* Suggestion how to "solve" the XML-reading problems in certain environments:

A workaround has been implemented where it is not tried any more to "directly
  parse the file" but rather the file is read into a memory buffer which then
  is parsed.
  For further information, see MUSR-122.

* Fixed a linking problem when only shared libraries are built on Cygwin
  (introduced with the split-off of libPUserFcnBase).

ChangeLog

@@ -10,6 +10,8 @@ NEW the chi^2 calculation in single-histogram and asymmetry fits is parallelized
     if musrfit is built using a compiler supporting OpenMP (e.g. GCC >= 4.2)
     Using --disable-omp this feature can be disabled on the configure level.
 NEW any2many: force the user to define the exact NeXus ouput format (HDF4,HDF5,XML)
+FIXED a linking problem when only shared libraries are built on Cygwin
+FIXED the problem that in certain environments XML files could not be parsed (MUSR-122)
 FIXED crash of musrview in case the XML startup file is present but cannot be parsed correctly
 FIXED crash in case a non-existing userFcn is called from an existing library (MUSR-159)
 FIXED slightly wrong chisq since the 0-bin entries were treated wrongly for scaled N0/Bkg data (MUSR-193)

src/any2many.cpp

@@ -418,6 +418,9 @@ int main(int argc, char *argv[])
   }
 
   // read startup file
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
   char startup_path_name[128];
   TSAXParser *saxParser = new TSAXParser();
   PStartupHandler *startupHandler = new PStartupHandler();
@@ -436,7 +439,23 @@ int main(int argc, char *argv[])
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
     saxParser->ConnectToHandler("PStartupHandler", startupHandler);
-    status = saxParser->ParseFile(startup_path_name);
+    //status = saxParser->ParseFile(startup_path_name);
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << ">> any2many **WARNING** Reading/parsing musrfit_startup.xml failed.";

src/classes/Makefile.am

@@ -89,7 +89,7 @@ CLEANFILES = *Dict.cpp *Dict.h *~ core
 lib_LTLIBRARIES = libPMusr.la libPUserFcnBase.la
 
 libPMusr_la_SOURCES = $(h_sources) $(cpp_sources) $(dict_h_sources) $(dict_cpp_sources)
-libPMusr_la_LIBADD = $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS) $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS)
+libPMusr_la_LIBADD = libPUserFcnBase.la $(LEM_LIBS) $(PSIBIN_LIBS) $(MUD_LIBS) $(PNEXUS_LIBS) $(FFTW3_LIBS) $(GSL_LIBS) $(ROOT_LIBS)
 libPMusr_la_LDFLAGS = -version-info $(MUSR_LIBRARY_VERSION) -release $(MUSR_RELEASE) $(AM_LDFLAGS)
 
 libPUserFcnBase_la_SOURCES = $(h_sources_userFcn) $(cpp_sources_userFcn) $(dict_h_sources_userFcn) $(dict_cpp_sources_userFcn)

src/classes/PMsr2Data.cpp

@@ -419,12 +419,31 @@ int PMsr2Data::SetRunNumbers(const string &runListFile)
  */
 int PMsr2Data::ParseXmlStartupFile()
 {
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
   int status;
   fSaxParser = new TSAXParser();
   fStartupHandler = new PStartupHandler();
   string startup_path_name(fStartupHandler->GetStartupFilePath().Data());
   fSaxParser->ConnectToHandler("PStartupHandler", fStartupHandler);
-  status = fSaxParser->ParseFile(startup_path_name.c_str());
+  //status = fSaxParser->ParseFile(startup_path_name.c_str());
+  // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+  xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+  if (xmlFile.is_open()) { // check if file has been opened successfully
+    xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+    xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+    xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+    xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+    xmlFile.close(); // close the XML file
+  }
+  if (!xmlBuffer) { // file has not been read into the buffer
+    status = 1;
+  } else {
+    status = fSaxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+    delete[] xmlBuffer; // free the buffer memory
+    xmlBuffer = 0;
+  }
   // check for parse errors
   if (status) { // error
     cerr << endl << ">> msr2data: **WARNING** Reading/parsing musrfit_startup.xml failed." << endl;

src/external/MagProximity/PMagProximityFitter.cpp

@@ -33,6 +33,7 @@
 #include <cmath>
 
 #include <iostream>
+#include <fstream>
 using namespace std;
 
