diff --git a/ippl/src/Message/CMakeLists.txt b/ippl/src/Message/CMakeLists.txt
index cfa937fa8553b1351a1f4aabab432b46b5c84191..784123741c329bd2f0996c0a22f259f07d691caf 100644
--- a/ippl/src/Message/CMakeLists.txt
+++ b/ippl/src/Message/CMakeLists.txt
@@ -1,23 +1,25 @@
set (_SRCS
CRC.cpp
- Communicate.cpp
CommCreator.cpp
CommMPI.cpp
+ Communicate.cpp
+ Format.cpp
MessageFunctions.cpp
- Formatter.cpp
+ MsgBuffer.cpp
)
set (_HDRS
+ CRC.h
CommCreator.h
CommMPI.h
Communicate.h
- CRC.h
DataTypes.h
- Formatter.h
- GlobalComm.hpp
+ Format.h
GlobalComm.h
- Message.hpp
+ GlobalComm.hpp
Message.h
+ Message.hpp
+ MsgBuffer.h
Operations.h
TagMaker.h
Tags.h
@@ -39,4 +41,4 @@ install (FILES ${_HDRS} DESTINATION include/Message)
# cmake-tab-width: 4
# indent-tabs-mode: nil
# require-final-newline: nil
-# End:
+# End:
\ No newline at end of file
diff --git a/ippl/src/Message/Format.cpp b/ippl/src/Message/Format.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..bd76adb26887dca024b9eda52aa1e33082e9ce8e
--- /dev/null
+++ b/ippl/src/Message/Format.cpp
@@ -0,0 +1,44 @@
+//
+// Class Format
+// Format class to allow serializing message objects into plain buffers
+// to send directly with mpi calls or similar means
+//
+// Copyright (c) 2008 - 2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
+#include "Message/Format.h"
+
+Format::Format(Message *msg)
+{
+ items = msg->size();
+ size = 0;
+
+ format_array.resize(2*items);
+ for (unsigned int i=0; i<items; ++i)
+ {
+ Message::MsgItem &msgitem = msg->item(i);
+ format_array[2*i+0] = msgitem.numElems();
+ format_array[2*i+1] = msgitem.numBytes();
+ size += format_array[2*i+1];
+ }
+}
+
+void Format::print()
+{
+ std::cout << "size: " << size << std::endl;
+ for (unsigned int i=0; i<items; ++i)
+ {
+ std::cout << "entry " << i << ": " << format_array[2*i+0]
+ << " elements " << format_array[2*i+1] << " bytes\n";
+ }
+}
\ No newline at end of file
diff --git a/ippl/src/Message/Format.h b/ippl/src/Message/Format.h
new file mode 100644
index 0000000000000000000000000000000000000000..5681662d0706b62f3f045c1ed3b0f0d53ecaf33f
--- /dev/null
+++ b/ippl/src/Message/Format.h
@@ -0,0 +1,53 @@
+//
+// Class Format
+// Format class to allow serializing message objects into plain buffers
+// to send directly with mpi calls or similar means
+//
+// Copyright (c) 2008 - 2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
+#ifndef FORMATTER_H
+#define FORMATTER_H
+
+#include <algorithm>
+#include <cstring>
+#include <vector>
+#include "Message/Message.h"
+
+class Format {
+public:
+ Format(Message*);
+ unsigned int getItemCount() {
+ return items;
+ }
+ unsigned int getSize() {
+ return size;
+ }
+ unsigned int getFormatSize() {
+ return 2 * items * sizeof(int);
+ }
+ unsigned int getItemElems(int i) {
+ return format_array[2 * i + 0];
+ }
+ unsigned int getItemBytes(int i) {
+ return format_array[2 * i + 1];
+ }
+
+ void print();
+
+private:
+ unsigned int items, size;
+ std::vector<unsigned int> format_array;
+};
+
+#endif
\ No newline at end of file
diff --git a/ippl/src/Message/Formatter.h b/ippl/src/Message/Formatter.h
deleted file mode 100644
index ce61ccd9f4c40b5cca30abb3fdbf057ba2c3309d..0000000000000000000000000000000000000000
--- a/ippl/src/Message/Formatter.h
+++ /dev/null
@@ -1,99 +0,0 @@
-// -*- C++ -*-
