From c46554551191a7a67439cd156cdfe563f1de3d6c Mon Sep 17 00:00:00 2001
From: wgodoy <wgodoy@wgodoy-desktop>
Date: Mon, 19 Jun 2017 00:23:28 -0400
Subject: [PATCH] Testing XML implementation with MPI
Initial implementation of XML running with helloBPWriter example
Corrected bug in ADIOS.cpp when detecting IO in ConfigFile
---
.../runtimeconfig/grandSchema.xml | 6 +-
examples/hello/bpWriter/CMakeLists.txt | 6 +
examples/hello/bpWriter/helloBPWriter.xml | 17 +-
examples/hello/bpWriter/helloBPWriterXML.cpp | 82 ++++
source/adios2/core/ADIOS.cpp | 14 +-
source/adios2/helper/adiosString.cpp | 4 +-
source/adios2/helper/adiosSystem.cpp | 21 +-
source/adios2/helper/adiosSystem.h | 3 +-
source/adios2/helper/adiosXML.cpp | 372 +++++++++---------
source/adios2/helper/adiosXML.h | 59 +--
10 files changed, 336 insertions(+), 248 deletions(-)
create mode 100644 examples/hello/bpWriter/helloBPWriterXML.cpp
diff --git a/examples/experimental/runtimeconfig/grandSchema.xml b/examples/experimental/runtimeconfig/grandSchema.xml
index e069a7764..71d80bd30 100644
--- a/examples/experimental/runtimeconfig/grandSchema.xml
+++ b/examples/experimental/runtimeconfig/grandSchema.xml
@@ -4,9 +4,9 @@
<io name="Output">
<var name="myArray"> <!-- provide a sequence of transforms -->
- <transform type="BZip2"> <!-- not implemented yet -->
+ <transform type='BZip2'> <!-- not implemented yet -->
BlockSize100K=3; <!-- must be a number between 0 and 9-->
- </transform>
+ </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-->
@@ -58,7 +58,7 @@
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-->
+ <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 -->
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index 56c647c17..17fc96c85 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -9,6 +9,12 @@ if(ADIOS_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})
+ target_link_libraries(hello_bpWriterXML adios2)
+
else()
add_executable(hello_bpWriter helloBPWriter_nompi.cpp)
endif()
diff --git a/examples/hello/bpWriter/helloBPWriter.xml b/examples/hello/bpWriter/helloBPWriter.xml
index 00afc9126..bda56e4c1 100644
--- a/examples/hello/bpWriter/helloBPWriter.xml
+++ b/examples/hello/bpWriter/helloBPWriter.xml
@@ -4,12 +4,17 @@
<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 shoudl depende on system) -->
- BufferGrowthFactor=2; <!-- exponential growth factor > 1, 1.5 (default), for this case: 1, 2, 4, 8, 16, 20 Mb-->
+ 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>
- </io>
-</adios-config>
+ <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 000000000..807b0c9c3
--- /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/source/adios2/core/ADIOS.cpp b/source/adios2/core/ADIOS.cpp
index ee373fb86..194dbdddb 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 90b6399b1..bc7841276 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 0dd5896d8..bc8acdcfb 100644
--- a/source/adios2/helper/adiosSystem.cpp
+++ b/source/adios2/helper/adiosSystem.cpp
@@ -79,10 +79,9 @@ std::string LocalTimeDate() noexcept
return std::string(std::ctime(&now));
}
-std::string BroadcastFileContents(const std::string &fileName,
- MPI_Comm mpiComm) noexcept
+std::string BroadcastString(const std::string &input, MPI_Comm mpiComm)
{
- std::string fileContents;
+ std::string receivedInput;
size_t characterCount = 0;
int rank;
@@ -90,15 +89,16 @@ std::string BroadcastFileContents(const std::string &fileName,
if (rank == 0) // sender
{
- fileContents = FileToString(fileName);
- characterCount = fileContents.size();
+ characterCount = input.size();
// broadcast size for allocation
MPI_Bcast(&characterCount, 1, ADIOS2_MPI_SIZE_T, 0, mpiComm);
// broadcast contents
