diff --git a/bindings/python/ADIOSPy.cpp b/bindings/python/ADIOSPy.cpp
index a64b2d8a281d572df963e604d4ef832a63448391..c7d161221a7b91bfbfad7e7957be707de8bb7a14 100644
--- a/bindings/python/ADIOSPy.cpp
+++ b/bindings/python/ADIOSPy.cpp
@@ -12,15 +12,30 @@
#include "adiosPyTypes.h"
+#include "adios2/ADIOSMPI.h"
+
namespace adios
{
-ADIOSPy::ADIOSPy(MPI_Comm mpiComm, const bool debug)
-: m_DebugMode(debug), m_ADIOS(mpiComm, debug)
+ADIOSPy::ADIOSPy(const std::string configFile, MPI_Comm mpiComm,
+ const bool debugMode)
+: m_DebugMode(debugMode), m_ADIOS(configFile, mpiComm, debugMode)
{
}
-ADIOSPy::ADIOSPy(const bool debug) : m_DebugMode(debug), m_ADIOS(debug) {}
+ADIOSPy::ADIOSPy(MPI_Comm mpiComm, const bool debugMode)
+: ADIOSPy("", mpiComm, debugMode)
+{
+}
+
+ADIOSPy::ADIOSPy(const std::string configFile, const bool debugMode)
+: ADIOSPy("", MPI_COMM_SELF, debugMode)
+{
+}
+
+ADIOSPy::ADIOSPy(const bool debugMode) : ADIOSPy("", MPI_COMM_SELF, debugMode)
+{
+}
IOPy ADIOSPy::DeclareIO(const std::string name)
{
diff --git a/bindings/python/ADIOSPy.h b/bindings/python/ADIOSPy.h
index d8cc68c9e453ebd5d840c07b369c75e3cf98107a..e1ed1f0e1964f600f87d229cadf55ae2b9acabf6 100644
--- a/bindings/python/ADIOSPy.h
+++ b/bindings/python/ADIOSPy.h
@@ -18,6 +18,7 @@
#include <adios2.h>
#include "IOPy.h"
+#include "adios2/ADIOSMPICommOnly.h"
namespace adios
{
@@ -26,8 +27,11 @@ class ADIOSPy
{
public:
- ADIOSPy(MPI_Comm mpiComm, const bool debug);
- ADIOSPy(const bool debug);
+ ADIOSPy(const std::string configFile, MPI_Comm mpiComm,
+ const bool debugMode);
+ ADIOSPy(MPI_Comm mpiComm, const bool debugMode);
+ ADIOSPy(const std::string configFile, const bool debugMode);
+ ADIOSPy(const bool debugMode);
~ADIOSPy() = default;
IOPy DeclareIO(const std::string name);
diff --git a/bindings/python/gluePyBind11.cpp b/bindings/python/gluePyBind11.cpp
index a257180426b998d9537b878bc836ffa97f9960dd..358d3778193bde08867ce9027f5de5afc858c9e8 100644
--- a/bindings/python/gluePyBind11.cpp
+++ b/bindings/python/gluePyBind11.cpp
@@ -25,6 +25,26 @@
#include "adiosPyTypes.h"
#ifdef ADIOS2_HAVE_MPI
+adios::ADIOSPy ADIOSPyInitConfig(const std::string configFile,
+ adios::pyObject &object, const bool debugMode)
+{
+ MPI_Comm *mpiCommPtr = PyMPIComm_Get(object.ptr());
+
+ if (import_mpi4py() < 0)
+ {
+ throw std::runtime_error("ERROR: could not import mpi4py "
+ "communicator, in call to ADIOS "
+ "constructor\n");
+ }
+
+ if (mpiCommPtr == nullptr)
+ {
+ throw std::runtime_error("ERROR: mpi4py communicator is null, in call "
+ "to ADIOS constructor\n");
+ }
+ return adios::ADIOSPy(configFile, *mpiCommPtr, debugMode);
+}
+
adios::ADIOSPy ADIOSPyInit(adios::pyObject &object, const bool debugMode)
{
MPI_Comm *mpiCommPtr = PyMPIComm_Get(object.ptr());
@@ -44,6 +64,12 @@ adios::ADIOSPy ADIOSPyInit(adios::pyObject &object, const bool debugMode)
return adios::ADIOSPy(*mpiCommPtr, debugMode);
}
#else
+adios::ADIOSPy ADIOSPyInitConfig(const std::string configFile,
+ const bool debugMode)
+{
+ return adios::ADIOSPy(debugMode);
+}
+
adios::ADIOSPy ADIOSPyInit(const bool debugMode)
{
return adios::ADIOSPy(debugMode);
@@ -69,6 +95,8 @@ PYBIND11_PLUGIN(adios2)
m.attr("OpenModeAppend") = static_cast<int>(adios::OpenMode::Append);
m.attr("OpenModeReadWrite") = static_cast<int>(adios::OpenMode::ReadWrite);
m.def("ADIOS", &ADIOSPyInit, "Function that creates an ADIOS class object");
+ m.def("ADIOS", &ADIOSPyInitConfig,
+ "Function that creates an ADIOS class object using a config file");
pybind11::class_<adios::ADIOSPy>(m, "ADIOSPy")
.def("DeclareIO", &adios::ADIOSPy::DeclareIO);
diff --git a/examples/experimental/runtimeconfig/grandSchema.xml b/examples/experimental/runtimeconfig/grandSchema.xml
new file mode 100644
index 0000000000000000000000000000000000000000..71d80bd30be8c3aff11cb1adf55e28493a71fb6d
--- /dev/null
+++ b/examples/experimental/runtimeconfig/grandSchema.xml
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<adios-config>
+
+ <io name="Output">
+
+ <var name="myArray"> <!-- provide a sequence of transforms -->
+ <transform type='BZip2'> <!-- not implemented yet -->
+ BlockSize100K=3; <!-- must be a number between 0 and 9-->
+ </transform>
+ <transform type="Zfp"> <!-- not implemented yet, mutually exclusive options -->
+ Tolerance=1e-3; <!-- must be a number between 0 and 9-->
+ <!-- Rate=1; --> <!-- must be a number between 0 and 9-->
+ <!-- Precision=1; --> <!-- must be a number between 0 and 9-->
+ </transform>
+ </var>
+
+ <engine type="BPSuperEngine">
+ Threads=4; <!-- for memory operations and asynchronous tasks -->
+ Verbose=4; <!-- 0 (default) to 5, not implemented -->
+ ProfileUnits=Microseconds; <!-- Microseconds (default), Milliseconds, Seconds, Minutes, Hours -->
+ MaxBufferSize=20Mb; <!-- XXKb, XXMb, or XXXGb supported, 16Mb (default should depend on system) -->
+ InitialBufferSize=1Mb; <!-- XXKb, XXMb, or XXXGb supported, 16Kb (default shoudl depende on system) -->
+ BufferGrowthFactor=2; <!-- exponential growth factor > 1, 1.5 (default), for this case: 1, 2, 4, 8, 16, 20 Mb-->
+ </engine>
+
+ <transport type="File">
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ Library=stdio; <!-- lowest level IO library, POSIX (default), stdio (C FILE*), fstream (C++), and interop: hdf5, netcdf? -->
+ CacheSize=8192; <!-- not to be confused with ADIOS heap buffer, this is the low-level setvbuffer, putsetbuf, default is 8192 bytes in most systems -->
+ CollectiveMetadata=Yes; <!-- this transport requires a collective/global metadata at the end, default = no -->
+ </transport>
+
+ <transport type="File">
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ Library=hdf5; <!-- lowest level IO library, POSIX (default), stdio (C FILE*), fstream (C++), and interop: hdf5, netcdf? -->
+ Name=data.h5; <!-- Mandatory if more than one File transport to avoid conflict -->
+ </transport>
+
+ <transport type="SharedMemory">
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ Library=SystemV; <!-- lowest level shared memory library: SystemV (default), Boost (interprocess), IPC (POSIX), IPCMMap (POSIX) -->
+ Name=data.shmem; <!-- Mandatory to create process key -->
+ SetSize=10Mb; <!-- Mandatory and fixed size (can't be extended) -->
+ </transport>
+
+ <transport type="NVRAM">
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ Library=POSIX; <!-- lowest level library -->
+ Name=/bb_location/data.bb; <!-- Mandatory -->
+ SetSize=10Mb; <!-- Mandatory and fixed size (can't be extended) -->
