-
- <adios-group name="solid">
- <var name="NX" type="integer"/>
- <var name="size" type="integer"/>
- <var name="rank" type="integer"/>
-
- <global-bounds dimensions="size,NX" offsets="rank,0">
- <var name="temperature" gwrite="solid.t" type="double" dimensions="1,NX"/>
- <var name="pressure" gwrite="solid.p" type="std::vector<double>" dimensions="1,NX"/>
- </global-bounds>
-
- <attribute name="temperature/description"
- value="Global array written from 'size' processes over several timesteps"
- type="string"/>
- </adios-group>
-
-
- <adios-group name="fluid">
- <var name="NX" type="integer"/>
- <var name="size" type="integer"/>
- <var name="rank" type="integer"/>
-
- <global-bounds dimensions="size,NX" offsets="rank,0">
- <var name="temperature" gwrite="fluid.t" type="double" dimensions="1,NX"/>
- <var name="pressure" gwrite="fluid.p" type="std::vector<double>" dimensions="1,NX"/>
- </global-bounds>
-
- <attribute name="temperature/description"
- value="Global array written from 'size' processes over several timesteps"
- type="string"/>
- </adios-group>
-
-
- <adios-group name="checkpoint">
- <!-- Add all variables from group 'solid' with a path-prefix 'solid/...'
- In adios write then one must refer to NX as "solid/NX", "solid/temperature", etc
- If prefix is not defined, the variables are simply merged in with their path, but
- then there should be no name collisions
- -->
- <add-group name="solid" prefix="solid" />
- <add-group name="fluid" prefix="fluid/" />
- </adios-group>
-
-
- <!-- Method is with what we create an Output. It specifies either
- 1. a group + a transport
- 2. a group + a data manager
- 3. a transport only
- 4. a data manager only
-
- 1 & 3. default manager is used
- 2 & 4. manager must have transports defined
- 3 & 4. each write needs explicit group + variable as argument
- -->
-
- <!-- Associate a single transport with a group.
- The manager will be the default manager when opening an output with this group
- The name of the method will be the same as the group ("checkpoint")
- This ensures full backward-compatibility for ADIOS-1 XML files
- -->
- <method group="solid" transport="POSIX">options to POSIX transport</method>
-
- <!-- the statement below is equivalent to the one above plus -->
- <method group="solid" >
- <transport="POSIX">options to POSIX transport</transport>
- </method>
-
- <method group="solid" <!-- engine="default-engine" --> >
- <transport="POSIX" fname="out_p.bp">options to POSIX transport</transport>
- <transport="MPI" fname="outsingle.bp">options to MPI transport</transport>
- <!-- filenames overwrite the value provided in Open() call -->
- </method>
-
- <!-- Same as above but we can name the method separately from group name.
- Hence multiple methods can be declared for one group
- -->
- <method name="viz1" group="viz" transport="STAGING"></method>
- <method name="viz2" group="viz" transport="MPI"></method>
-
- <!-- Associate an engine with a group and parameterize it here
- The manager will define the transport(s) used in an output
- -->
- <method name="fluid" group="fluid" engine="sirius" fname="x.bp">
- <level transport="SHMEM">options to SHMEM transport</level>
- <level target="ssd" target-path="/ssd/pnorbert/" transport="POSIX"/>
- <level target="wan" transport="ICEE" />
- </method>
-
- <method group="checkpoint" transport="MPI_AGGREGATE">
- num_aggregators=1;num_ost=1
- </method>
-
- <!-- We can set a transport to a group which is not defined yet.
- The group can/should be defined in the source code before use.
- -->
- <method group="grouptobe" transport="POSIX">options to transport</method>
-
- <!-- We can set a transport/engine without any group
- All variables at writing should come from some existing group.