-/***************************************************************************
- *
- * The IPPL Framework
- *
- *
- * Visit http://people.web.psi.ch/adelmann/ for more details
- *
- ***************************************************************************/
-
-#ifndef FORMATTER_H
-#define FORMATTER_H
-
-#include "Message/Message.h"
-#include <cstring>
-#include <vector>
-#include <algorithm>
-
-/*
- * Format and MsgBuffer class to allow serializing message objects into plain buffers
- * to send directly with mpi calls or similar means
- */
-
-class Format
-{
-public:
- Format(Message*);
- unsigned int getItemCount()
- {
- return items;
- }
- unsigned int getSize()
- {
- return size;
- }
- unsigned int getFormatSize()
- {
- return 2*items*sizeof(int);
- }
- unsigned int getItemElems(int i)
- {
- return format_array[2*i+0];
- }
- unsigned int getItemBytes(int i)
- {
- return format_array[2*i+1];
- }
-
- void print();
-
-private:
- unsigned int items, size;
- std::vector<unsigned int> format_array;
-};
-
-
-class MsgBuffer
-{
-public:
- //creates buffer with space to hold count messages of format f
- MsgBuffer(Format *f, int count, int offset = 0);
- MsgBuffer(Format *f, char* d, int size);
-
- bool add(Message*);
- Message* get();
-
- template<class T>
- void get(T &v)
- {
- std::memcpy(&v, data.data()+readpos, sizeof(T));
- readpos += sizeof(T);
- }
-
- template<class T>
- void put(T &v)
- {
- std::memcpy(data.data()+writepos, &v, sizeof(T));
- writepos += sizeof(T);
- }
-
- int getSize()
- {
- return writepos;
- }
- void* getBuffer()
- {
- return data.data();
- }
-
- Format* getFormat() { return format; }
-
- ~MsgBuffer();
-private:
- Format *format;
- unsigned int datasize, writepos, readpos;
- std::vector<char> data;
-};
-
-#endif // FORMATTER_H
diff --git a/ippl/src/Message/Formatter.cpp b/ippl/src/Message/MsgBuffer.cpp
similarity index 70%
rename from ippl/src/Message/Formatter.cpp
rename to ippl/src/Message/MsgBuffer.cpp
index 2e21ab7652ac4476b111aff03385f2459595edb6..b3a6ed2b560c1acb9f623ab8bb678385d0b2e37b 100644
--- a/ippl/src/Message/Formatter.cpp
+++ b/ippl/src/Message/MsgBuffer.cpp
@@ -1,29 +1,24 @@
-#include "Message/Formatter.h"
-
-Format::Format(Message *msg)
-{
- items = msg->size();
- size = 0;
-
- format_array.resize(2*items);
- for (unsigned int i=0; i<items; ++i)
- {
- Message::MsgItem &msgitem = msg->item(i);
- format_array[2*i+0] = msgitem.numElems();
- format_array[2*i+1] = msgitem.numBytes();
- size += format_array[2*i+1];
- }
-}
-
-void Format::print()
-{
- std::cout << "size: " << size << std::endl;
- for (unsigned int i=0; i<items; ++i)
- {
- std::cout << "entry " << i << ": " << format_array[2*i+0]
- << " elements " << format_array[2*i+1] << " bytes\n";
- }
-}
+//
+// Class MsgBuffer
+// MsgBuffer class to allow serializing message objects into plain buffers
+// to send directly with mpi calls or similar means
+//
+// Copyright (c) 2008 - 2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
+#include "Message/MsgBuffer.h"
+
+#include "Message/Format.h"
MsgBuffer::MsgBuffer(Format *f, int count, int offset)
: format(f), writepos(0), readpos(0)
@@ -94,4 +89,4 @@ Message* MsgBuffer::get()
}
return msg;
-}
+}
\ No newline at end of file
diff --git a/ippl/src/Message/MsgBuffer.h b/ippl/src/Message/MsgBuffer.h
new file mode 100644