+ </transport>
+
+ <transport type="WAN">
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ IPAddress=128.219.4.85; <!-- Mandatory -->
+ Port=500; <!-- Default=500? -->
+ Library=zmq; <!-- lowest level IO library, zmq, UDP, etc. -->
+ CacheSize=8192; <!-- not to be confused with ADIOS heap buffer, this is transport library cache, always in bytes -->
+ </transport>
+
+ <transport type="RDMA"> <!-- Staging gets more complex depending on library requirements-->
+ ProfileUnits=Microseconds; <!-- Microseconds, Milliseconds, Seconds, Minutes, Hours -->
+ Library=ibverbs; <!-- SST (default), Flexpath, Dataspaces, ibverbs -->
+ Port=18515; <!-- ibverbs -->
+ IBPort=1; <!-- ibverbs -->
+ SetSize=1Mb; <!-- Mandatory and fixed size (can't be extended) -->
+ TXDepth=100; <!-- ibverbs -->
+ SocketFD=-1; <!-- ibverbs -->
+ ServerName=NULL; <!-- ibverbs -->
+ RemoteConnection=NULL; <!-- ibverbs -->
+ IBDev=NULL; <!-- ibverbs -->
+ </transport>
+
+ </io>
+
+</adios-config>
\ No newline at end of file
diff --git a/examples/experimental/runtimeconfig/multipleIOResolutions.xml b/examples/experimental/runtimeconfig/multipleIOResolutions.xml
new file mode 100644
index 0000000000000000000000000000000000000000..28fe854084bc7e8126f68f2a3b70aa65b7dfc6af
--- /dev/null
+++ b/examples/experimental/runtimeconfig/multipleIOResolutions.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<adios-config>
+
+ <io name="LowResolution">
+ <var name="myArray"> <!-- provide a sequence of transforms -->
+ <transform type="Zfp"> <!-- not implemented yet, mutually exclusive options -->
+ Tolerance=1e-2; <!-- must be a number between 0 and 9-->
+ <!-- Rate=1; --> <!-- must be a number between 0 and 9-->
+ <!-- Precision=1; --> <!-- must be a number between 0 and 9-->
+ </transform>
+ </var>
+ </io>
+
+ <io name="HighResolution">
+ <var name="myArray"> <!-- provide a sequence of transforms -->
+ <transform type="Zfp"> <!-- not implemented yet, mutually exclusive options -->
+ Tolerance=1e-5; <!-- must be a number between 0 and 9-->
+ <!-- Rate=1; --> <!-- must be a number between 0 and 9-->
+ <!-- Precision=1; --> <!-- must be a number between 0 and 9-->
+ </transform>
+ </var>
+ </io>
+
+</adios-config>
\ No newline at end of file
diff --git a/examples/experimental/runtimeconfig/multipleTransformedVariables.xml b/examples/experimental/runtimeconfig/multipleTransformedVariables.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8338320d5ce13b1fd8cd5be57c639d52ff58fb5e
--- /dev/null
+++ b/examples/experimental/runtimeconfig/multipleTransformedVariables.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<adios-config>
+
+ <io name="LowResolution">
+ <transform type="Zfp"> <!-- not implemented yet, mutually exclusive options -->
+ Tolerance=1e-2; <!-- must be a number between 0 and 9 -->
+ <!-- Rate=1; --> <!-- must be a number between 0 and 9 -->
+ <!-- Precision=1; --> <!-- must be a number between 0 and 9 -->
+ <variable name="myArray1"></variable>
+ <variable name="myArray2"></variable>
+ <variable name="myArray3"></variable>
+ </transform>
+ </io>
+
+ <io name="HighResolution">
+ <transform type="Zfp"> <!-- not implemented yet, mutually exclusive options -->
+ Tolerance=1e-5; <!-- must be a number between 0 and 9 -->
+ <!-- Rate=1; --> <!-- must be a number between 0 and 9 -->
+ <!-- Precision=1; --> <!-- must be a number between 0 and 9 -->
+ <variable name="myArray1"></variable>
+ <variable name="myArray2"></variable>
+ <variable name="myArray3"></variable>
+ </transform>
+ </io>
+
+</adios-config>
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index a3d4cd35a3f9ffd3e32239d26fbda027e69ca8b1..c5707cdf0ed9b9ac1d0de36b7bd77b20f70d9c6f 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -9,7 +9,16 @@ if(ADIOS2_HAVE_MPI)
add_executable(hello_bpWriter helloBPWriter.cpp)
target_include_directories(hello_bpWriter PRIVATE ${MPI_C_INCLUDE_PATH})
target_link_libraries(hello_bpWriter ${MPI_C_LIBRARIES})
+
+ add_executable(hello_bpWriterXML helloBPWriterXML.cpp)
+ target_include_directories(hello_bpWriterXML PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_bpWriterXML ${MPI_C_LIBRARIES})
+
else()
add_executable(hello_bpWriter helloBPWriter_nompi.cpp)
+ add_executable(hello_bpWriterXML helloBPWriterXML_nompi.cpp)
+
endif()
+
+target_link_libraries(hello_bpWriterXML adios2)
target_link_libraries(hello_bpWriter adios2)
diff --git a/examples/hello/bpWriter/config.xml b/examples/hello/bpWriter/config.xml
deleted file mode 100644
index 10dfa830e33baed86ec3c2667f0bd6b67b2c8aa1..0000000000000000000000000000000000000000
--- a/examples/hello/bpWriter/config.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0"?>
-<adios-config>
-
- <io name="Output">
- <engine name="BPFileWriter">verbose=4;profile_units=mus</engine>
- <transport name= "File">
- profile_units=mus;
- abort_on_error;
- have_metadata_file
- =
- no;
- </transport>
-
- <!-- Create a named transform and add variables to it here.
- name is optional, required only if it is used outside the definition
- options is optional to pass parameters to the transformation
- -->
- <transform name="LossyCompression" transform="zfp" options="accuracy=0.001">
- <var name="myMatrix"/>
- <var name="ThisVarDoesNotExists"/>
- </transform>
-
- <!-- Unnamed transformation -->
- <transform transform="bzip2">
- <var name="myMatrix2"/>
- </transform>
-
- <!-- A variable can have its own private transform definition.
- Also its own ordered chain of transformations.
- Also can refer to a transform defined previously
- -->
- <var name="myDoubles">
- <transform transform="identity">verbose=DEBUG</transform>
- <transform name="LossyCompression"/>
- </var>
-
- <buffer max-size-MB="20"/>
- </io>
-
-</adios-config>
-
diff --git a/examples/hello/bpWriter/helloBPWriter.py b/examples/hello/bpWriter/helloBPWriter.py
index 780507684e067c519173210be2e3f8a855a67082..7332f5e7333b159d00187035f4d3911c239a3f53 100644
--- a/examples/hello/bpWriter/helloBPWriter.py
+++ b/examples/hello/bpWriter/helloBPWriter.py
@@ -1,32 +1,35 @@
-# clang-format off
#
# Distributed under the OSI-approved Apache License, Version 2.0. See
# accompanying file Copyright.txt for details.
#
-# test_hello.py
+# helloBPWriter.py
# Created on: Feb 2, 2017
# Author: William F Godoy godoywf@ornl.gov
from mpi4py import MPI
+import numpy
import adios2
-import numpy as np
+
+# MPI
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
# User data
-myArray = np.array([1., 2., 3., 4., 5., 6.])