- Each write call needs to add an extra argument to identify the variable's group
- -->
- <method name="groupless" transport="POSIX">options to transport</method>
- <method name="groupless" >
- <transport="POSIX">options to POSIX transport</transport>
- </method>
-
- <!-- Global options for ADIOS that are not tied to a specific method -->
- <options>verbose=2</options>
-
- <buffer max-size-MB="1"/>
-
-</adios-config>
-
diff --git a/examples/solidfluid/solidfluid_read.cpp b/examples/solidfluid/solidfluid_read.cpp
deleted file mode 100644
index f451ff12d76a37317ebca73477997943b8c22247..0000000000000000000000000000000000000000
--- a/examples/solidfluid/solidfluid_read.cpp
+++ /dev/null
@@ -1,314 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * globalArrayXML.cpp
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <mpi.h>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include "adios2/ADIOS_OOP.h"
-
-struct MYDATA
-{
- int NX;
- double *t;
- std::vector<double> p;
-};
-
-const int N = 10;
-struct MYDATA solid, fluid;
-MPI_Comm comm = MPI_COMM_WORLD;
-int rank, size;
-
-void read_ckpt(adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid)
-{
- try
- {
- // Open an input which was written with an expected Method
- // 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
- auto ckptfile = adios.Open("checkpoint.bp", "r", comm, "checkpoint");
- // We can also manually set the read transport
- // auto 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);
- // 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
- ckptfile->Read("fluid/NX", &fluid.NX);
- // fluid.NX is filled at this point
-
- solid.t = new double(solid.NX);
- solid.p = std::vector<double>(solid.NX);
-
- fluid.t = new double(fluid.NX);
- fluid.p = std::vector<double>(fluid.NX);
-
- adios::ADIOS_SELECTION_WRITEBLOCK sel(rank);
- adios.Read(ckptfile, sel, "solid/temperature", solid.t);
- adios.Read(ckptfile, sel, "solid/pressure", solid.p);
- adios.Read(ckptfile, sel, "fluid/temperature", fluid.t);
- // force checking if the allocated space equals to the size of the
- // selection:
- adios.Read(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
- {
- if (rank == 0)
- {
- std::cout << e.what() << "\n";
- }
- }
-}
-
-void read_solid(adios::ADIOS adios, struct MYDATA &solid)
-{
- float timeout_sec = 1.0;
- int retval = 0;
-
- try
- {
- // 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 = adios.InqVar(solidfile, "temperature");
- v.GetBlockInfo();
-
- printf("ndim = %d\n", v.ndim);
- // printf ("nsteps = %d\n", v.nsteps);
- printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
-
- uint64_t slice_size = v.dims[0] / size;
-
- if (rank == size - 1)
- slice_size = slice_size + v.dims[0] % size;
-
- start[0] = rank * slice_size;
- count[0] = slice_size;
- start[1] = 0;
- count[1] = v.dims[1];
-
- auto data = std::make_unique<double[]>(slice_size * v.dims[1] * 8);
-
- adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
-
- /* Processing loop over the steps (we are already in the first one) */
- while (adios_errno != err_end_of_stream)
- {
- steps++; // steps start counting from 1
-
- solidfile.ScheduleRead(sel, "temperature", solid.t);
- solidfile.Read(true);
-
- if (rank == 0)
- printf("--------- Step: %d --------------------------------\n",
- solidfile.getCurrentStep());
-
- printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank,
- v.dims[0], v.dims[1]);
- for (i = 0; i < slice_size; i++)
- {
- printf(" [");
- for (j = 0; j < v.dims[1]; j++)
- {
- printf("%g ", *((double *)data + i * v.dims[1] + j));
- }
- printf("]");
- }
- printf(" ]\n\n");
-
- // advance to 1) next available step with 2) blocking wait
- solidfile.AdvanceStep(false, timeout_sec);
- if (adios_errno == err_step_notready)
- {
- printf("rank %d: No new step arrived within the timeout. Quit. "
- "%s\n",
- rank, adios_errmsg());
- break; // quit while loop
- }
- }
- solidfile.Close();
- }
- catch (std::exception &e)
- {
- if (adios_errno == err_file_not_found)
- {