index 0000000000000000000000000000000000000000..3d2c29a9f43571080c30e3b69bc6af16c7ea6f9c
--- /dev/null
+++ b/ippl/src/Message/MsgBuffer.h
@@ -0,0 +1,71 @@
+//
+// Class MsgBuffer
+// MsgBuffer class to allow serializing message objects into plain buffers
+// to send directly with mpi calls or similar means
+//
+// Copyright (c) 2008 - 2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// You should have received a copy of the GNU General Public License
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
+//
+#ifndef MSGBUFFER_H
+#define MSGBUFFER_H
+
+#include <algorithm>
+#include <cstring>
+#include <vector>
+#include "Message/Message.h"
+
+class Format;
+
+class MsgBuffer {
+public:
+ // creates buffer with space to hold count messages of format f
+ MsgBuffer(Format* f, int count, int offset = 0);
+ MsgBuffer(Format* f, char* d, int size);
+
+ bool add(Message*);
+ Message* get();
+
+ template <class T>
+ void get(T& v) {
+ std::memcpy(&v, data.data() + readpos, sizeof(T));
+ readpos += sizeof(T);
+ }
+
+ template <class T>
+ void put(T& v) {
+ std::memcpy(data.data() + writepos, &v, sizeof(T));
+ writepos += sizeof(T);
+ }
+
+ int getSize() {
+ return writepos;
+ }
+
+ void* getBuffer() {
+ char* data_ptr = data.empty() ? static_cast<char*>(0) : &(data[0]);
+ return data_ptr;
+ }
+
+ Format* getFormat() {
+ return format;
+ }
+
+ ~MsgBuffer();
+
+private:
+ Format* format;
+ unsigned int datasize, writepos, readpos;
+ std::vector<char> data;
+};
+
+#endif
\ No newline at end of file
diff --git a/ippl/src/Particle/BoxParticleCachingPolicy.h b/ippl/src/Particle/BoxParticleCachingPolicy.h
index 78884d0de83f05126b132685687332db3f8c78dc..ca5a8745cb6362010725fa8f4a9306851806c0cc 100644
--- a/ippl/src/Particle/BoxParticleCachingPolicy.h
+++ b/ippl/src/Particle/BoxParticleCachingPolicy.h
@@ -14,7 +14,8 @@
#include "Message/Message.h"
#include "Message/Communicate.h"
-#include "Message/Formatter.h"
+#include "Message/Format.h"
+#include "Message/MsgBuffer.h"
template <class T, unsigned Dim, class Mesh, class CachingPolicy> class ParticleSpatialLayout;
@@ -233,7 +234,8 @@ template<class C>
}
//wait for communication to finish and clean up buffers
- MPI_Waitall(requests.size(), &(requests[0]), MPI_STATUSES_IGNORE);
+ MPI_Request* requests_ptr = requests.empty()? static_cast<MPI_Request*>(0): &(requests[0]);
+ MPI_Waitall(requests.size(), requests_ptr, MPI_STATUSES_IGNORE);
for (unsigned int j = 0; j<buffers.size(); ++j)
{
delete buffers[j]->getFormat();
@@ -259,4 +261,4 @@ private:
std::map<unsigned, std::list<std::pair<NDRegion<T,Dim>, Offset_t> > > regions;
};
-#endif
\ No newline at end of file
+#endif
diff --git a/ippl/src/Particle/IpplParticleBase.h b/ippl/src/Particle/IpplParticleBase.h
index fa5e4a1639b8e8fdf6f6f90a6d45f2c475795ebe..b38aef195506839fc4080392f62204ef9bb17bb4 100644
--- a/ippl/src/Particle/IpplParticleBase.h
+++ b/ippl/src/Particle/IpplParticleBase.h
@@ -98,7 +98,8 @@
#include "AppTypes/Vektor.h"
#include "DataSource/DataSource.h"
#include "DataSource/MakeDataSource.h"
-#include "Message/Formatter.h"
+#include "Message/Format.h"
+#include "Message/MsgBuffer.h"
#include <vector>
#include <algorithm> // Include algorithms
#include <utility>
@@ -398,4 +399,4 @@ private:
* $RCSfile: IpplParticleBase.h,v $ $Author: adelmann $
* $Revision: 1.1.1.1 $ $Date: 2003/01/23 07:40:28 $