+myArray = numpy.array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
+Nx = myArray.size
-# ADIOS
-adios = adios2.ADIOS(MPI.COMM_WORLD, adios2.DebugON)
+# ADIOS MPI Communicator, debug mode
+adios = adios2.ADIOS(comm, adios2.DebugON)
-# IO
-bpIO = adios.DeclareIO("BPN2N")
+# ADIOS IO
+bpIO = adios.DeclareIO("BPFile_N2N")
-# Variable
+# ADIOS Variable name, shape, start, offset, constant dims
ioArray = bpIO.DefineVariable(
- "bpArray", [myArray.size], [0], [myArray.size], adios2.ConstantDims)
+ "bpArray", [size * Nx], [rank * Nx], [Nx], adios2.ConstantDims)
-# Engine
-bpFileWriter = bpIO.Open("myArray.bp", adios2.OpenModeWrite)
-# bpFileWriter = bpIO.Open("myArray.bp", adiosOpenModeWrite,
-# MPI.COMM_WORLD) //doesn't work
+# ADIOS Engine
+bpFileWriter = bpIO.Open("npArray.bp", adios2.OpenModeWrite)
bpFileWriter.Write(ioArray, myArray)
bpFileWriter.Close()
diff --git a/examples/hello/bpWriter/helloBPWriter.xml b/examples/hello/bpWriter/helloBPWriter.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bda56e4c18b67f1c4a68d0558c470b80e8c9b616
--- /dev/null
+++ b/examples/hello/bpWriter/helloBPWriter.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<adios-config>
+
+ <io name="BPFile_N2N">
+ <engine type="BPFileWriter">
+ Threads=1; <!-- for vectorized memory operations and asynchronous tasks -->
+ ProfileUnits=Microseconds; <!-- Microseconds (default), Milliseconds, Seconds, Minutes, Hours -->
+ MaxBufferSize=20Mb; <!-- XXKb, XXMb, or XXXGb supported, 16Mb (default should depend on system) -->
+ InitialBufferSize=1Mb; <!-- XXKb, XXMb, or XXXGb supported, 16Kb (default should depend on system) -->
+ BufferGrowthFactor=2; <!-- exponential growth factor > 1, 1.5 (default, e.g. STL default=2), for this case: 1, 2, 4, 8, 16, 20 Mb-->
+ </engine>
+
+ <transport type="File">
+ Library=POSIX;
+ ProfileUnits=Milliseconds;
+ </transport>
+
+ </io>
+
+</adios-config>
\ No newline at end of file
diff --git a/examples/hello/bpWriter/helloBPWriterXML.cpp b/examples/hello/bpWriter/helloBPWriterXML.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..807b0c9c32f948dc2aebe694fdd194664eef8653
--- /dev/null
+++ b/examples/hello/bpWriter/helloBPWriterXML.cpp
@@ -0,0 +1,82 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * helloBPWriter.cpp: Simple self-descriptive example of how to write a variable
+ * to a BP File that lives in several MPI processes.
+ *
+ * Created on: Feb 16, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#include <ios> //std::ios_base::failure
+#include <iostream> //std::cout
+#include <mpi.h>
+#include <stdexcept> //std::invalid_argument std::exception
+#include <vector>
+
+#include <adios2.h>
+
+int main(int argc, char *argv[])
+{
+ MPI_Init(&argc, &argv);
+ int rank, size;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &size);
+
+ /** Application variable */
+ std::vector<float> myFloats = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myFloats.size();
+
+ try
+ {
+ /** ADIOS class factory of IO class objects, DebugON is recommended */
+ adios::ADIOS adios("helloBPWriter.xml", MPI_COMM_WORLD, adios::DebugON);
+
+ /*** IO class object: settings and factory of Settings: Variables,
+ * Parameters, Transports, and Execution: Engines */
+ adios::IO &bpIO = adios.DeclareIO("BPFile_N2N");
+
+ /** global array : name, { shape (total) }, { start (local) }, { count
+ * (local) }, all are constant dimensions */
+ adios::Variable<float> &bpFloats = bpIO.DefineVariable<float>(
+ "bpFloats", {size * Nx}, {rank * Nx}, {Nx}, adios::ConstantDims);
+
+ /** Engine derived class, spawned to start IO operations */
+ auto bpWriter = bpIO.Open("myVector.bp", adios::OpenMode::Write);
+
+ if (!bpWriter)
+ {
+ throw std::ios_base::failure(
+ "ERROR: bpWriter not created at Open\n");
+ }
+
+ /** Write variable for buffering */
+ bpWriter->Write<float>(bpFloats, myFloats.data());
+
+ /** Create bp file, engine becomes unreachable after this*/
+ bpWriter->Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM from rank "
+ << rank << "\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout
+ << "IO System base failure exception, STOPPING PROGRAM from rank "
+ << rank << "\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM from rank " << rank << "\n";
+ std::cout << e.what() << "\n";
+ }
+
+ MPI_Finalize();
+
+ return 0;
+}
diff --git a/examples/hello/bpWriter/helloBPWriterXML.py b/examples/hello/bpWriter/helloBPWriterXML.py
new file mode 100644
index 0000000000000000000000000000000000000000..2d81dd0bd990693198d92fed91eca035e3b81548
--- /dev/null
+++ b/examples/hello/bpWriter/helloBPWriterXML.py
@@ -0,0 +1,36 @@
+#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#
+# helloBPWriterXML.py
+# Created on: Feb 2, 2017
+# Author: William F Godoy godoywf@ornl.gov
+
+from mpi4py import MPI
+import adios2
+import numpy
+
+# MPI
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
+
+# User data
+myArray = numpy.array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
+Nx = myArray.size
+
+# ADIOS config file, MPI communicator, debug mode
+adios = adios2.ADIOS("helloBPWriter.xml", comm, adios2.DebugON)
+
+# ADIOS IO, name must be the same as in helloBPWriter.xml for runtime settings
+bpIO = adios.DeclareIO("BPFile_N2N")
+
+# Variable name, shape, start, count, ConstantDims = True
+ioArray = bpIO.DefineVariable(
+ "bpArray", [size * Nx], [rank * Nx], [Nx], adios2.ConstantDims)
+
+# Engine name, open mode
+bpFileWriter = bpIO.Open("npArray.bp", adios2.OpenModeWrite)
+# Write variable, numpy object
+bpFileWriter.Write(ioArray, myArray)
+bpFileWriter.Close()
diff --git a/examples/hello/bpWriter/helloBPWriterXML_nompi.cpp b/examples/hello/bpWriter/helloBPWriterXML_nompi.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..8028787a699932f8f7c4079f30b5de9c67f61630
--- /dev/null
+++ b/examples/hello/bpWriter/helloBPWriterXML_nompi.cpp
@@ -0,0 +1,71 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * helloBPWriterXML_nompi.cpp: sequential non-mpi version of helloBPWriterXML
+ *
+ * Created on: Feb 16, 2017
+ * Author: William F Godoy godoywf@ornl.gov
+ */
+
+#include <ios> //std::ios_base::failure
+#include <iostream> //std::cout
+#include <mpi.h>
+#include <stdexcept> //std::invalid_argument std::exception
+#include <vector>
+
+#include <adios2.h>
+
+int main(int argc, char *argv[])
+{
+ /** Application variable */
+ std::vector<float> myFloats = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myFloats.size();
+
+ try
+ {
+ /** ADIOS class factory of IO class objects, DebugON is recommended */
