replace &(someVector[0]) with someVector.data() where the vector written but...

replace &(someVector[0]) with someVector.data() where the vector written but only read and where we can't be sure that if it has elements

CMakeLists.txt

@@ -99,6 +99,9 @@ elseif (${CMAKE_CXX_COMPILER_ID} MATCHES "GNU")
         add_link_options (-fopenmp)
     endif ()
 
+    # Enables extra error checking in the form of precondition assertion, such
+    # as bounds checking and null pointer checks when dereferencing smart pointers
+    add_compile_options(-Wp,-D_GLIBCXX_ASSERTIONS)
 else ()
     message (STATUS "Unknown C++ compiler. Please use the GNU or Intel compiler, if you are having problems.")
 endif ()
@@ -271,4 +274,4 @@ install (
     FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config_install.cmake
     DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/cmake/${PROJECT_NAME}"
     RENAME ${PROJECT_NAME}Config.cmake
-    )
+    )
\ No newline at end of file

ippl/src/Message/CMakeLists.txt

 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
@@ -30,4 +32,4 @@ include_directories (
 add_ippl_sources (${_SRCS})
 add_ippl_headers (${_HDRS})
 
-install (FILES ${_HDRS} DESTINATION include/Message)
+install (FILES ${_HDRS} DESTINATION include/Message)
\ No newline at end of file

ippl/src/Message/Format.cpp

+//
+// 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

ippl/src/Message/Format.h

+//
+// 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

ippl/src/Message/Formatter.h

-// -*- 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

ippl/src/Message/Formatter.cpp → ippl/src/Message/MsgBuffer.cpp

-#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

ippl/src/Message/MsgBuffer.h

+//
+// 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

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

ippl/src/Particle/IpplParticleBase.h

@@ -100,7 +100,8 @@
 #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 <utility>
 #include <iostream>
@@ -400,4 +401,4 @@ 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
+ ***************************************************************************/

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;
     }

src/Amr/BoxLibLayout.hpp

@@ -38,7 +38,8 @@
 
 #include "BoxLibLayout.h"
 
-#include "Message/Formatter.h"
+#include "Message/Format.h"
+#include "Message/MsgBuffer.h"
 #include "Utility/PAssert.h"
 #include "Utilities/OpalException.h"
 
@@ -348,7 +349,8 @@ 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 +481,7 @@ 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()",
@@ -856,4 +858,4 @@ void BoxLibLayout<T, Dim>::initBaseBox_m(int nGridPoints,
     this->m_nlevels = ba.size();
 }
 
-#endif
\ No newline at end of file
+#endif

src/CMakeLists.txt

@@ -161,4 +161,4 @@ set (HDRS
     changes.h
     )
 
-install (FILES ${HDRS} DESTINATION "${CMAKE_INSTALL_PREFIX}/include/src")
+install (FILES ${HDRS} DESTINATION "${CMAKE_INSTALL_PREFIX}/include/src")
\ No newline at end of file

src/Classic/Structure/LossDataSink.cpp

@@ -399,22 +399,22 @@ 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;
@@ -711,4 +711,4 @@ SetStatistics LossDataSink::computeSetStatistics(unsigned int setIdx) {
     stat.rprms_m = stat.rpsum_m * stat.fac_m;
 
     return stat;
-}
+}
\ No newline at end of file

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>

src/Distribution/Distribution.cpp

@@ -1007,26 +1007,26 @@ size_t Distribution::getNumberOfParticlesInFile(std::ifstream &inputFile) {
 }
 
 void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, double massIneV) {
-
     // Data input file is only read by node 0.
     std::ifstream inputFile;
     std::string fileName = Attributes::getString(itsAttr[Attrib::Distribution::FNAME]);
     if (!boost::filesystem::exists(fileName)) {
-        throw OpalException("Distribution::createDistributionFromFile",
-                            "Open file operation failed, please check if \""
-                            + fileName +
-                            "\" really exists.");
+        throw OpalException(
+            "Distribution::createDistributionFromFile",
+            "Open file operation failed, please check if \"" + fileName + "\" really exists.");
     }
     if (Ippl::myNode() == 0) {
         inputFile.open(fileName.c_str());
     }
 
     *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;
 
     size_t numberOfParticlesRead = getNumberOfParticlesInFile(inputFile);
     /*
@@ -1037,26 +1037,25 @@ 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;
-
-    data.reserve(dataSize);
+    size_t singleDataSize            = 6;
+    unsigned int dataSize            = distributeFrequency * singleDataSize;
+    std::vector<double> data(dataSize);
 
-    const char* buffer;
     if (Ippl::myNode() == 0) {
-        char lineBuffer[1024];
-        unsigned int numParts = 0;
+        constexpr unsigned int bufferSize = 1024;
+        char lineBuffer[bufferSize];