* IPPL_VERSION_ID: $Id: IpplParticleBase.h,v 1.1.1.1 2003/01/23 07:40:28 adelmann Exp $
- ***************************************************************************/
\ No newline at end of file
+ ***************************************************************************/
diff --git a/ippl/src/Particle/ParticleSpatialLayout.h b/ippl/src/Particle/ParticleSpatialLayout.h
index edd0b63c525c4b6e44543848dcd0c5c482f6c422..cc392eee5fa39d541eabff6a932aa67c62b27013 100644
--- a/ippl/src/Particle/ParticleSpatialLayout.h
+++ b/ippl/src/Particle/ParticleSpatialLayout.h
@@ -26,6 +26,8 @@
#include "Particle/IpplParticleBase.h"
#include "Region/RegionLayout.h"
#include "Message/Message.h"
+#include "Message/Format.h"
+#include "Message/MsgBuffer.h"
#include "FieldLayout/FieldLayoutUser.h"
#include "Utility/IpplException.h"
@@ -39,7 +41,6 @@
#include "BoxParticleCachingPolicy.h"
-#include "Message/Formatter.h"
#include <mpi.h>
// forward declarations
@@ -1197,7 +1198,8 @@ protected:
}
//wait for communication to finish and clean up buffers
- MPI_Waitall(requests.size(), &(requests[0]), MPI_STATUSES_IGNORE);
+ MPI_Request* requests_ptr = requests.empty()? static_cast<MPI_Request*>(0): &(requests[0]);
+ MPI_Waitall(requests.size(), requests_ptr, MPI_STATUSES_IGNORE);
return LocalNum;
}
@@ -1326,7 +1328,8 @@ protected:
}
//wait for communication to finish and clean up buffers
- MPI_Waitall(requests.size(), &(requests[0]), 0);
+ MPI_Request* requests_ptr = requests.empty()? static_cast<MPI_Request*>(0): &(requests[0]);
+ MPI_Waitall(requests.size(), requests_ptr, 0);
return LocalNum;
}
diff --git a/src/Amr/BoxLibLayout.hpp b/src/Amr/BoxLibLayout.hpp
index c898753d4f07a595418b9644f66103a487dcaeca..4ad6635909653b2dc60ab02320544c1b68f21f6a 100644
--- a/src/Amr/BoxLibLayout.hpp
+++ b/src/Amr/BoxLibLayout.hpp
@@ -38,7 +38,9 @@
#include "BoxLibLayout.h"
-#include "Message/Formatter.h"
+#include "Message/Format.h"
+#include "Message/MsgBuffer.h"
+#include "Utility/PAssert.h"
#include "Utilities/OpalException.h"
#include <cassert>
@@ -348,7 +350,8 @@ void BoxLibLayout<T, Dim>::update(AmrParticleBase< BoxLibLayout<T,Dim> >& PData,
}
//wait for communication to finish and clean up buffers
- MPI_Waitall(requests.size(), &(requests[0]), MPI_STATUSES_IGNORE);
+ MPI_Request* requests_ptr = requests.empty()? static_cast<MPI_Request*>(0): &(requests[0]);
+ MPI_Waitall(requests.size(), requests_ptr, MPI_STATUSES_IGNORE);
for (unsigned int j = 0; j<buffers.size(); ++j)
{
delete buffers[j];
@@ -479,7 +482,7 @@ void BoxLibLayout<T, Dim>::clearLevelMask(int lev) {
template <class T, unsigned Dim>
-const std::unique_ptr<typename BoxLibLayout<T, Dim>::mask_t>&
+const std::unique_ptr<typename BoxLibLayout<T, Dim>::mask_t>&
BoxLibLayout<T, Dim>::getLevelMask(int lev) const {
if ( lev >= (int)masks_m.size() ) {
throw OpalException("BoxLibLayout::getLevelMask()",
diff --git a/src/Classic/Structure/LossDataSink.cpp b/src/Classic/Structure/LossDataSink.cpp
index 866a39b3f62bb7a7a416c1bf6c8a21f3ada5f123..2096fec53719436d9b69e692def25986092d8d1c 100644
--- a/src/Classic/Structure/LossDataSink.cpp
+++ b/src/Classic/Structure/LossDataSink.cpp
@@ -368,22 +368,22 @@ void LossDataSink::saveH5(unsigned int setIdx) {
WRITE_STEPATTRIB_INT64("GlobalTrackStep", &(globalTrackStep_m[setIdx]), 1);