- MPI_Bcast(const_cast<char *>(fileContents.c_str()),
+ MPI_Bcast(const_cast<char *>(input.c_str()),
static_cast<int>(characterCount), MPI_CHAR, 0, mpiComm);
+
+ return input;
}
else // receivers
{
@@ -106,15 +106,14 @@ std::string BroadcastFileContents(const std::string &fileName,
MPI_Bcast(&characterCount, 1, ADIOS2_MPI_SIZE_T, 0, mpiComm);
// allocate receiver
- std::vector<char> fileContentsReceiver(characterCount);
- MPI_Bcast(fileContentsReceiver.data(), static_cast<int>(characterCount),
+ std::vector<char> stringReceiver(characterCount);
+ MPI_Bcast(stringReceiver.data(), static_cast<int>(characterCount),
MPI_CHAR, 0, mpiComm);
- fileContents.assign(fileContentsReceiver.begin(),
- fileContentsReceiver.end());
+ receivedInput.assign(stringReceiver.begin(), stringReceiver.end());
}
- return fileContents;
+ return receivedInput;
}
} // end namespace adios
diff --git a/source/adios2/helper/adiosSystem.h b/source/adios2/helper/adiosSystem.h
index acbae391d..389e095dd 100644
--- a/source/adios2/helper/adiosSystem.h
+++ b/source/adios2/helper/adiosSystem.h
@@ -50,8 +50,7 @@ std::string LocalTimeDate() noexcept;
* @param mpiComm
* @return fileContents as a single string
*/
-std::string BroadcastFileContents(const std::string &fileName,
- MPI_Comm mpiComm) noexcept;
+std::string BroadcastString(const std::string &input, MPI_Comm mpiComm);
} // end namespace adios
diff --git a/source/adios2/helper/adiosXML.cpp b/source/adios2/helper/adiosXML.cpp
index 8107a4104..d52968e1e 100644
--- a/source/adios2/helper/adiosXML.cpp
+++ b/source/adios2/helper/adiosXML.cpp
@@ -16,145 +16,163 @@
/// \endcond
#include "adios2/ADIOSTypes.h"
-#include "adios2/helper/adiosSystem.h"
+#include "adios2/helper/adiosString.h"
namespace adios
{
-std::string GetSubString(const std::string initialTag,
- const std::string finalTag, const std::string &content,
- 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 subString;
-
- 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() == ' ')
+ {
+ name.pop_back();
+ }
+
+ auto openingStart = lf_SetPositions("<" + name, content, position);
+ auto openingEnd = lf_SetPositions(">", content, position);
+
+ if (openingStart == std::string::npos || openingEnd == std::string::npos)
+ {
+ tagXML.IsFull = false;
+ return tagXML;
+ }
+
+ tagXML.Header = content.substr(openingStart, openingEnd + 1 - openingStart);
+
+ auto closingStart =
+ GetStringPositionXML("</" + name + ">", content, position);
+
+ if (closingStart == std::string::npos)
{
- lf_Wipe(subString, currentPosition);
- return subString;
+ throw std::invalid_argument(
+ "ERROR: could not find closing tag </" + name +
+ "> in XML config file, in call to ADIOS constructor\n");
}
- currentPosition = start;
+ 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 end(content.find(finalTag, currentPosition));
- if (end == content.npos)
+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)
{
- lf_Wipe(subString, currentPosition);
- return subString;
+ return foundPosition;
}
- // make sure the finalTag is not a value surrounded by " " or ' ',
- // if so find next
- bool isValue = true;
+ // check if it is not inside " " or ' '
+ std::string::size_type currentPosition(startPosition);
- while (isValue)
+ while (foundPosition != content.npos)
{
- std::string::size_type singleQuotePosition =
- content.find('\'', currentPosition);
- std::string::size_type doubleQuotePosition =
- content.find('\"', currentPosition);
+ 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 can't find closing it's open until the end
if (closingQuotePosition == content.npos)
{
- lf_Wipe(subString, currentPosition);
- return subString;
+ currentPosition == content.npos;
+ break;
}
currentPosition = closingQuotePosition + 1;