+ adios::ADIOS adios("helloBPWriter.xml", adios::DebugON);
+
+ /*** IO class object: settings and factory of Settings: Variables,
+ * Parameters, Transports, and Execution: Engines */
+ adios::IO &bpIO = adios.DeclareIO("BPFile_N2N");
+
+ /** global array : name, { shape (total) }, { start (local) }, { count
+ * (local) }, all are constant dimensions */
+ adios::Variable<float> &bpFloats = bpIO.DefineVariable<float>(
+ "bpFloats", {}, {}, {Nx}, adios::ConstantDims);
+
+ /** Engine derived class, spawned to start IO operations */
+ auto bpWriter = bpIO.Open("myVector.bp", adios::OpenMode::Write);
+
+ if (!bpWriter)
+ {
+ throw std::ios_base::failure(
+ "ERROR: bpWriter not created at Open\n");
+ }
+
+ /** Write variable for buffering */
+ bpWriter->Write<float>(bpFloats, myFloats.data());
+
+ /** Create bp file, engine becomes unreachable after this*/
+ 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 << "IO System base failure exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM from rank\n";
+ std::cout << e.what() << "\n";
+ }
+
+ return 0;
+}
diff --git a/examples/hello/bpWriter/helloBPWriterXML_nompi.py b/examples/hello/bpWriter/helloBPWriterXML_nompi.py
new file mode 100644
index 0000000000000000000000000000000000000000..0373d1e67294ef45e72ff7e1ef04e9f767098da7
--- /dev/null
+++ b/examples/hello/bpWriter/helloBPWriterXML_nompi.py
@@ -0,0 +1,30 @@
+#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#
+# helloBPWriterXML_nompi.py serial non-MPI version of helloBPWriter.py
+# Created on: Feb 2, 2017
+# Author: William F Godoy godoywf@ornl.gov
+
+import numpy
+import adios2
+
+
+# User data
+myArray = numpy.array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
+Nx = myArray.size
+
+# ADIOS config file, debug mode
+adios = adios2.ADIOS("helloBPWriter.xml", adios2.DebugON)
+
+# ADIOS IO, name must be the same as in helloBPWriter.xml for runtime settings
+bpIO = adios.DeclareIO("BPFile_N2N")
+
+# ADIOS local array: Variable name, shape, start, offset
+ioArray = bpIO.DefineVariable(
+ "bpArray", [], [], [Nx], adios2.ConstantDims)
+
+# ADIOS Engine
+bpFileWriter = bpIO.Open("npArray.bp", adios2.OpenModeWrite)
+bpFileWriter.Write(ioArray, myArray)
+bpFileWriter.Close()
diff --git a/source/adios2/ADIOSMPI.h b/source/adios2/ADIOSMPI.h
index 3524532d34ee3e5b81ef977f6269cf25a813047e..95ae7619aebdb9b32af02a9f6adbd7b2488f06a3 100644
--- a/source/adios2/ADIOSMPI.h
+++ b/source/adios2/ADIOSMPI.h
@@ -14,4 +14,17 @@
#include "adios2/mpidummy.h"
#endif
+#include <climits> //UXXX_MAX
+#include <cstdint> //SIZE_MAX
+
+#if SIZE_MAX == UINT_MAX
+#define ADIOS2_MPI_SIZE_T MPI_UNSIGNED
+#elif SIZE_MAX == ULONG_MAX
+#define ADIOS2_MPI_SIZE_T MPI_UNSIGNED_LONG
+#elif SIZE_MAX == ULLONG_MAX
+#define ADIOS2_MPI_SIZE_T MPI_UNSIGNED_LONG_LONG
+#else
+#error "size_t could not be mapped to a MPI Type"
+#endif
+
#endif /* ADIOS2_ADIOSMPI_H_ */
diff --git a/source/adios2/core/ADIOS.cpp b/source/adios2/core/ADIOS.cpp
index ee373fb869ae75a4d98457b0624646fbfb31af55..194dbdddbf081a4f511cf95c17c632a143fe8c79 100644
--- a/source/adios2/core/ADIOS.cpp
+++ b/source/adios2/core/ADIOS.cpp
@@ -19,6 +19,7 @@
/// \endcond
#include "adios2/ADIOSMPI.h"
+#include "adios2/helper/adiosFunctions.h"
namespace adios
{
@@ -31,9 +32,14 @@ ADIOS::ADIOS(const std::string configFile, MPI_Comm mpiComm,
{
CheckMPI();
}
- // XML to be implemented later
- // InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage,
- // m_Transforms, m_Groups );
+ if (!configFile.empty())
+ {
+ if (configFile.substr(configFile.size() - 3) == "xml")
+ {
+ InitXML(configFile, m_MPIComm, m_DebugMode, m_Transforms, m_IOs);
+ }
+ // TODO expand for other formats
+ }
}
ADIOS::ADIOS(const std::string configFile, const bool debugMode)
@@ -56,7 +62,7 @@ IO &ADIOS::DeclareIO(const std::string ioName)
{
if (m_DebugMode)
{
- if (itIO->second.InConfigFile())
+ if (!itIO->second.InConfigFile())
{
throw std::invalid_argument(
"ERROR: IO class object with name " + ioName +
diff --git a/source/adios2/helper/adiosString.cpp b/source/adios2/helper/adiosString.cpp
index 90b6399b131dd8f19b513e6d37236d3d63b3a65d..bc7841276e0f8e0490ac6006134e1d618940919b 100644
--- a/source/adios2/helper/adiosString.cpp
+++ b/source/adios2/helper/adiosString.cpp
@@ -24,9 +24,9 @@ std::string FileToString(const std::string &fileName)
{
std::ifstream fileStream(fileName);
- if (!fileStream.good())
+ if (!fileStream)
{
- throw std::ios_base::failure(
+ throw std::invalid_argument(
"ERROR: file " + fileName +
" could not be opened. Check permissions or existence\n");
}
diff --git a/source/adios2/helper/adiosSystem.cpp b/source/adios2/helper/adiosSystem.cpp
index 9836130796bb035d886d0d8c60bd334c20748ac5..bc8acdcfbd07366e149c0d79f6aa86d9eba3f2b4 100644
--- a/source/adios2/helper/adiosSystem.cpp
+++ b/source/adios2/helper/adiosSystem.cpp
@@ -16,7 +16,9 @@
#include <chrono> //system_clock, now
#include <ctime> //std::ctime
+#include "adios2/ADIOSMPI.h"
#include "adios2/ADIOSTypes.h"
+#include "adios2/helper/adiosString.h"
namespace adios
{
@@ -77,4 +79,41 @@ std::string LocalTimeDate() noexcept
return std::string(std::ctime(&now));
}
+std::string BroadcastString(const std::string &input, MPI_Comm mpiComm)
+{
+ std::string receivedInput;
+ size_t characterCount = 0;
+
+ int rank;
+ MPI_Comm_rank(mpiComm, &rank);
+
+ if (rank == 0) // sender
+ {
+ characterCount = input.size();
+
+ // broadcast size for allocation
+ MPI_Bcast(&characterCount, 1, ADIOS2_MPI_SIZE_T, 0, mpiComm);
+
+ // broadcast contents
+ MPI_Bcast(const_cast<char *>(input.c_str()),
+ static_cast<int>(characterCount), MPI_CHAR, 0, mpiComm);
+
+ return input;
+ }
+ else // receivers
+ {
+ // receive size
+ MPI_Bcast(&characterCount, 1, ADIOS2_MPI_SIZE_T, 0, mpiComm);
+
+ // allocate receiver
+ std::vector<char> stringReceiver(characterCount);
+ MPI_Bcast(stringReceiver.data(), static_cast<int>(characterCount),
+ MPI_CHAR, 0, mpiComm);
+
+ receivedInput.assign(stringReceiver.begin(), stringReceiver.end());
+ }
+
+ return receivedInput;
+}
+
} // end namespace adios
diff --git a/source/adios2/helper/adiosSystem.h b/source/adios2/helper/adiosSystem.h
index 9374d160370839377b6c4897f3b489fbb850216e..389e095dd838048a5503549abe4fea970dbc0eb4 100644
--- a/source/adios2/helper/adiosSystem.h
+++ b/source/adios2/helper/adiosSystem.h
@@ -17,6 +17,8 @@
#include <vector>
/// \endcond
+#include "adios2/ADIOSMPICommOnly.h"
+
namespace adios
{
@@ -41,6 +43,15 @@ bool IsLittleEndian() noexcept;
*/
std::string LocalTimeDate() noexcept;
+/**
+ * Rank 0: opens file, dumps contents string and broadcast.