- printf("rank %d: Stream not found after waiting %f seconds: %s\n",
- rank, timeout_sec, adios_errmsg());
- retval = adios_errno;
- }
- else if (adios_errno == err_end_of_stream)
- {
- printf("rank %d: Stream terminated before open. %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
- }
- else if (f == NULL)
- {
- printf("rank %d: Error at opening stream: %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
- }
- }
-}
-
-void read_fluid(adios::ADIOS adios, struct MYDATA &fluid)
-{
- 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 fluidfile(comm, "r");
-
- try
- {
- fluidfile.Open("fluid.bp"); //, ADIOS_LOCKMODE_NONE, timeout_sec);
-
- /* process file here... */
- const adios::ADIOS_VARINFO &v = fluidfile.InqVar("temperature");
- v.GetBlockInfo();
-
- printf("ndim = %d\n", v.ndim);
- // printf ("nsteps = %d\n", v.nsteps);
- printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
-
- uint64_t slice_size = v.dims[0] / size;
-
- if (rank == size - 1)
- slice_size = slice_size + v.dims[0] % size;
-
- start[0] = rank * slice_size;
- count[0] = slice_size;
- start[1] = 0;
- count[1] = v.dims[1];
-
- data = malloc(slice_size * v.dims[1] * 8);
-
- adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
-
- /* Processing loop over the steps (we are already in the first one) */
- while (adios_errno != err_end_of_stream)
- {
- steps++; // steps start counting from 1
-
- fluidfile.ScheduleRead(sel, "temperature", fluid.t);
- fluidfile.Read(true);
-
- if (rank == 0)
- printf("--------- Step: %d --------------------------------\n",
- fluidfile.getCurrentStep());
-
- printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank,
- v.dims[0], v.dims[1]);
- for (i = 0; i < slice_size; i++)
- {
- printf(" [");
- for (j = 0; j < v.dims[1]; j++)
- {
- printf("%g ", *((double *)data + i * v.dims[1] + j));
- }
- printf("]");
- }
- printf(" ]\n\n");
-
- // advance to 1) next available step with 2) blocking wait
- fluidfile.AdvanceStep(false, timeout_sec);
- if (adios_errno == err_step_notready)
- {
- printf("rank %d: No new step arrived within the timeout. Quit. "
- "%s\n",
- rank, adios_errmsg());
- break; // quit while loop
- }
- }
- fluidfile.Close();
- }
- catch (std::exception &e)
- {
- if (adios_errno == err_file_not_found)
- {
- printf("rank %d: Stream not found after waiting %f seconds: %s\n",
- rank, timeout_sec, adios_errmsg());
- retval = adios_errno;
- }
- else if (adios_errno == err_end_of_stream)
- {
- printf("rank %d: Stream terminated before open. %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
- }
- else if (f == NULL)
- {
- printf("rank %d: Error at opening stream: %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
- }
- }
-}
-
-int main(int argc, char **argv)
-{
-
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayXML.xml", comm, true);
-
- read_ckpt(adios, solid, fluid);
-
- read_solid(adios, solid);
-
- read_fluid(adios, fluid);
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << e.what() << "\n";
- }
- }
- if (rank == 0)
- printf("We have processed %d steps\n", steps);
-
- free(data);
- MPI_Finalize();
-
- return retval;
-}
diff --git a/examples/solidfluid/solidfluid_write.cpp b/examples/solidfluid/solidfluid_write.cpp
deleted file mode 100644
index a746dd52b6312dce6524f318690ee369cd288ccd..0000000000000000000000000000000000000000
--- a/examples/solidfluid/solidfluid_write.cpp
+++ /dev/null
@@ -1,249 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * solid fluid example
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include <adios2.h>
-
-using adiosFile = std::shared_ptr<adios::Engine>;
-
-struct MYDATA
-{
- int NX;
- double *t;
- std::vector<double> p;
-};
-
-const int N = 10;
-struct MYDATA solid, fluid;
-MPI_Comm comm = MPI_COMM_WORLD;
-int rank, size;
-
-void write_data(adiosFile writer, struct MYDATA &data)
-{
- writer->Write("NX", &data.NX);
- writer->Write("rank", &rank);
- writer->Write("size", &size);
- writer->Write("temperature", data.t);
- writer->Write("pressure", data.p.data());
- // writer->Flush(); AdvanceStep()???