}
// Write all data
- WRITE_DATA_FLOAT64 ("x", &x_m[startIdx]);
- WRITE_DATA_FLOAT64 ("y", &y_m[startIdx]);
- WRITE_DATA_FLOAT64 ("z", &z_m[startIdx]);
- WRITE_DATA_FLOAT64 ("px", &px_m[startIdx]);
- WRITE_DATA_FLOAT64 ("py", &py_m[startIdx]);
- WRITE_DATA_FLOAT64 ("pz", &pz_m[startIdx]);
+ WRITE_DATA_FLOAT64 ("x", x_m.data() + startIdx);
+ WRITE_DATA_FLOAT64 ("y", y_m.data() + startIdx);
+ WRITE_DATA_FLOAT64 ("z", z_m.data() + startIdx);
+ WRITE_DATA_FLOAT64 ("px", px_m.data() + startIdx);
+ WRITE_DATA_FLOAT64 ("py", py_m.data() + startIdx);
+ WRITE_DATA_FLOAT64 ("pz", pz_m.data() + startIdx);
/// Write particle id numbers.
std::vector<h5_int64_t> larray(id_m.begin() + startIdx, id_m.end() );
- WRITE_DATA_INT64 ("id", &larray[0]);
+ WRITE_DATA_INT64 ("id", larray.data());
if (hasTimeAttribute()) {
- WRITE_DATA_FLOAT64 ("time", &time_m[startIdx]);
+ WRITE_DATA_FLOAT64 ("time", time_m.data() + startIdx);
larray.assign (turn_m.begin() + startIdx, turn_m.end() );
- WRITE_DATA_INT64 ("turn", &larray[0]);
+ WRITE_DATA_INT64 ("turn", larray.data());
larray.assign (bunchNum_m.begin() + startIdx, bunchNum_m.end() );
- WRITE_DATA_INT64 ("bunchNumber", &larray[0]);
+ WRITE_DATA_INT64 ("bunchNumber", larray.data());
}
++ H5call_m;
@@ -688,4 +688,4 @@ SetStatistics LossDataSink::computeSetStatistics(unsigned int setIdx) {
// c-basic-offset: 4
// indent-tabs-mode: nil
// require-final-newline: nil
-// End:
+// End:
\ No newline at end of file
diff --git a/src/Classic/Utilities/Util.h b/src/Classic/Utilities/Util.h
index 44816c5a14fb74d097b343aeeea91d2952c61930..96a6ca110ed81b997f40ff1b6b02fdcf1225eca2 100644
--- a/src/Classic/Utilities/Util.h
+++ b/src/Classic/Utilities/Util.h
@@ -196,6 +196,13 @@ namespace Util {
std::string base64_encode(const std::string &string_to_encode);//unsigned char const* , unsigned int len);
std::string base64_decode(std::string const& s);
+
+ template<typename T, typename A>
+ T* c_data(std::vector<T,A>& v) { return v.empty() ? static_cast<T*>(0) : &(v[0]); }
+
+ template<typename T, typename A>
+ T const* c_data(std::vector<T,A> const& v) { return v.empty() ? static_cast<T const*>(0) : &(v[0]); }
+
}
template <typename T>
diff --git a/src/Distribution/Distribution.cpp b/src/Distribution/Distribution.cpp
index 1cf37f4dbaa88696e7dc0fab1833f8c3b3679aa7..629dbe02777f63fe3c9de722e20fb6e4e5b0a157 100644
--- a/src/Distribution/Distribution.cpp
+++ b/src/Distribution/Distribution.cpp
@@ -1003,11 +1003,13 @@ size_t Distribution::getNumberOfParticlesInFile(std::ifstream &inputFile) {
void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, double massIneV) {
*gmsg << level3 << "\n"
- << "------------------------------------------------------------------------------------\n";
+ << "-------------------------------------------------------------------"
+ "-----------------\n";
*gmsg << "READ INITIAL DISTRIBUTION FROM FILE \""
- << Attributes::getString(itsAttr[Attrib::Distribution::FNAME])
- << "\"\n";
- *gmsg << "------------------------------------------------------------------------------------\n" << endl;
+ << Attributes::getString(itsAttr[Attrib::Distribution::FNAME]) << "\"\n";
+ *gmsg << "-------------------------------------------------------------------"
+ "-----------------\n"
+ << endl;
// Data input file is only read by node 0.