 #include <TSAXParser.h>
@@ -64,10 +65,30 @@ PMagProximityFitterGlobal::PMagProximityFitterGlobal()
   PMPStartupHandler *fStartupHandler = new PMPStartupHandler();
   strcpy(startup_path_name, fStartupHandler->GetStartupFilePath().Data());
   saxParser->ConnectToHandler("PMPStartupHandler", fStartupHandler);
-  Int_t status = saxParser->ParseFile(startup_path_name);
+  //Int_t status = saxParser->ParseFile(startup_path_name);
+  // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
+  xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+  if (xmlFile.is_open()) { // check if file has been opened successfully
+    xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+    xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+    xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+    xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+    xmlFile.close(); // close the XML file
+  }
+  Int_t status;
+  if (!xmlBuffer) { // file has not been read into the buffer
+    status = 1;
+  } else {
+    status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+    delete[] xmlBuffer; // free the buffer memory
+    xmlBuffer = 0;
+  }
   // check for parse errors
   if (status) { // error
-    cout << endl << ">> PMagProximityFitterGlobal::PMagProximityFitterGlobal: **WARNING** reading/parsing mag_proximity_startup.xml.";
+    cout << endl << ">> PMagProximityFitterGlobal::PMagProximityFitterGlobal: **WARNING** Reading/parsing mag_proximity_startup.xml failed.";
     cout << endl;
     fValid = false;
   }

src/external/Nonlocal/PNL_PippardFitter.cpp

@@ -33,6 +33,7 @@
 #include <cmath>
 
 #include <iostream>
+#include <fstream>
 using namespace std;
 
 #include <TSAXParser.h>
@@ -63,10 +64,30 @@ PNL_PippardFitterGlobal::PNL_PippardFitterGlobal()
   PNL_StartupHandler *fStartupHandler = new PNL_StartupHandler();
   strcpy(startup_path_name, fStartupHandler->GetStartupFilePath().Data());
   saxParser->ConnectToHandler("PNL_StartupHandler", fStartupHandler);
-  Int_t status = saxParser->ParseFile(startup_path_name);
+  //Int_t status = saxParser->ParseFile(startup_path_name);
+  // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
+  xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+  if (xmlFile.is_open()) { // check if file has been opened successfully
+    xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+    xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+    xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+    xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+    xmlFile.close(); // close the XML file
+  }
+  Int_t status;
+  if (!xmlBuffer) { // file has not been read into the buffer
+    status = 1;
+  } else {
+    status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+    delete[] xmlBuffer; // free the buffer memory
+    xmlBuffer = 0;
+  }
   // check for parse errors
   if (status) { // error
-    cout << endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal: **WARNING** reading/parsing nonlocal_startup.xml.";
+    cout << endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal: **WARNING** Reading/parsing nonlocal_startup.xml failed.";
     cout << endl;
     fValid = false;
   }

src/external/libFitPofB/classes/TLondon1D.cpp

@@ -30,6 +30,7 @@
 
 #include "TLondon1D.h"
 #include <iostream>
+#include <fstream>
 #include <cassert>
 #include <cmath>
 using namespace std;
@@ -153,7 +154,27 @@ TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -301,7 +322,27 @@ TLondon1D1L::TLondon1D1L() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -484,7 +525,27 @@ TLondon1D2L::TLondon1D2L() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -654,7 +715,27 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -801,7 +882,27 @@ TLondon1D3L::TLondon1D3L() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -970,7 +1071,27 @@ TLondon1D3LS::TLondon1D3LS() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -1139,7 +1260,27 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
 //     TSAXParser *saxParser = new TSAXParser();
 //     BMWStartupHandler *startupHandler = new BMWStartupHandler();
 //     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-//     int status (saxParser->ParseFile(startup_path_name.c_str()));
+//     //int status (saxParser->ParseFile(startup_path_name.c_str()));
+//     // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+//     fstream xmlFile;
+//     unsigned int xmlSize = 0;
+//     char *xmlBuffer = 0;
+//     xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+//     if (xmlFile.is_open()) { // check if file has been opened successfully
+//       xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+//       xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+//       xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+//       xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+//       xmlFile.close(); // close the XML file
+//     }
+//     int status;
+//     if (!xmlBuffer) { // file has not been read into the buffer
+//       status = 1;
+//     } else {
+//       status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+//       delete[] xmlBuffer; // free the buffer memory
+//       xmlBuffer = 0;
+//     }
 //     // check for parse errors
 //     if (status) { // error
 //       cout << endl << "**WARNING** Reading/parsing " << startup_path_name << " failed." << endl;