- if (closingQuotePosition < end)
+ if (closingQuotePosition < foundPosition)
{
continue;
}
-
- // if this point is reached it means it's a value inside " " or ' ',
- // move to the next end
- end = content.find(finalTag, currentPosition);
- }
-
- currentPosition = end;
- subString = content.substr(start, end - start + finalTag.size());
- return subString;
-}
-
-std::string GetOpeningTag(const std::string tagName,
- const std::string &tagContents,
- std::string::size_type &position,
- const bool debugMode)
-{
- std::string openingTag(
- GetSubString("<" + tagName + " ", ">", tagContents, position));
-
- const std::string::size_type elementsStartPosition(position);
-
- if (debugMode)
- {
- if (openingTag.size() < 2)
+ else
{
- throw std::invalid_argument("ERROR: wrong XML tag <" + tagName +
- ", in call to ADIOS constructor\n");
+ // if this point is reached it means it's a value inside " " or ' ',
+ // iterate
+ foundPosition = content.find(input, currentPosition);
+ currentPosition = foundPosition;
}
}
- // eliminate < >
- openingTag = openingTag.substr(1, openingTag.size() - 2);
- return openingTag;
+ return foundPosition;
}
-Params GetTagAttributes(const std::string &fileContent, const std::string &tag)
+Params GetTagAttributesXML(const std::string &tagHeader)
{
auto lf_GetQuotedValue = [](const char quote,
const std::string::size_type "ePosition,
@@ -170,8 +188,9 @@ Params GetTagAttributes(const std::string &fileContent, const std::string &tag)
"...check XML file, in call to ADIOS constructor\n");
}
+ const std::string value(currentTag.substr(0, nextQuotePosition));
currentTag = currentTag.substr(nextQuotePosition + 1);
- return currentTag.substr(0, nextQuotePosition);
+ return value;
};
auto lf_GetAttributes = [&](const std::string &tag) -> Params {
@@ -199,6 +218,10 @@ Params GetTagAttributes(const std::string &fileContent, const std::string &tag)
{
value = lf_GetQuotedValue(quote, equalPosition + 1, currentTag);
}
+ else
+ {
+ // throw exception here?
+ }
attributes.emplace(key, value);
}
@@ -207,105 +230,80 @@ Params GetTagAttributes(const std::string &fileContent, const std::string &tag)
// BODY of function starts here
Params attributes;
+ // eliminate < >
+ std::string openingTag = tagHeader.substr(1, tagHeader.size() - 2);
- if (tag.back() == '/') // last char is / --> "XML empty tag"
+ if (tagHeader.back() == '/') // last char is / --> "XML empty tag"
{
- attributes = lf_GetAttributes(tag);
+ // attributes = lf_GetAttributes(openingTag);
+ // throw exception here, ADIOS2 doesn't allow XML empty tags
}
- else if (tag[0] == '/') // first char is / ---> closing tag
+ else if (tagHeader[0] == '/') // first char is / ---> closing tag
{
- attributes = lf_GetAttributes(tag);
+ attributes = lf_GetAttributes(openingTag);
if (attributes.size() > 0)
{
throw std::invalid_argument(
- "ERROR: closing tag " + tag +
+ "ERROR: closing tag " + tagHeader +
" can't have attributes, in call to ADIOS constructor\n");
}
}
else // opening tag
{
- const std::string tagName(tag.substr(0, tag.find_first_of(" \t\n\r")));
- // look for closing tagName
- const std::string closingTagName("</" + tagName + ">");
-
- if (fileContent.find(closingTagName) == fileContent.npos)
- {
- throw std::invalid_argument(
- "ERROR: closing tag missing for " + closingTagName +
- " check XML config file, in call to ADIOS constructor\n");
- }
-
- attributes = lf_GetAttributes(tag);
+ attributes = lf_GetAttributes(openingTag);
}
return attributes;
}
-void RemoveXMLComments(std::string ¤tContent) noexcept
-{
- 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("<!--");
- }
-}
-
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)
{
- // if using collective IO only?