std::ifstream inputFile;
@@ -1030,26 +1032,25 @@ void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, doub
pmean_m = 0.0;
- size_t numPartsToSend = 0;
unsigned int distributeFrequency = 1000;
- size_t singleDataSize = (/*sizeof(int) +*/ 6 * sizeof(double));
- unsigned int dataSize = distributeFrequency * singleDataSize;
- std::vector<char> data;
+ size_t singleDataSize = 6;
+ unsigned int dataSize = distributeFrequency * singleDataSize;
+ std::vector<double> data(dataSize);
- data.reserve(dataSize);
-
- const char* buffer;
if (Ippl::myNode() == 0) {
- char lineBuffer[1024];
- unsigned int numParts = 0;
+ constexpr unsigned int bufferSize = 1024;
+ char lineBuffer[bufferSize];
+ unsigned int numParts = 0;
+ std::vector<double>::iterator currentPosition = data.begin();
while (!inputFile.eof()) {
- inputFile.getline(lineBuffer, 1024);
+ inputFile.getline(lineBuffer, bufferSize);
Vector_t R(0.0), P(0.0);
std::istringstream line(lineBuffer);
line >> R(0);
- if (line.rdstate()) break;
+ if (line.rdstate())
+ break;
line >> P(0);
line >> R(1);
line >> P(1);
@@ -1068,19 +1069,14 @@ void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, doub
pmean_m += P;
if (saveProcessor > 0u) {
- buffer = reinterpret_cast<const char*>(&R[0]);
- data.insert(data.end(), buffer, buffer + 3 * sizeof(double));
- buffer = reinterpret_cast<const char*>(&P[0]);
- data.insert(data.end(), buffer, buffer + 3 * sizeof(double));
- ++ numPartsToSend;
+ currentPosition = std::copy(&(R[0]), &(R[0]) + 3, currentPosition);
+ currentPosition = std::copy(&(P[0]), &(P[0]) + 3, currentPosition);
- if (numPartsToSend % distributeFrequency == 0) {
+ if (currentPosition == data.end()) {
MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
- MPI_Bcast(&data[0], dataSize, MPI_CHAR, 0, Ippl::getComm());
- numPartsToSend = 0;
+ MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
- std::vector<char>().swap(data);
- data.reserve(dataSize);
+ currentPosition = data.begin();
}
} else {
xDist_m.push_back(R(0));
@@ -1091,53 +1087,49 @@ void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, doub
pzDist_m.push_back(P(2));
}
- ++ numParts;
- ++ saveProcessor;
+ ++numParts;
+ ++saveProcessor;
}
- dataSize = (numberOfParticlesRead == numParts? data.size(): std::numeric_limits<unsigned int>::max());
+ dataSize =
+ (numberOfParticlesRead == numParts ? currentPosition - data.begin()
+ : std::numeric_limits<unsigned int>::max());
+
MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
if (numberOfParticlesRead != numParts) {
- throw OpalException("Distribution::createDistributionFromFile",
- "Found " +
- std::to_string(numParts) +
- " particles in file '" +
- fileName +
- "' instead of " +
- std::to_string(numberOfParticlesRead));
+ throw OpalException(
+ "Distribution::createDistributionFromFile",
+ "Found " + std::to_string(numParts) + " particles in file '" + fileName
+ + "' instead of " + std::to_string(numberOfParticlesRead));
}
- MPI_Bcast(&data[0], dataSize, MPI_CHAR, 0, Ippl::getComm());
+ MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
} else {
do {
MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
if (dataSize == std::numeric_limits<unsigned int>::max()) {
- throw OpalException("Distribution::createDistributionFromFile",
- "Couldn't find " +