-}
-
-void write_checkpoint(adiosFile ckptfile, const struct MYDATA &solid,
- const struct MYDATA &fluid)
-{
- try
- {
- ckptfile->Write("solid/NX", &solid.NX);
- ckptfile->Write("solid/rank", &rank);
- ckptfile->Write("solid/size", &size);
- ckptfile->Write("solid/temperature", solid.t);
- ckptfile->Write("solid/pressure", &solid.p[0]);
-
- ckptfile->Write("fluid/NX", &fluid.NX);
- ckptfile->Write("fluid/rank", &rank);
- ckptfile->Write("fluid/size", &size);
- ckptfile->Write("fluid/temperature", fluid.t);
- ckptfile->Write("fluid/pressure", fluid.p.data());
- // ckptfile->AdvanceStep(); ??
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << "ERROR: caught an exception from write_checkpoint\n";
- std::cout << e.what() << "\n";
- }
- }
-}
-
-void write_viz(std::shared_ptr<adios::Engine> vizstream, struct MYDATA &solid,
- struct MYDATA &fluid)
-{
- // 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
- // An array variable's dimension definitions are also re-defined with
- // dimensions <groupname>/<dimensionvar>
-
- // vizstream->Write ("solid", "NX", &solid.NX);
- // vizstream->Write ("solid", "rank", &rank);
- // vizstream->Write ("solid", "size", &size);
-
- // write solid group's temperature simply as temperature, risking
- // overloading
- // the 'temperature' variable when
- // reading from a file
-
- // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
-
- // vizstream->Write ("fluid", "NX", &fluid.NX);
- // vizstream->Write ("fluid", "rank", &rank);
- // vizstream->Write ("fluid", "size", &size);
-
- // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
-
- // vizstream->Flush(); // flushes all data to disk; required operation
- // vizstream.AdvanceStep();
-}
-
-void compute(int it, struct MYDATA &solid, struct MYDATA &fluid)
-{
- for (int i = 0; i < solid.NX; i++)
- {
- solid.t[i] = it * 100.0 + rank * solid.NX + i;
- solid.p[i] = it * 1000.0 + rank * solid.NX + i;
- }
- for (int i = 0; i < fluid.NX; i++)
- {
- fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
- fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
- }
-}
-
-int main(int argc, char *argv[])
-{
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- solid.NX = N;
- solid.t = new double[N];
- solid.p = std::vector<double>(N);
-
- fluid.NX = N;
- fluid.t = new double[N];
- fluid.p = std::vector<double>(N);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios(comm, true);
-
- adios::Method &fileSettings =
- adios.DeclareMethod("Reusable"); // default engine is BP writer
- fileSettings.AddTransport("POSIX", "have_metadata_file=no");
-
- // Open a file with a Method which has selected a group and a transport
- // in
- // the XML.
- // "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?
-
- auto solidfile = adios.Open("solid.bp", "w", comm, fileSettings);
-
- // "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?
- // solidfile.Open("solid.bp");
-
- // Open a file with a Method that has selected a group and an engine in
- // the
- // XML
- // The transport method(s) are (must be) associated with the engines
- // "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?
