Merge branch 'develop' into feature/hadrons

lib/parallelIO/BinaryIO.h

@@ -372,7 +372,7 @@ class BinaryIO {
 	std::cout << GridLogMessage <<"IOobject: C++ read I/O " << file << " : "
                   << iodata.size() * sizeof(fobj) << " bytes" << std::endl;
         std::ifstream fin;
-        fin.open(file, std::ios::binary | std::ios::in);
+	fin.open(file, std::ios::binary | std::ios::in);
         if (control & BINARYIO_MASTER_APPEND)
         {
           fin.seekg(-sizeof(fobj), fin.end);
@@ -453,11 +453,15 @@ class BinaryIO {
 	std::ofstream fout; 
 	fout.exceptions ( std::fstream::failbit | std::fstream::badbit );
 	try {
-	  fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
+	  if (offset) { // Must already exist and contain data
+	    fout.open(file,std::ios::binary|std::ios::out|std::ios::in);
+	  } else {     // Allow create
+	    fout.open(file,std::ios::binary|std::ios::out);
+	  }
 	} catch (const std::fstream::failure& exc) {
 	  std::cout << GridLogError << "Error in opening the file " << file << " for output" <<std::endl;
 	  std::cout << GridLogError << "Exception description: " << exc.what() << std::endl;
-	  std::cout << GridLogError << "Probable cause: wrong path, inaccessible location "<< std::endl;
+	  //	  std::cout << GridLogError << "Probable cause: wrong path, inaccessible location "<< std::endl;
 #ifdef USE_MPI_IO
 	  MPI_Abort(MPI_COMM_WORLD,1);
 #else

lib/parallelIO/IldgIO.h

@@ -350,26 +350,36 @@ class GridLimeWriter : public BinaryIO {
     // iv) fseek on FILE * to end of this disjoint section.
     //  v) Continue writing scidac record.
     ////////////////////////////////////////////////////////////////////
-
+    
+    GridBase *grid = field._grid;
     ////////////////////////////////////////////
     // Create record header
     ////////////////////////////////////////////
     typedef typename vobj::scalar_object sobj;
     int err;
     uint32_t nersc_csum,scidac_csuma,scidac_csumb;
-    uint64_t PayloadSize = sizeof(sobj) * field._grid->_gsites;
+    uint64_t PayloadSize = sizeof(sobj) * grid->_gsites;
     createLimeRecordHeader(record_name, 0, 0, PayloadSize);
-
+    fflush(File);
+    
     //    std::cout << "W sizeof(sobj)"      <<sizeof(sobj)<<std::endl;
     //    std::cout << "W Gsites "           <<field._grid->_gsites<<std::endl;
     //    std::cout << "W Payload expected " <<PayloadSize<<std::endl;
 
-    fflush(File);
+    ////////////////////////////////////////////////
+    // Check all nodes agree on file position
+    ////////////////////////////////////////////////
+    uint64_t offset1 = ftello(File);    
+
+    uint64_t compare = offset1;
+    grid->Broadcast(0,(void *)&compare,sizeof(compare));
+
+    assert(compare == offset1 ); 
 
     ///////////////////////////////////////////
     // Write by other means into the binary record
     ///////////////////////////////////////////
-    uint64_t offset1 = ftello(File);    //    std::cout << " Writing to offset "<<offset1 << std::endl;
+
     std::string format = getFormatString<vobj>();
     BinarySimpleMunger<sobj,sobj> munge;
     BinaryIO::writeLatticeObject<vobj,sobj>(field, filename, munge, offset1, format,nersc_csum,scidac_csuma,scidac_csumb);
@@ -380,7 +390,15 @@ class GridLimeWriter : public BinaryIO {
     fseek(File,0,SEEK_END);             
     uint64_t offset2 = ftello(File);     //    std::cout << " now at offset "<<offset2 << std::endl;
 
-    assert((offset2-offset1) == PayloadSize);
+    /////////////////////////////////////////////////////////////
+    // Must synchronise the nodes so no race between nodes
+    /////////////////////////////////////////////////////////////
+    grid->Barrier();
+
+    /////////////////////////////////////////////////////////////
+    // Check MPI-2 I/O did what we expect to file
+    /////////////////////////////////////////////////////////////
+    assert( (offset2-offset1) == PayloadSize);
 
     err=limeWriterCloseRecord(LimeW);  assert(err>=0);
 

lib/parallelIO/IldgIOtypes.h

@@ -136,8 +136,9 @@ struct scidacRecord : Serializable {
 				  int, typesize,
 				  int, datacount);
 
-  scidacRecord() { version =1.0; }
-
+  scidacRecord()
+  : version(1.0), recordtype(0), colors(0), spins(0), typesize(0), datacount(0)
+  {}
 };
 
 ////////////////////////

lib/parallelIO/MetaData.h

@@ -81,18 +81,16 @@ namespace Grid {
 				      std::string, creation_date,
 				      std::string, archive_date,
 				      std::string, floating_point);
-      FieldMetaData(void) { 
-	nd=4;
-	dimension.resize(4);
-	boundary.resize(4);
-	scidac_checksuma=0;
-	scidac_checksumb=0;
-	checksum=0;
-      }
+      // WARNING: non-initialised values might lead to twisted parallel IO
+      // issues, std::string are fine because they initliase to size 0
+      // as per C++ standard.
+      FieldMetaData(void) 
+      : nd(4), dimension(4,0), boundary(4, ""), data_start(0),
+      link_trace(0.), plaquette(0.), checksum(0),
+      scidac_checksuma(0), scidac_checksumb(0), sequence_number(0)
+      {}
     };
 
-
-
   namespace QCD {
 
     using namespace Grid;