+ * Others: receive std::vector<char> and copy to a string
+ * @param fileName
+ * @param mpiComm
+ * @return fileContents as a single string
+ */
+std::string BroadcastString(const std::string &input, MPI_Comm mpiComm);
+
} // end namespace adios
#endif /* ADIOS2_HELPER_ADIOSSYSTEM_H_ */
diff --git a/source/adios2/helper/adiosXML.cpp b/source/adios2/helper/adiosXML.cpp
index 746a436145472b910e58d2dccec7e6adc8b9d363..d52968e1ecfc1e24989269973d320b4a2b1dfb4b 100644
--- a/source/adios2/helper/adiosXML.cpp
+++ b/source/adios2/helper/adiosXML.cpp
@@ -11,386 +11,457 @@
#include "adiosXML.h"
/// \cond EXCLUDE_FROM_DOXYGEN
+#include <sstream>
#include <stdexcept> //std::invalid_argument
/// \endcond
+#include "adios2/ADIOSTypes.h"
+#include "adios2/helper/adiosString.h"
+
namespace adios
{
-void GetSubString(const std::string initialTag, const std::string finalTag,
- const std::string content, std::string &subString,
- std::string::size_type ¤tPosition)
+void RemoveCommentsXML(std::string ¤tContent) noexcept
{
- auto lf_Wipe = [](std::string &subString,
- std::string::size_type ¤tPosition) {
- subString.clear();
- currentPosition = std::string::npos;
- };
+ std::string::size_type startComment(currentContent.find("<!--"));
+ while (startComment != currentContent.npos)
+ {
+ std::string::size_type endComment(currentContent.find("-->"));
+ currentContent.erase(startComment, endComment - startComment + 3);
+ startComment = currentContent.find("<!--");
+ }
+}
+
+TagXML GetTagXML(const std::string tagName, const std::string &content,
+ std::string::size_type &position)
+{
auto lf_SetPositions =
- [](const char quote, const std::string::size_type quotePosition,
- const std::string &content, std::string::size_type ¤tPosition,
- std::string::size_type &closingQuotePosition) {
- currentPosition = quotePosition;
- closingQuotePosition = content.find(quote, currentPosition + 1);
- };
-
- // BODY OF FUNCTION STARTS HERE
- std::string::size_type start(content.find(initialTag, currentPosition));
- if (start == content.npos)
+ [](const std::string input, const std::string &content,
+ std::string::size_type &position) -> std::string::size_type {
+
+ const std::string::size_type inputPosition =
+ GetStringPositionXML(input, content, position);
+
+ if (inputPosition != std::string::npos)
+ {
+ position = inputPosition + input.size();
+ }
+ return inputPosition;
+ };
+
+ TagXML tagXML;
+
+ std::string name(tagName);
+ if (name.back() == ' ')
{
- lf_Wipe(subString, currentPosition);
- return;
+ name.pop_back();
}
- currentPosition = start;
- std::string::size_type end(content.find(finalTag, currentPosition));
- if (end == content.npos)
+ auto openingStart = lf_SetPositions("<" + name, content, position);
+ auto openingEnd = lf_SetPositions(">", content, position);
+
+ if (openingStart == std::string::npos || openingEnd == std::string::npos)
{
- lf_Wipe(subString, currentPosition);
- return;
+ tagXML.IsFull = false;
+ return tagXML;
}
- // here make sure the finalTag is not a value surrounded by " " or ' ', if
- // so
- // find next
- bool isValue = true;
+ tagXML.Header = content.substr(openingStart, openingEnd + 1 - openingStart);
+
+ auto closingStart =
+ GetStringPositionXML("</" + name + ">", content, position);
- while (isValue)
+ if (closingStart == std::string::npos)
{
- std::string::size_type singleQuotePosition =
- content.find('\'', currentPosition);
- std::string::size_type doubleQuotePosition =
- content.find('\"', currentPosition);
+ throw std::invalid_argument(
+ "ERROR: could not find closing tag </" + name +
+ "> in XML config file, in call to ADIOS constructor\n");
+ }
+ tagXML.IsFull = true;
+ tagXML.Elements =
+ content.substr(openingEnd + 1, closingStart - (openingEnd + 1));
+
+ // std::cout << "START..." << tagXML.Header << "...";
+ // std::cout << tagXML.Elements << "...END\n";
+
+ return tagXML;
+}
+
+std::string::size_type
+GetStringPositionXML(const std::string input, const std::string &content,
+ const std::string::size_type &startPosition) noexcept
+{
+ std::string::size_type foundPosition(content.find(input, startPosition));
+ if (foundPosition == content.npos)
+ {
+ return foundPosition;
+ }
+
+ // check if it is not inside " " or ' '
+ std::string::size_type currentPosition(startPosition);
+
+ while (foundPosition != content.npos)
+ {
+ const std::string::size_type singleQuotePosition(
+ content.find('\'', currentPosition));
+ const std::string::size_type doubleQuotePosition(
+ content.find('\"', currentPosition));
if ((singleQuotePosition == content.npos &&
doubleQuotePosition == content.npos) ||
(singleQuotePosition == content.npos &&
- end < doubleQuotePosition) ||
+ foundPosition < doubleQuotePosition) ||
(doubleQuotePosition == content.npos &&
- end < singleQuotePosition) ||
- (end < singleQuotePosition && end < doubleQuotePosition))
+ foundPosition < singleQuotePosition) ||
+ (foundPosition < singleQuotePosition &&
+ foundPosition < doubleQuotePosition))
{
break;
}
-
// find the closing corresponding quote
std::string::size_type closingQuotePosition;
- if (singleQuotePosition == content.npos)
- { // no ' anywhere
- lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
- closingQuotePosition);
+ if (singleQuotePosition != content.npos &&
+ doubleQuotePosition == content.npos)
+ {
+ currentPosition = singleQuotePosition;
+ closingQuotePosition = content.find('\'', currentPosition + 1);
}
- else if (doubleQuotePosition == content.npos)
- { // no " anywhere
- lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
- closingQuotePosition);
+ else if (singleQuotePosition == content.npos &&
+ doubleQuotePosition != content.npos)
+ {
+ currentPosition = doubleQuotePosition;
+ closingQuotePosition = content.find('\"', currentPosition + 1);
}
else
{
if (singleQuotePosition < doubleQuotePosition)
{
- lf_SetPositions('\'', singleQuotePosition, content,
- currentPosition, closingQuotePosition);
+ currentPosition = singleQuotePosition;
+ closingQuotePosition = content.find('\'', currentPosition + 1);
}
else
- { // find the closing "
- lf_SetPositions('\"', doubleQuotePosition, content,
- currentPosition, closingQuotePosition);
+ {
+ currentPosition = doubleQuotePosition;
+ closingQuotePosition = content.find('\"', currentPosition + 1);
}
}
-
- if (closingQuotePosition ==
- content.npos) // if can't find closing it's open until the end
+ // if can't find closing it's open until the end
+ if (closingQuotePosition == content.npos)
{
- lf_Wipe(subString, currentPosition);
- return;
+ currentPosition == content.npos;
+ break;
}
currentPosition = closingQuotePosition + 1;
- if (closingQuotePosition < end)
+ if (closingQuotePosition < foundPosition)
{
continue;
}
+ else
+ {
+ // if this point is reached it means it's a value inside " " or ' ',
+ // iterate
+ foundPosition = content.find(input, currentPosition);
+ currentPosition = foundPosition;
+ }
+ }
+
+ return foundPosition;
+}
+
+Params GetTagAttributesXML(const std::string &tagHeader)
+{
+ auto lf_GetQuotedValue = [](const char quote,
+ const std::string::size_type "ePosition,
+ std::string ¤tTag) -> std::string {
+
+ currentTag = currentTag.substr(quotePosition + 1);
+ auto nextQuotePosition = currentTag.find(quote);
+
+ if (nextQuotePosition == currentTag.npos)
+ {
+ throw std::invalid_argument(
+ "ERROR: Invalid attribute in..." + currentTag +
+ "...check XML file, in call to ADIOS constructor\n");
+ }
+
+ const std::string value(currentTag.substr(0, nextQuotePosition));
+ currentTag = currentTag.substr(nextQuotePosition + 1);
+ return value;
+ };
+
+ auto lf_GetAttributes = [&](const std::string &tag) -> Params {
+ Params attributes;
+ std::string currentTag(tag.substr(tag.find_first_of(" \t\n")));
+
+ while (currentTag.find('=') != currentTag.npos) // equalPosition
+ {
+ currentTag =
+ currentTag.substr(currentTag.find_first_not_of(" \t\n"));
+ auto equalPosition = currentTag.find('=');
+ if (currentTag.size() <= equalPosition + 1)
+ {
+ throw std::invalid_argument(
+ "ERROR: tag " + tag +
+ " is incomplete, check XML config file, "
+ "in call to ADIOS constructor\n");
+ }
+
+ const std::string key(currentTag.substr(0, equalPosition));
+ std::string value;
+
+ const char quote = currentTag[equalPosition + 1];
+ if (quote == '\'' || quote == '"')
+ {
+ value = lf_GetQuotedValue(quote, equalPosition + 1, currentTag);
+ }
+ else
+ {
+ // throw exception here?