- auto fluidfile = adios.Open("fluid.bp", "w", comm, fileSettings);
-
- auto checkpointFile =
- adios.Open("checkpoint.bp", "w", comm, fileSettings);
-
- // 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");
- auto vizstream = adios.Open("stream.bp", "w", comm, fileSettings);
-
- // This creates an empty group inside, and we can write all kinds of
- // variables to it
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorVariables(logStream);
-
- int checkPointSteps = 10;
-
- for (int it = 1; it <= 100; it++)
- {
- compute(it, solid, fluid);
-
- write_data(solidfile, solid);
- write_data(fluidfile, fluid);
-
- if (it % checkPointSteps == 0)
- {
- write_checkpoint(checkpointFile, solid, fluid);
-
- MPI_Barrier(comm);
- if (rank == 0)
- {
- std::cout
- << "New checkpoint step, current = " << checkPointSteps
- << "\n";
- std::cin >> checkPointSteps;
- MPI_Bcast(&checkPointSteps, 1, MPI_INT, 0, comm);
- }
- MPI_Barrier(comm);
- }
-
- write_viz(vizstream, solid, fluid);
-
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
- }
-
- solidfile->Close();
- fluidfile->Close();
- vizstream->Close();
-
- // need barrier before we destroy the ADIOS object here automatically
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << "ERROR: " << e.what() << "\n";
- }
- }
-
- delete[] solid.t;
- delete[] fluid.t;
-
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
-}
diff --git a/examples/solidfluid/solidfluid_write_nompi.cpp b/examples/solidfluid/solidfluid_write_nompi.cpp
deleted file mode 100644
index ef8732ca2d5b951b65315298007ec30a813aa4a4..0000000000000000000000000000000000000000
--- a/examples/solidfluid/solidfluid_write_nompi.cpp
+++ /dev/null
@@ -1,242 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * solid fluid example
- *
- * Created on: Oct 31, 2016
- * Author: pnorbert
- */
-
-#include <fstream>
-#include <iostream>
-#include <stdexcept>
-#include <string>
-#include <vector>
-
-#include <adios2.h>
-
-using adiosFile = std::shared_ptr<adios::Engine>;
-
-struct MYDATA
-{
- int NX;
- double *t;
- std::vector<double> p;
-};
-
-const int N = 10;
-struct MYDATA solid, fluid;
-int rank = 0, size = 1;
-
-void set_io_variables(adios::ADIOS &adios, const std::string process)
-{
- adios.DefineVariable<int>(process + "/NX");
- adios.DefineVariable<int>(process + "/rank");
- adios.DefineVariable<int>(process + "/size");
- adios.DefineVariable<double>(process + "/temperature", adios::Dims{N});
- adios.DefineVariable<double>(process + "/pressure", adios::Dims{N});
-}
-
-void write_data(adiosFile writer, const std::string process,
- struct MYDATA &data)
-{
- writer->Write(process + "/NX", &data.NX);
- writer->Write(process + "/rank", &rank);
- writer->Write(process + "/size", &size);
- writer->Write(process + "/temperature", data.t);
- writer->Write(process + "/pressure", data.p.data());
- // writer->Flush(); AdvanceStep()???
-}
-
-void write_checkpoint(adiosFile ckptfile, const struct MYDATA &solid,
- const struct MYDATA &fluid)
-{
- try
- {
- ckptfile->Write("solid/NX", &solid.NX);
- ckptfile->Write("solid/rank", &rank);
- ckptfile->Write("solid/size", &size);
- ckptfile->Write("solid/temperature", solid.t);
- ckptfile->Write("solid/pressure", &solid.p[0]);
-
- ckptfile->Write("fluid/NX", &fluid.NX);
- ckptfile->Write("fluid/rank", &rank);
- ckptfile->Write("fluid/size", &size);
- ckptfile->Write("fluid/temperature", fluid.t);
- ckptfile->Write("fluid/pressure", fluid.p.data());
- // ckptfile->AdvanceStep(); ??
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
- {
- std::cout << "ERROR: caught an exception from write_checkpoint\n";
- std::cout << e.what() << "\n";
- }
- }
-}
-
-void write_viz(adiosFile vizstream, struct MYDATA &solid, struct MYDATA &fluid)
-{
- // 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
- // An array variable's dimension definitions are also re-defined with
- // dimensions <groupname>/<dimensionvar>
-
- // vizstream->Write ("solid", "NX", &solid.NX);
- // vizstream->Write ("solid", "rank", &rank);
- // vizstream->Write ("solid", "size", &size);
-
- // write solid group's temperature simply as temperature, risking
- // overloading
- // the 'temperature' variable when
- // reading from a file
-
- // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
-
- // vizstream->Write ("fluid", "NX", &fluid.NX);
- // vizstream->Write ("fluid", "rank", &rank);
- // vizstream->Write ("fluid", "size", &size);
-
- // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
-
- // vizstream->Flush(); // flushes all data to disk; required operation
- // vizstream.AdvanceStep();
-}
-
-void compute(int it, struct MYDATA &solid, struct MYDATA &fluid)
-{
- for (int i = 0; i < solid.NX; i++)
- {
- solid.t[i] = it * 100.0 + rank * solid.NX + i;
- solid.p[i] = it * 1000.0 + rank * solid.NX + i;
- }
- for (int i = 0; i < fluid.NX; i++)
- {
- fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
- fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
- }
-}
-
-int main(int argc, char *argv[])
-{
- solid.NX = N;
- solid.t = new double[N];
- solid.p = std::vector<double>(N);
-
- fluid.NX = N;
- fluid.t = new double[N];
- fluid.p = std::vector<double>(N);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios(true);
- set_io_variables(adios, "solid");
- set_io_variables(adios, "fluid");
-
- adios::Method &fileSettings =
- adios.DeclareMethod("Reusable"); // default engine is BP writer
- fileSettings.AddTransport("POSIX", "have_metadata_file=no");
-
- // Open a file with a Method which has selected a group and a transport
- // in
- // the XML.