- std::to_string(numberOfParticlesRead) +
- " particles in file '" +
- fileName + "'");
+ throw OpalException(
+ "Distribution::createDistributionFromFile",
+ "Couldn't find " + std::to_string(numberOfParticlesRead)
+ + " particles in file '" + fileName + "'");
}
- MPI_Bcast(&data[0], dataSize, MPI_CHAR, 0, Ippl::getComm());
+ MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
size_t i = 0;
while (i < dataSize) {
-
- if (saveProcessor + 1 == (unsigned) Ippl::myNode()) {
- const double *tmp = reinterpret_cast<const double*>(&data[i]);
+ if (saveProcessor + 1 == (unsigned)Ippl::myNode()) {
+ const double* tmp = &(data[i]);
xDist_m.push_back(tmp[0]);
yDist_m.push_back(tmp[1]);
tOrZDist_m.push_back(tmp[2]);
pxDist_m.push_back(tmp[3]);
pyDist_m.push_back(tmp[4]);
pzDist_m.push_back(tmp[5]);
- i += 6 * sizeof(double);
- } else {
- i += singleDataSize;
}
+ i += singleDataSize;
- ++ saveProcessor;
- if (saveProcessor + 1 >= (unsigned) Ippl::getNodes()) {
+ ++saveProcessor;
+ if (saveProcessor + 1 >= (unsigned)Ippl::getNodes()) {
saveProcessor = 0;
}
}
@@ -1151,7 +1143,6 @@ void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, doub
inputFile.close();
}
-
void Distribution::createMatchedGaussDistribution(size_t numberOfParticles,
double massIneV,
double charge)
@@ -4462,4 +4453,4 @@ void Distribution::adjustPhaseSpace(double massIneV) {
// c-basic-offset: 4
// indent-tabs-mode: nil
// require-final-newline: nil
-// End:
+// End:
\ No newline at end of file
diff --git a/src/Structure/H5PartWrapper.cpp b/src/Structure/H5PartWrapper.cpp
index 109ef19225d6963ed66a089614a8b338f0c06435..f16d32a0e076a6f6ad7b33bbcc9441287e9c5cd0 100644
--- a/src/Structure/H5PartWrapper.cpp
+++ b/src/Structure/H5PartWrapper.cpp
@@ -459,10 +459,11 @@ void H5PartWrapper::copyStepData(
REPORTONERROR(H5PartSetNumParticles(file_m, numParticles));
std::vector<char> buffer(numParticles * sizeof(h5_float64_t));
- h5_float32_t *f32buffer = reinterpret_cast<h5_float32_t*>(&buffer[0]);
- h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(&buffer[0]);
- h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(&buffer[0]);
- h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(&buffer[0]);
+ char* buffer_ptr = Util::c_data(buffer);
+ h5_float32_t *f32buffer = reinterpret_cast<h5_float32_t*>(buffer_ptr);
+ h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
+ h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(buffer_ptr);
+ h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(buffer_ptr);
h5_ssize_t numDatasets = H5PartGetNumDatasets(source);
@@ -533,4 +534,4 @@ size_t H5PartWrapper::getNumParticles() const {
// c-basic-offset: 4
// indent-tabs-mode: nil
// require-final-newline: nil
-// End:
+// End:
\ No newline at end of file
diff --git a/src/Structure/H5PartWrapperForPC.cpp b/src/Structure/H5PartWrapperForPC.cpp
index 09fc259388965d6faed06d8822852a14dee4b1d0..3229b4857a2eb1c7f4b5fbe69cf3bc657fdca78b 100644
--- a/src/Structure/H5PartWrapperForPC.cpp
+++ b/src/Structure/H5PartWrapperForPC.cpp
@@ -163,7 +163,9 @@ void H5PartWrapperForPC::readStepData(PartBunchBase<double, 3>* bunch,
numParticles = lastParticle - firstParticle + 1;
std::vector<char> buffer(numParticles * sizeof(h5_float64_t));
- h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(&buffer[0]);