+ }
+
+ attributes.emplace(key, value);
+ }
+ return attributes;
+ };
+
+ // BODY of function starts here
+ Params attributes;
+ // eliminate < >
+ std::string openingTag = tagHeader.substr(1, tagHeader.size() - 2);
+
+ if (tagHeader.back() == '/') // last char is / --> "XML empty tag"
+ {
+ // attributes = lf_GetAttributes(openingTag);
+ // throw exception here, ADIOS2 doesn't allow XML empty tags
+ }
+ else if (tagHeader[0] == '/') // first char is / ---> closing tag
+ {
+ attributes = lf_GetAttributes(openingTag);
+ if (attributes.size() > 0)
+ {
+ throw std::invalid_argument(
+ "ERROR: closing tag " + tagHeader +
+ " can't have attributes, in call to ADIOS constructor\n");
+ }
+ }
+ else // opening tag
+ {
+ attributes = lf_GetAttributes(openingTag);
+ }
+ return attributes;
+}
+
+void InitXML(const std::string configXML, const MPI_Comm mpiComm,
+ const bool debugMode,
+ std::vector<std::shared_ptr<Transform>> &transforms,
+ std::map<std::string, IO> &ios)
+{
+ // independent IO
+ std::string fileContents(FileToString(configXML));
+ RemoveCommentsXML(fileContents);
+
+ // adios-config
+ std::string::size_type position(0);
+ const TagXML adiosConfigXML(
+ GetTagXML("adios-config", fileContents, position));
+
+ // process transforms, not yet implemented
+
+ while (position != std::string::npos)
+ {
+ const TagXML transformXML(
+ GetTagXML("transform ", adiosConfigXML.Elements, position));
- // if this point is reached it means it's a value inside " " or ' ',
- // move to
- // the next end
- end = content.find(finalTag, currentPosition);
+ if (transformXML.Header.empty())
+ {
+ break;
+ }
+ // InitTransform(transformTag, debugMode, transforms);
}
- subString = content.substr(start, end - start + finalTag.size());
- currentPosition = end;
+ position = 0;
+ // process IOs
+ while (position != std::string::npos)
+ {
+ // io
+ const TagXML ioXML(GetTagXML("io ", adiosConfigXML.Elements, position));
+
+ if (ioXML.Header.empty()) // no more groups to find
+ {
+ break;
+ }
+ InitIOXML(ioXML, mpiComm, debugMode, transforms, ios);
+ }
}
-void GetQuotedValue(const char quote,
- const std::string::size_type "ePosition,
- std::string ¤tTag, std::string &value)
+void InitIOXML(const TagXML &ioXML, const MPI_Comm mpiComm,
+ const bool debugMode,
+ std::vector<std::shared_ptr<Transform>> &transforms,
+ std::map<std::string, IO> &ios)
{
- currentTag = currentTag.substr(quotePosition + 1);
- auto nextQuotePosition = currentTag.find(quote);
+ const Params ioAttributes(GetTagAttributesXML(ioXML.Header));
+
+ std::string ioName;
+ for (const auto &ioAttribute : ioAttributes)
+ {
+ if (ioAttribute.first == "name")
+ {
+ ioName = ioAttribute.second;
+ }
+ }
+
+ if (debugMode)
+ {
+ if (ioName.empty())
+ {
+ throw std::invalid_argument(
+ "ERROR: io name=\"value\" attribute not found in opening XML "
+ "tag " +
+ ioXML.Header +
+ ", check XML config file, in call to ADIOS constructor\n");
+ }
+
+ if (ios.count(ioName) == 1) // io exists
+ {
+ throw std::invalid_argument("ERROR: io name " + ioName +
+ " must be unique in XML config file, "
+ "in call to ADIOS constructor\n");
+ }
+ }
+
+ // emplace io with inConfigFile argument as true
+ auto itIO = ios.emplace(ioName, IO(ioName, mpiComm, true, debugMode));
+
+ // process engine
+ std::string::size_type position(0);
+
+ TagXML engineXML(GetTagXML("engine ", ioXML.Elements, position));
+ if (!engineXML.Header.empty()) // found first one
+ {
+ InitEngineXML(engineXML, debugMode, itIO.first->second);
+ }
- if (nextQuotePosition == currentTag.npos)
+ if (debugMode)
{
- throw std::invalid_argument("ERROR: Invalid attribute in..." +
- currentTag + "...check XML file\n");
+ // try finding a 2nd one from current position
+ TagXML engineXML(GetTagXML("engine ", ioXML.Elements, position));
+ if (!engineXML.Header.empty()) // found first one
+ {
+ throw std::invalid_argument(
+ "ERROR: more than one engine found in <io name=" + ioName +
+ "...>, only one per io tag is allowed in XML "
+ "config file, in call to "
+ "ADIOS constructor\n");
+ }
}
- value = currentTag.substr(0, nextQuotePosition);
- currentTag = currentTag.substr(nextQuotePosition + 1);
+ position = 0;
+ // process transports
+ while (position != std::string::npos)
+ {
+ TagXML transportXML(GetTagXML("transport", ioXML.Elements, position));
+
+ if (transportXML.Header.empty()) // no more groups to find
+ {
+ break;
+ }
+ InitTransportXML(transportXML, debugMode, itIO.first->second);
+ }
}
-void GetPairs(const std::string tag,
- std::vector<std::pair<const std::string, const std::string>>
- &pairs) noexcept
+void InitEngineXML(const TagXML &engineXML, const bool debugMode, IO &io)
{
- std::string currentTag(
- tag.substr(tag.find_first_of(" \t\n"))); // initialize current tag
+ const Params attributes = GetTagAttributesXML(engineXML.Header);
- while (currentTag.find('=') != currentTag.npos) // equalPosition
+ std::string type;
+ for (const auto &attribute : attributes)
{
- currentTag = currentTag.substr(currentTag.find_first_not_of(" \t\n"));
- auto equalPosition = currentTag.find('=');
- const std::string field(
- currentTag.substr(0, equalPosition)); // get field
- std::string value;
-
- const char quote = currentTag[equalPosition + 1];
- if (quote == '\'' || quote == '"') // single quotes
+ if (attribute.first == "type")
{
- GetQuotedValue(quote, equalPosition + 1, currentTag, value);
+ type = attribute.second;
+ break;
}
+ }
- pairs.push_back(
- std::pair<const std::string, const std::string>(field, value));
+ if (!type.empty())
+ {
+ io.SetEngine(type);
}
+
+ io.SetParameters(ParseParamsXML(engineXML.Elements, debugMode));
}
-void GetPairsFromTag(
- const std::string &fileContent, const std::string tag,
- std::vector<std::pair<const std::string, const std::string>> &pairs)
+void InitTransportXML(const TagXML &transportXML, const bool debugMode, IO &io)
{
- if (tag.back() == '/') // last char is / --> "XML empty tag"
+ const Params attributes = GetTagAttributesXML(transportXML.Header);
+
+ std::string type;
+ for (const auto &attribute : attributes)
{
- GetPairs(tag, pairs);
+ if (attribute.first == "type")
+ {
+ type = attribute.second;
+ break;
+ }
}
- else if (tag[0] == '/') // first char is / ---> closing tag
+
+ if (type.empty())
{
+ throw std::invalid_argument(
+ "ERROR: missing transport type in " + transportXML.Header +
+ ", in XML config file, in call to ADIOS constructor\n");
}
- else // opening tag
+
+ io.AddTransport(type, ParseParamsXML(transportXML.Elements, debugMode));
+}
+
+Params ParseParamsXML(const std::string &tagElements, const bool debugMode)
+{
+ auto start = tagElements.find_first_not_of(" \t\n");