- std::string fileContents = BroadcastFileContents(configXML, mpiComm);
+ // independent IO
+ std::string fileContents(FileToString(configXML));
+ RemoveCommentsXML(fileContents);
// adios-config
- std::string::size_type currentPosition(0);
- std::string currentContent(GetSubString("<adios-config ", "</adios-config>",
- fileContents, currentPosition));
- RemoveXMLComments(currentContent);
+ std::string::size_type position(0);
+ const TagXML adiosConfigXML(
+ GetTagXML("adios-config", fileContents, position));
// process transforms, not yet implemented
- while (currentPosition != std::string::npos)
+
+ while (position != std::string::npos)
{
- std::string transformTag(GetSubString("<transform ", "</transform>",
- currentContent, currentPosition));
+ const TagXML transformXML(
+ GetTagXML("transform ", adiosConfigXML.Elements, position));
- if (transformTag.empty()) // no more transforms
+ if (transformXML.Header.empty())
{
break;
}
// InitTransform(transformTag, debugMode, transforms);
}
- currentPosition = 0;
+ position = 0;
// process IOs
- while (currentPosition != std::string::npos)
+ while (position != std::string::npos)
{
// io
- std::string ioTag(
- GetSubString("<io ", "</io>", currentContent, currentPosition));
+ const TagXML ioXML(GetTagXML("io ", adiosConfigXML.Elements, position));
- if (ioTag.empty()) // no more groups to find
+ if (ioXML.Header.empty()) // no more groups to find
{
break;
}
- InitIOXML(ioTag, mpiComm, debugMode, transforms, ios);
+ InitIOXML(ioXML, mpiComm, debugMode, transforms, ios);
}
}
-void InitIOXML(const std::string &ioTag, const MPI_Comm mpiComm,
+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)
{
- std::string::size_type position(0);
- const std::string openingTag(
- GetOpeningTag("io", ioTag, position, debugMode));
- const std::string::size_type elementsStart(position);
-
- Params ioAttributes = GetTagAttributes(ioTag, openingTag);
+ const Params ioAttributes(GetTagAttributesXML(ioXML.Header));
std::string ioName;
for (const auto &ioAttribute : ioAttributes)
@@ -323,7 +321,7 @@ void InitIOXML(const std::string &ioTag, const MPI_Comm mpiComm,
throw std::invalid_argument(
"ERROR: io name=\"value\" attribute not found in opening XML "
"tag " +
- openingTag +
+ ioXML.Header +
", check XML config file, in call to ADIOS constructor\n");
}
@@ -339,49 +337,45 @@ void InitIOXML(const std::string &ioTag, const MPI_Comm mpiComm,
auto itIO = ios.emplace(ioName, IO(ioName, mpiComm, true, debugMode));
// process engine
- std::string engineTag(
- GetSubString("<engine ", "</engine>", ioTag, position));
+ std::string::size_type position(0);
- if (!engineTag.empty()) // no more groups to find
+ TagXML engineXML(GetTagXML("engine ", ioXML.Elements, position));
+ if (!engineXML.Header.empty()) // found first one
{
- InitEngineXML(engineTag, debugMode, itIO.first->second);
+ InitEngineXML(engineXML, debugMode, itIO.first->second);
}
if (debugMode)
{
- // try finding a 2nd one
- std::string engineTag(
- GetSubString("<engine ", "</engine>", ioTag, position));
- if (!engineTag.empty())
+ // 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: two engine tags found in IO " +
- ioName + ", only one is allowed in XML "
- "config file, in call to "
- "ADIOS constructor\n");
+ 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");
}
}
- position = elementsStart;
+ position = 0;
// process transports
while (position != std::string::npos)
{
- std::string transportTag(
- GetSubString("<transport ", "</transport>", ioTag, position));
+ TagXML transportXML(GetTagXML("transport", ioXML.Elements, position));
- if (transportTag.empty()) // no more groups to find
+ if (transportXML.Header.empty()) // no more groups to find
{
break;
}
+ InitTransportXML(transportXML, debugMode, itIO.first->second);
}
}
-void InitEngineXML(const std::string &engineTag, const bool debugMode, IO &io)
+void InitEngineXML(const TagXML &engineXML, const bool debugMode, IO &io)
{
- std::string::size_type position(0);
- const std::string openingTag(
- GetOpeningTag("engine", engineTag, position, debugMode));
- const std::string::size_type elementsStartPosition(position);
- Params attributes = GetTagAttributes(engineTag, openingTag);
+ const Params attributes = GetTagAttributesXML(engineXML.Header);
std::string type;
for (const auto &attribute : attributes)
@@ -389,22 +383,21 @@ void InitEngineXML(const std::string &engineTag, const bool debugMode, IO &io)