+ char* buffer_ptr = Util::c_data(buffer);
+ h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
+ h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(buffer_ptr);
READDATA(Float64, file_m, "x", f64buffer);
for(long int n = 0; n < numParticles; ++ n) {
@@ -207,16 +209,12 @@ void H5PartWrapperForPC::readStepData(PartBunchBase<double, 3>* bunch,
}
if ( bunch->getNumBunch() > 1 ) {
- std::vector<char> ibuffer(numParticles * sizeof(h5_int64_t));
- h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(&ibuffer[0]);
READDATA(Int64, file_m, "bin", i64buffer);
for(long int n = 0; n < numParticles; ++ n) {
bunch->Bin[n] = i64buffer[n];
}
}
- std::vector<char> ibuffer(numParticles * sizeof(h5_int64_t));
- h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(&ibuffer[0]);
READDATA(Int64, file_m, "bunchNumber", i64buffer);
for(long int n = 0; n < numParticles; ++ n) {
bunch->bunchNum[n] = i64buffer[n];
@@ -488,8 +486,9 @@ void H5PartWrapperForPC::writeStepData(PartBunchBase<double, 3>* bunch) {
const size_t skipID = IDZero;
std::vector<char> buffer(numLocalParticles * sizeof(h5_float64_t));
- h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(&buffer[0]);
- h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*> (&buffer[0]);
+ char* buffer_ptr = Util::c_data(buffer);
+ h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
+ h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*> (buffer_ptr);
REPORTONERROR(H5PartSetNumParticles(file_m, numLocalParticles));
diff --git a/src/Structure/H5PartWrapperForPT.cpp b/src/Structure/H5PartWrapperForPT.cpp
index 8fe3529b4308a97f2fd90ae006f1aac7c8dc3dfe..da36c82fa1440bbcd43e47c832365b1fff79b6d1 100644
--- a/src/Structure/H5PartWrapperForPT.cpp
+++ b/src/Structure/H5PartWrapperForPT.cpp
@@ -141,8 +141,9 @@ void H5PartWrapperForPT::readStepData(PartBunchBase<double, 3>* bunch, h5_ssize_
numParticles = lastParticle - firstParticle + 1;
std::vector<char> buffer(numParticles * sizeof(h5_float64_t));
- h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(&buffer[0]);
- h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(&buffer[0]);
+ char* buffer_ptr = Util::c_data(buffer);
+ h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
+ h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(buffer_ptr);
READDATA(Float64, file_m, "x", f64buffer);
for(long int n = 0; n < numParticles; ++ n) {
@@ -389,9 +390,10 @@ void H5PartWrapperForPT::writeStepData(PartBunchBase<double, 3>* bunch) {
REPORTONERROR(H5PartSetNumParticles(file_m, numLocalParticles));
std::vector<char> buffer(numLocalParticles * sizeof(h5_float64_t));
- h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(&buffer[0]);
- h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(&buffer[0]);
- h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(&buffer[0]);
+ char* buffer_ptr = Util::c_data(buffer);
+ h5_float64_t *f64buffer = reinterpret_cast<h5_float64_t*>(buffer_ptr);
+ h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(buffer_ptr);
+ h5_int32_t *i32buffer = reinterpret_cast<h5_int32_t*>(buffer_ptr);
for(size_t i = 0; i < numLocalParticles; ++ i)
f64buffer[i] = bunch->R[i](0);
@@ -498,4 +500,4 @@ void H5PartWrapperForPT::writeStepData(PartBunchBase<double, 3>* bunch) {
reportOnError(herr, __FILE__, __LINE__);
}
-}
+}
\ No newline at end of file