+ auto end = tagElements.find_last_not_of(" \t\n");
+
+ std::string parametersString(tagElements.substr(start, end - start + 1));
+ if (debugMode)
{
- const std::string tagName(tag.substr(0, tag.find_first_of(" \t\n\r")));
- const std::string closingTagName("</" + tagName +
- ">"); // check for closing tagName
+ if (parametersString.back() != ';')
+ {
+ throw std::invalid_argument(
+ "ERROR: parameters in config XML file must end with a ; " +
+ tagElements + ", in call to ADIOS constructor\n");
+ }
+ }
+
+ std::istringstream parametersSS(parametersString);
+ std::string pair;
+
+ Params parameters;
+
+ while (std::getline(parametersSS, pair, ';'))
+ {
+ pair = pair.substr(pair.find_first_not_of(" \t\n"));
+ auto equalPosition = pair.find("=");
- if (fileContent.find(closingTagName) == fileContent.npos)
+ if (debugMode)
{
- throw std::invalid_argument("ERROR: closing tag " + closingTagName +
- " missing, check XML file\n");
+ if (equalPosition == std::string::npos ||
+ equalPosition == pair.size())
+ {
+ throw std::invalid_argument("ERROR: wrong parameter " + pair +
+ " format is "
+ "key=value in XML config file, in "
+ "call to ADIOS constructor\n");
+ }
}
- GetPairs(tag, pairs);
+ const std::string key(pair.substr(0, equalPosition));
+ const std::string value(pair.substr(equalPosition + 1));
+ parameters.emplace(key, value);
}
+ return parameters;
}
-// void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
-// const bool debugMode,
-// std::string& hostLanguage, std::vector<
-// std::shared_ptr<Transform> >& transforms,
-// std::map< std::string, Group >& groups )
-//{
-// //adios-config
-// std::string currentContent;
-// std::string::size_type currentPosition( 0 );
-// GetSubString( "<adios-config ", "</adios-config>", fileContent,
-// currentContent, currentPosition );
-//
-// //remove comment sections
-// std::string::size_type startComment ( currentContent.find( "<!--" ) );
-//
-// while( startComment != currentContent.npos )
-// {
-// std::string::size_type endComment( currentContent.find( "-->") );
-// currentContent.erase( startComment, endComment-startComment+3 );
-// startComment = currentContent.find( "<!--" );
-// }
-//
-// //Tag <adios-config
-// currentPosition = 0;
-//
-// std::string tag; //use for < > tags
-// GetSubString( "<adios-config", ">", currentContent, tag, currentPosition
-// );
-// tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
-//
-// std::vector< std::pair<const std::string, const std::string> > pairs; //
-// pairs in tag
-// GetPairsFromTag( currentContent, tag, pairs );
-//
-// for( auto& pair : pairs )
-// if( pair.first == "host-language" )
-// hostLanguage = pair.second;
-//
-// if( debugMode )
-// {
-// if( Support::HostLanguages.count( hostLanguage ) == 0 )
-// throw std::invalid_argument("ERROR: host language " + hostLanguage
-// + " not supported.\n" );
-//
-// if( hostLanguage.empty() )
-// throw std::invalid_argument("ERROR: host language is empty.\n" );
-// }
-//
-// //adios-group
-// currentPosition = 0;
-//
-// while( currentPosition != std::string::npos )
-// {
-// std::string xmlGroup;
-// GetSubString("<adios-group ", "</adios-group>", currentContent,
-// xmlGroup, currentPosition ); //Get all group contents
-//
-// if( xmlGroup.empty() ) //no more groups to find
-// break;
-//
-// //get group name
-// std::string::size_type groupPosition( 0 );
-// GetSubString( "<adios-group ", ">", xmlGroup, tag, groupPosition );
-// if( debugMode )
-// {
-// if( tag.size() < 2 )
-// throw std::invalid_argument( "ERROR: wrong tag " + tag + " in
-// adios-group\n" ); //check < or <=
-// }
-//
-// tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
-// GetPairsFromTag( xmlGroup, tag, pairs );
-// std::string groupName;
-//
-// for( auto& pair : pairs )
-// {
-// if( pair.first == "name")
-// groupName = pair.second;
-// }
-//
-// if( debugMode )
-// {
-// if( groupName.empty() )
-// throw std::invalid_argument( "ERROR: group name not found. \n"
-// );
-//
-// if( groups.count( groupName ) == 1 ) //group exists
-// throw std::invalid_argument( "ERROR: group " + groupName + "
-// defined twice.\n" );
-// }
-//
-// groups.emplace( groupName, Group( groupName, xmlGroup, transforms,
-// debugMode ) );
-//
-// currentContent.erase( currentContent.find( xmlGroup ), xmlGroup.size()
-// );
-// currentPosition = 0;
-// }
-//
-// //transport
-// //lambda function to check priority and iteration casting to unsigned int
-// auto lf_UIntCheck = []( const std::string method, const std::string
-// fieldStr, const std::string fieldName,
-// const bool debugMode, int& field )
-// {
-// field = 0;
-// if( !fieldStr.empty())
-// {
-// field = std::stoi( fieldStr ); //throws invalid_argument
-//
-// if( debugMode )
-// {
-// if( field < 0 )
-// throw std::invalid_argument("ERROR: " + fieldName + " in
-// transport " + method + " can't be negative\n" );
-// }
-// }
-// };
-//
-// //this section will have to change, doing nothing for now
-// currentPosition = 0;
-// while( currentPosition != std::string::npos )
-// {
-// GetSubString( "<transport ", ">", currentContent, tag, currentPosition
-// );
-// if( tag.empty() ) break;
-// tag = tag.substr( 1, tag.size() - 2 ); //eliminate < >
-// pairs.clear();
-// GetPairsFromTag( currentContent, tag, pairs );
-//
-// std::string groupName, method, priorityStr, iterationStr;
-// for( auto& pair : pairs )
-// {
-// if( pair.first == "group" ) groupName = pair.second;
-// else if( pair.first == "method" ) method = pair.second;
-// else if( pair.first == "priority" ) priorityStr = pair.second;
-// else if( pair.first == "iteration" ) iterationStr = pair.second;
-// }
-//
-// auto itGroup = groups.find( groupName );
-// if( debugMode )
-// {
-// if( itGroup == groups.end() ) //not found
-// throw std::invalid_argument( "ERROR: in transport " + method +
-// " group " + groupName + " not found.\n" );
-// }
-//
-// int priority, iteration;
-// lf_UIntCheck( method, priorityStr, "priority", debugMode, priority );
-// lf_UIntCheck( method, iterationStr, "iteration", debugMode, iteration
-// );
-// //here do something with the capsule
-// }
-//}
-
-// void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const
-// bool debugMode,
-// std::string& hostLanguage, std::vector<
-// std::shared_ptr<Transform> >& transforms,
-// std::map< std::string, Group >& groups )
-//{
-// int xmlFileContentSize;
-// std::string xmlFileContent;
-//
-// int rank;
-// MPI_Comm_rank( mpiComm, &rank );
-//
-// if( rank == 0 ) //serial part
-// {
-// DumpFileToString( xmlConfigFile, xmlFileContent ); //in
-// ADIOSFunctions.h dumps all XML Config File to xmlFileContent