src/external/libFitPofB/classes/TVortex.cpp

@@ -30,6 +30,7 @@
 
 #include "TVortex.h"
 #include <iostream>
+#include <fstream>
 #include <cassert>
 #include <cmath>
 using namespace std;
@@ -165,7 +166,27 @@ TBulkTriVortexLondon::TBulkTriVortexLondon() : fCalcNeeded(true), fFirstCall(tru
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -222,7 +243,27 @@ TBulkSqVortexLondon::TBulkSqVortexLondon() : fCalcNeeded(true), fFirstCall(true)
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -449,7 +490,27 @@ TBulkTriVortexML::TBulkTriVortexML() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -585,7 +646,27 @@ TBulkTriVortexAGL::TBulkTriVortexAGL() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -720,7 +801,27 @@ TBulkTriVortexAGLII::TBulkTriVortexAGLII() : fCalcNeeded(true), fFirstCall(true)
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -868,7 +969,27 @@ TBulkTriVortexNGL::TBulkTriVortexNGL() : fCalcNeeded(true), fFirstCall(true) {
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -1020,7 +1141,27 @@ TBulkAnisotropicTriVortexLondonGlobal::TBulkAnisotropicTriVortexLondonGlobal() :
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -1259,7 +1400,27 @@ TBulkAnisotropicTriVortexMLGlobal::TBulkAnisotropicTriVortexMLGlobal() : fCalcNe
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -1498,7 +1659,27 @@ TBulkAnisotropicTriVortexAGLGlobal::TBulkAnisotropicTriVortexAGLGlobal() : fCalc
     TSAXParser *saxParser = new TSAXParser();
     BMWStartupHandler *startupHandler = new BMWStartupHandler();
     saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-    int status (saxParser->ParseFile(startup_path_name.c_str()));
+    //int status (saxParser->ParseFile(startup_path_name.c_str()));
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    fstream xmlFile;
+    unsigned int xmlSize = 0;
+    char *xmlBuffer = 0;
+    xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    int status;
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \

src/external/libLFRelaxation/TLFRelaxation.cpp

@@ -35,6 +35,7 @@
 #include <cassert>
 #include <sys/time.h>
 #include <iostream>
+#include <fstream>
 #include <cmath>
 
 #ifdef HAVE_GOMP
@@ -201,7 +202,27 @@ TLFDynGssKT::TLFDynGssKT() : fCalcNeeded(true), fFirstCall(true), fCounter(0) {
   TSAXParser *saxParser = new TSAXParser();
   BMWStartupHandler *startupHandler = new BMWStartupHandler();
   saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-  int status (saxParser->ParseFile(startup_path_name.c_str()));
+  //int status (saxParser->ParseFile(startup_path_name.c_str()));
+  // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
+  xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+  if (xmlFile.is_open()) { // check if file has been opened successfully
+    xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+    xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+    xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+    xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+    xmlFile.close(); // close the XML file
+  }
+  int status;
+  if (!xmlBuffer) { // file has not been read into the buffer
+    status = 1;
+  } else {
+    status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+    delete[] xmlBuffer; // free the buffer memory
+    xmlBuffer = 0;
+  }
   // check for parse errors
   if (status) { // error
     cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
@@ -523,7 +544,27 @@ TLFDynExpKT::TLFDynExpKT() : fCalcNeeded(true), fFirstCall(true), fCounter(0), f
   TSAXParser *saxParser = new TSAXParser();
   BMWStartupHandler *startupHandler = new BMWStartupHandler();
   saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
-  int status (saxParser->ParseFile(startup_path_name.c_str()));
+  //int status (saxParser->ParseFile(startup_path_name.c_str()));
+  // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
+  xmlFile.open(startup_path_name.c_str(), ios::in | ios::ate); // open file for reading and go to the end of the file
+  if (xmlFile.is_open()) { // check if file has been opened successfully
+    xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+    xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+    xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+    xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+    xmlFile.close(); // close the XML file
+  }
+  int status;
+  if (!xmlBuffer) { // file has not been read into the buffer
+    status = 1;
+  } else {
+    status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+    delete[] xmlBuffer; // free the buffer memory
+    xmlBuffer = 0;
+  }
   // check for parse errors
   if (status) { // error
     cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \

src/musrfit.cpp

@@ -424,6 +424,9 @@ int main(int argc, char *argv[])
   }
 
   // read startup file
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
   char startup_path_name[128];
   TSAXParser *saxParser = new TSAXParser();
   PStartupHandler *startupHandler = new PStartupHandler();
@@ -442,7 +445,23 @@ int main(int argc, char *argv[])
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
     saxParser->ConnectToHandler("PStartupHandler", startupHandler);
-    status = saxParser->ParseFile(startup_path_name);
+    //status = saxParser->ParseFile(startup_path_name);
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << ">> musrfit **WARNING** Reading/parsing musrfit_startup.xml failed.";

src/musrt0.cpp

@@ -34,6 +34,7 @@
 #include <string.h>
 
 #include <iostream>
+#include <fstream>
 using namespace std;
 
 #include <TApplication.h>
@@ -275,6 +276,9 @@ Int_t main(Int_t argc, Char_t *argv[])
   }
 
   // read startup file
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
   Char_t startup_path_name[128];
   TSAXParser *saxParser = new TSAXParser();
   PStartupHandler *startupHandler = new PStartupHandler();
@@ -293,10 +297,26 @@ Int_t main(Int_t argc, Char_t *argv[])
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
     saxParser->ConnectToHandler("PStartupHandler", startupHandler);
-    status = saxParser->ParseFile(startup_path_name);
+    //status = saxParser->ParseFile(startup_path_name);
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
-      cerr << endl << ">> musrt0 **WARNING** reading/parsing musrfit_startup.xml.";
+      cerr << endl << ">> musrt0 **WARNING** Reading/parsing musrfit_startup.xml failed.";
       cerr << endl;
       // clean up
       if (saxParser) {

src/musrview.cpp

@@ -34,6 +34,7 @@
 #include <string.h>
 
 #include <iostream>
+#include <fstream>
 using namespace std;
 
 #include <TApplication.h>
@@ -158,6 +159,9 @@ int main(int argc, char *argv[])
   }
 
   // read startup file
+  fstream xmlFile;
+  unsigned int xmlSize = 0;
+  char *xmlBuffer = 0;
   char startup_path_name[128];
   TSAXParser *saxParser = new TSAXParser();
   PStartupHandler *startupHandler = new PStartupHandler();
@@ -176,7 +180,23 @@ int main(int argc, char *argv[])
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
     saxParser->ConnectToHandler("PStartupHandler", startupHandler);
-    status = saxParser->ParseFile(startup_path_name);
+    //status = saxParser->ParseFile(startup_path_name);
+    // parsing the file as above seems to lead to problems in certain environments; try working around through a buffer as follows
+    xmlFile.open(startup_path_name, ios::in | ios::ate); // open file for reading and go to the end of the file
+    if (xmlFile.is_open()) { // check if file has been opened successfully
+      xmlSize = xmlFile.tellg(); // get the position within the stream == size of the file (since we are at the end)
+      xmlFile.seekg(0, ios::beg); // go back to the beginning of the stream
+      xmlBuffer = new char[xmlSize]; // allocate buffer memory for the whole XML file
+      xmlFile.read(xmlBuffer, xmlSize); // read in the whole XML file into the buffer
+      xmlFile.close(); // close the XML file
+    }
+    if (!xmlBuffer) { // file has not been read into the buffer
+      status = 1;
+    } else {
+      status = saxParser->ParseBuffer(xmlBuffer, xmlSize); // parse buffer
+      delete[] xmlBuffer; // free the buffer memory
+      xmlBuffer = 0;
+    }
     // check for parse errors
     if (status) { // error
       cerr << endl << ">> musrview **WARNING** Reading/parsing musrfit_startup.xml failed.";