if (attribute.first == "type")
{
type = attribute.second;
+ break;
}
}
- io.SetEngine(type);
- io.SetParameters(
- ParseParamsXML(engineTag, elementsStartPosition, debugMode));
+ if (!type.empty())
+ {
+ io.SetEngine(type);
+ }
+
+ io.SetParameters(ParseParamsXML(engineXML.Elements, debugMode));
}
-void InitTransportXML(const std::string &transportTag, const bool debugMode,
- IO &io)
+void InitTransportXML(const TagXML &transportXML, const bool debugMode, IO &io)
{
- std::string::size_type position(0);
- const std::string openingTag(
- GetOpeningTag("transport", transportTag, position, debugMode));
- const std::string::size_type elementsStartPosition(position);
- Params attributes = GetTagAttributes(transportTag, openingTag);
+ const Params attributes = GetTagAttributesXML(transportXML.Header);
std::string type;
for (const auto &attribute : attributes)
@@ -412,24 +405,44 @@ void InitTransportXML(const std::string &transportTag, const bool debugMode,
if (attribute.first == "type")
{
type = attribute.second;
+ break;
}
}
- io.AddTransport(
- type, ParseParamsXML(transportTag, elementsStartPosition, debugMode));
+ if (type.empty())
+ {
+ throw std::invalid_argument(
+ "ERROR: missing transport type in " + transportXML.Header +
+ ", in XML config file, in call to ADIOS constructor\n");
+ }
+
+ io.AddTransport(type, ParseParamsXML(transportXML.Elements, debugMode));
}
-Params ParseParamsXML(const std::string &tag,
- const std::string::size_type elementsStartPosition,
- const bool debugMode)
+Params ParseParamsXML(const std::string &tagElements, const bool debugMode)
{
- std::istringstream parametersSS(tag.substr(elementsStartPosition));
+ 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)
+ {
+ 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 (debugMode)
@@ -443,6 +456,7 @@ Params ParseParamsXML(const std::string &tag,
"call to ADIOS constructor\n");
}
}
+
const std::string key(pair.substr(0, equalPosition));
const std::string value(pair.substr(equalPosition + 1));
parameters.emplace(key, value);
diff --git a/source/adios2/helper/adiosXML.h b/source/adios2/helper/adiosXML.h
index 30ae76222..22d6abd89 100644
--- a/source/adios2/helper/adiosXML.h
+++ b/source/adios2/helper/adiosXML.h
@@ -25,43 +25,23 @@
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
- */
-std::string GetSubString(const std::string initialTag,
- const std::string finalTag, const std::string &content,
- std::string::size_type ¤tPosition);
+struct TagXML
+{
+ std::string Header;
+ std::string Elements;
+ bool IsFull;
+};
-/**
- * Determine tag type ( opening, empty, closing ), populates and returns Params
- * (map<string,string>) object with xml tag attributes
- * @param fileContent to check for missing tag closing
- * @param tag single string: key0="value0" ... keyN="valueN"
- * @return std::map of attributes: { { "key0", "value0" } ,..., { "keyN",
- * "valueN" } }
- */
-Params GetTagAttributes(const std::string &fileContent, const std::string &tag);
+void RemoveCommentsXML(std::string ¤tContent) 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
- */
+TagXML GetTagXML(const std::string tagName, const std::string &content,
+ std::string::size_type &position);
+
+std::string::size_type
+GetStringPositionXML(const std::string input, const std::string &content,
+ const std::string::size_type &startPosition) noexcept;
-void RemoveXMLComments(std::string ¤tContent) noexcept;
+Params GetTagAttributesXML(const std::string &tagHeader);
/**
* Called inside the ADIOS XML constructors to get contents from file,
@@ -77,19 +57,16 @@ void InitXML(const std::string configXML, const MPI_Comm mpiComm,
std::vector<std::shared_ptr<Transform>> &transforms,
std::map<std::string, IO> &ios);
-void InitIOXML(const std::string &ioTag, const MPI_Comm mpiComm,
+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 std::string &engineTag, const bool debugMode, IO &io);
+void InitEngineXML(const TagXML &engineXML, const bool debugMode, IO &io);
-void InitTransportXML(const std::string &transportTag, const bool debugMode,
- IO &io);
+void InitTransportXML(const TagXML &transportXML, const bool debugMode, IO &io);
-Params ParseParamsXML(const std::string &tag,
- const std::string::size_type elementsStartPosition,
- const bool debugMode);
+Params ParseParamsXML(const std::string &tagContents, const bool debugMode);
}
#endif /* ADIOS2_HELPER_ADIOSXML_H_ */
--
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