- // "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?
-
- auto solidfile = adios.Open("solid.bp", "w", fileSettings);
-
- // "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?
- // solidfile.Open("solid.bp");
-
- // Open a file with a Method that has selected a group and an engine in
- // the
- // XML
- // The transport method(s) are (must be) associated with the engines
- // "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?
- auto fluidfile = adios.Open("fluid.bp", "w", fileSettings);
-
- auto checkpointFile = adios.Open("checkpoint.bp", "w", fileSettings);
-
- // 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");
- auto vizstream = adios.Open("stream.bp", "w", fileSettings);
-
- // This creates an empty group inside, and we can write all kinds of
- // variables to it
-
- // Get Monitor info
- std::ofstream logStream("info_nompi.log");
- adios.MonitorVariables(logStream);
-
- int checkPointSteps = 10;
-
- for (int it = 1; it <= 100; it++)
- {
- compute(it, solid, fluid);
-
- write_data(solidfile, "solid", solid);
- write_data(fluidfile, "fluid", fluid);
-
- if (it % checkPointSteps == 0)
- {
- write_checkpoint(checkpointFile, solid, fluid);
-
- {
- std::cout
- << "New checkpoint step, current = " << checkPointSteps
- << "\n";
- std::cin >> checkPointSteps;
- }
- }
-
- write_viz(vizstream, solid, fluid);
-
- std::cout << "Timestep " << it << " written\n";
- }
-
- solidfile->Close();
- fluidfile->Close();
- vizstream->Close();
- checkpointFile->Close();
-
- // need barrier before we destroy the ADIOS object here automatically
- // ...no!
- std::cout << "Finalize adios\n";
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- std::cout << e.what() << "\n";
- }
-
- delete[] solid.t;
- delete[] fluid.t;
-
- return 0;
-}
diff --git a/examples/xmlParser/xmlParser.cpp b/examples/xmlParser/xmlParser.cpp
deleted file mode 100644
index e19295e5dc59196895a40b4ff57900c079aa24cb..0000000000000000000000000000000000000000
--- a/examples/xmlParser/xmlParser.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0. See
- * accompanying file Copyright.txt for details.
- *
- * xmlParser.cpp
- *
- * Created on: Nov 2, 2016
- * Author: wfg
- */
-
-#include <iostream>
-#include <stdexcept>
-#include <string>
-
-#include "adios2/../../include/ADIOS.h"
-
-#ifdef HAVE_MPI
-#include <mpi.h>
-#else
-#include "adios2/../../include/mpidummy.h"
-using namespace adios;
-#endif
-
-static void Usage();
-
-int main(int argc, char *argv[])
-{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-
- try
- {
- if (argc != 2)
- {
- Usage();
- }
- else
- {
- const std::string xmlConfigFile(argv[1]);
- adios::ADIOS adios(xmlConfigFile, MPI_COMM_WORLD, true);
- adios.MonitorGroups(std::cout);
- }
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "ERROR: exception caught\n";
- std::cout << e.what() << "\n";
- }
- }
-
- MPI_Finalize();
- return 0;
-}
-
-static void Usage()
-{
- std::cout << "Program to test XML Config file parsing\n";
- std::cout << "Usage: \n";
- std::cout << "\t MPI version: ./xmlParser_mpi xmlConfigFile\n";
- std::cout << "\t Non-MPI version: ./xmlParser_nompi xmlConfigFile\n";
-}