-// xmlFileContentSize = xmlFileContent.size( ) + 1; // add one for the
-// null character
-//
-// MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, mpiComm ); //broadcast
-// size for allocation
-// MPI_Bcast( (char*)xmlFileContent.c_str(), xmlFileContentSize,
-// MPI_CHAR, 0, mpiComm ); //broadcast contents
-// }
-// else
-// {
-// MPI_Bcast( &xmlFileContentSize, 1, MPI_INT, 0, mpiComm ); //receive
-// size
-//
-// char* xmlFileContentMPI = new char[ xmlFileContentSize ]; //allocate
-// xml C-char
-// MPI_Bcast( xmlFileContentMPI, xmlFileContentSize, MPI_CHAR, 0, mpiComm
-// ); //receive xml C-char
-// xmlFileContent.assign( xmlFileContentMPI ); //copy to a string
-//
-// delete []( xmlFileContentMPI ); //delete char* needed for MPI, might
-// add size is moving to C++14 for optimization, avoid memory leak
-// }
-//
-// SetMembers( xmlFileContent, mpiComm, debugMode, hostLanguage, transforms,
-// groups );
-//}
-
} // end namespace adios
diff --git a/source/adios2/helper/adiosXML.h b/source/adios2/helper/adiosXML.h
index f3df2990549ed646f2f66457e82a3b2ec5ad55f0..22d6abd8904d0cf1eb39523a6e68e7730ebb76a0 100644
--- a/source/adios2/helper/adiosXML.h
+++ b/source/adios2/helper/adiosXML.h
@@ -12,95 +12,61 @@
#define ADIOS2_HELPER_ADIOSXML_H_
/// \cond EXCLUDE_FROM_DOXYGEN
+#include <map>
+#include <memory> //std::shared_ptr
#include <string>
#include <utility> //std::pair
#include <vector>
/// \endcond
+#include "adios2/core/IO.h"
+#include "adios2/core/Transform.h"
+
namespace adios
{
-/**
- * Extracts a substring between two tags from content
- * @param initialTag
- * @param finalTag
- * @param content full string
- * @param subString if found return substring between initialTag and finalTag,
- * otherwise returns empty
- * @param currentPosition to start the search, moved forward to finalTag
- * position
- */
-void GetSubString(const std::string initialTag, const std::string finalTag,
- const std::string content, std::string &subString,
- std::string::size_type ¤tPosition);
+struct TagXML
+{
+ std::string Header;
+ std::string Elements;
+ bool IsFull;
+};
-/**
- * Extracts the value inside quotes in a string currentTag ( Example: currentTag
- * --> field1="value1" field2="value2" )
- * @param quote double " or single '
- * @param quotePosition position of the opening quote in currentTag
- * @param currentTag initial tag value, modified by cutting the first found " "
- * portion, currentTag --> field2="value2"
- * @param value value1 in the example above
- */
-void GetQuotedValue(const char quote,
- const std::string::size_type "ePosition,
- std::string ¤tTag, std::string &value);
+void RemoveCommentsXML(std::string ¤tContent) noexcept;
-/**
- * Get attributes field1="value1" field2="value2" by looping through a single
- * XML tag
- * @param tag field0="value0" field1="value1" in a single string
- * @param pairs pairs[0].first=field0 pairs[0].second=value0
- * pairs[1].first=field1 pairs[1].second=value1
- */
-void GetPairs(const std::string tag,
- std::vector<std::pair<const std::string, const std::string>>
- &pairs) noexcept;
+TagXML GetTagXML(const std::string tagName, const std::string &content,
+ std::string::size_type &position);
-/**
- * Determine tag type and call GetPairs to populate pairs
- * @param fileContent file Content in a single string
- * @param tag field0="value0" field1="value1" in a single string
- * @param pairs pairs[0].first=field0 pairs[0].second=value0
- * pairs[1].first=field1 pairs[1].second=value1
- */
-void GetPairsFromTag(
- const std::string &fileContent, const std::string tag,
- std::vector<std::pair<const std::string, const std::string>> &pairs);
+std::string::size_type
+GetStringPositionXML(const std::string input, const std::string &content,
+ const std::string::size_type &startPosition) noexcept;
-/**
- * Set members m_Groups and m_HostLanguage from XML file content, called within
- * Init functions
- * @param fileContent file Content in a single string
- * @param mpiComm MPI Communicator passed from application passed to Transport
- * method if required
- * @param hostLanguage return the host language from fileContent
- * @param transforms return the modified transforms vector if there are
- * variables with transformations
- * @param groups passed returns the map of groups defined in fileContent
- */
-// void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
-// std::string& hostLanguage, std::vector<
-// std::shared_ptr<Transform> >& transforms,
-// std::map< std::string, Group >& groups );
+Params GetTagAttributesXML(const std::string &tagHeader);
/**
- * Called inside the ADIOS XML constructors to get contents from file, broadcast
- * and set hostLanguage and groups from ADIOS class
- * @param xmlConfigFile xml config file name
- * @param mpiComm communicator used from broadcasting
- * @param debugMode from ADIOS m_DebugMode passed to CGroup in groups
- * @param hostLanguage set from host-language in xml file
- * @param transforms return the modified transforms vector if there are
- * variables with transformations
- * @param groups passed returns the map of groups defined in fileContent
+ * Called inside the ADIOS XML constructors to get contents from file,
+ * broadcast and fill transforms and ios
+ * @param configXMLFile
+ * @param mpiComm
+ * @param debugMode
+ * @param transforms
+ * @param ios
*/
-// void InitXML( const std::string xmlConfigFile, const MPI_Comm mpiComm, const
-// bool debugMode,
-// std::string& hostLanguage, std::vector<
-// std::shared_ptr<Transform> >& transforms,
-// std::map< std::string, Group >& groups );
+void InitXML(const std::string configXML, const MPI_Comm mpiComm,
+ const bool debugMode,
+ std::vector<std::shared_ptr<Transform>> &transforms,
+ std::map<std::string, IO> &ios);
+
+void InitIOXML(const TagXML &ioXML, const MPI_Comm mpiComm,
+ const bool debugMode,
+ std::vector<std::shared_ptr<Transform>> &transforms,
+ std::map<std::string, IO> &ios);
+
+void InitEngineXML(const TagXML &engineXML, const bool debugMode, IO &io);
+
+void InitTransportXML(const TagXML &transportXML, const bool debugMode, IO &io);
+
+Params ParseParamsXML(const std::string &tagContents, const bool debugMode);
}
#endif /* ADIOS2_HELPER_ADIOSXML_H_ */
diff --git a/source/adios2/mpidummy.h b/source/adios2/mpidummy.h
index ed2b120584d2a334de31a43edfe6811cbce58dbb..249f9206f653020379d046dc729c7ae429045cf3 100644
--- a/source/adios2/mpidummy.h
+++ b/source/adios2/mpidummy.h
@@ -54,6 +54,9 @@ typedef int MPI_Fint;
#define MPI_INT 1
#define MPI_CHAR 2
#define MPI_DOUBLE 3
+#define MPI_UNSIGNED 4
+#define MPI_UNSIGNED_LONG 5
+#define MPI_UNSIGNED_LONG_LONG 6
#define MPI_ANY_SOURCE 0
#define MPI_ANY_TAG 0