git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11323 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MPIIO/dump_atom_mpiio.cpp

@@ -38,9 +38,7 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg) :
-                  DumpAtom(lmp, narg, arg)
+  DumpAtom(lmp, narg, arg) {}
-{
-}
 
 /* ---------------------------------------------------------------------- */
 

src/MPIIO/dump_atom_mpiio.h

@@ -11,13 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-/* ----------------------------------------------------------------------
-   Contributing author: Paul Coffman (IBM)
-------------------------------------------------------------------------- */
-
 #ifdef DUMP_CLASS
 
-DumpStyle(atom_mpiio,DumpAtomMPIIO)
+DumpStyle(atom/mpiio,DumpAtomMPIIO)
 
 #else
 

src/MPIIO/dump_custom_mpiio.cpp

@@ -59,22 +59,19 @@ enum{INT,DOUBLE,STRING};    // same as in DumpCFG
 /* ---------------------------------------------------------------------- */
 
 DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg) :
-                  DumpCustom(lmp, narg, arg)
+  DumpCustom(lmp, narg, arg) {}
-{
-}
 
 /* ---------------------------------------------------------------------- */
 
 DumpCustomMPIIO::~DumpCustomMPIIO()
 {
-  if (multifile == 0)    MPI_File_close(&mpifh);
+  if (multifile == 0) MPI_File_close(&mpifh);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void DumpCustomMPIIO::openfile()
 {
-
   if (singlefile_opened) { // single file already opened, so just return after resetting filesize
     mpifo = currentFileSize;
     MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
@@ -140,7 +137,6 @@ void DumpCustomMPIIO::openfile()
 
 void DumpCustomMPIIO::write()
 {
-
   if (domain->triclinic == 0) {
     boxxlo = domain->boxlo[0];
     boxxhi = domain->boxhi[0];
@@ -504,7 +500,6 @@ void DumpCustomMPIIO::header_item_triclinic(bigint ndump)
 
 void DumpCustomMPIIO::write_data(int n, double *mybuf)
 {
-
   (this->*write_choice)(n,mybuf);
 }
 
@@ -512,7 +507,6 @@ void DumpCustomMPIIO::write_data(int n, double *mybuf)
 
 void DumpCustomMPIIO::write_binary(int n, double *mybuf)
 {
-
   MPI_Status mpiStatus;
   n *= size_one;
 

src/MPIIO/dump_custom_mpiio.h

@@ -11,13 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-/* ----------------------------------------------------------------------
-   Contributing author: Paul Coffman (IBM)
-------------------------------------------------------------------------- */
-
 #ifdef DUMP_CLASS
 
-DumpStyle(custom_mpiio,DumpCustomMPIIO)
+DumpStyle(custom/mpiio,DumpCustomMPIIO)
 
 #else
 
@@ -42,6 +38,7 @@ class DumpCustomMPIIO : public DumpCustom {
   MPI_Offset mpifo,offsetFromHeader,headerSize, currentFileSize;
   int performEstimate; // switch for write_data and write_header methods to use for gathering data and detemining filesize for preallocation vs actually writing the data
   char *filecurrent;  // name of file for this round (with % and * replaced)
+
 #if defined(_OPENMP)
   int convert_string_omp(int, double *);  // multithreaded version of convert_string
 #endif
@@ -63,8 +60,6 @@ class DumpCustomMPIIO : public DumpCustom {
   FnPtrData write_choice;              // ptr to write data functions
   void write_binary(int, double *);
   void write_string(int, double *);
-
-
 };
 
 }

src/MPIIO/dump_xyz_mpiio.cpp

@@ -59,15 +59,13 @@ enum{INT,DOUBLE,STRING};    // same as in DumpCFG
 /* ---------------------------------------------------------------------- */
 
 DumpXYZMPIIO::DumpXYZMPIIO(LAMMPS *lmp, int narg, char **arg) :
-                  DumpXYZ(lmp, narg, arg)
+  DumpXYZ(lmp, narg, arg) {}
-{
-}
 
 /* ---------------------------------------------------------------------- */
 
 DumpXYZMPIIO::~DumpXYZMPIIO()
 {
-  if (multifile == 0)    MPI_File_close(&mpifh);
+  if (multifile == 0) MPI_File_close(&mpifh);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -251,7 +249,6 @@ void DumpXYZMPIIO::init_style()
 
 void DumpXYZMPIIO::write_header(bigint n)
 {
-
   MPI_Status mpiStatus;
 
   if (performEstimate) {
@@ -275,7 +272,6 @@ void DumpXYZMPIIO::write_header(bigint n)
 
 void DumpXYZMPIIO::write_data(int n, double *mybuf)
 {
-
   (this->*write_choice)(n,mybuf);
 }
 
@@ -287,7 +283,6 @@ void DumpXYZMPIIO::write_string(int n, double *mybuf)
 
   if (performEstimate) {
 
-
 #if defined(_OPENMP)
     int nthreads = omp_get_max_threads();
     if (nthreads > 1)

src/MPIIO/dump_xyz_mpiio.h

@@ -11,13 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-/* ----------------------------------------------------------------------
-   Contributing author: Paul Coffman (IBM)
-------------------------------------------------------------------------- */
-
 #ifdef DUMP_CLASS
 
-DumpStyle(xyz_mpiio,DumpXYZMPIIO)
+DumpStyle(xyz/mpiio,DumpXYZMPIIO)
 
 #else
 

src/MPIIO/restart_mpiio.cpp

@@ -38,7 +38,7 @@ RestartMPIIO::RestartMPIIO(LAMMPS *lmp) : Pointers(lmp)
 
 void RestartMPIIO::openForRead(char *filename)
 {
-  int err = MPI_File_open(world, filename, MPI_MODE_RDONLY , 
+  int err = MPI_File_open(world, filename, MPI_MODE_RDONLY ,
                           MPI_INFO_NULL, &mpifh);
   if (err != MPI_SUCCESS) {
     char str[MPI_MAX_ERROR_STRING+128];
@@ -58,7 +58,7 @@ void RestartMPIIO::openForRead(char *filename)
 
 void RestartMPIIO::openForWrite(char *filename)
 {
-  int err = MPI_File_open(world, filename, MPI_MODE_APPEND | MPI_MODE_WRONLY, 
+  int err = MPI_File_open(world, filename, MPI_MODE_APPEND | MPI_MODE_WRONLY,
                           MPI_INFO_NULL, &mpifh);
   if (err != MPI_SUCCESS) {
     char str[MPI_MAX_ERROR_STRING+128];
@@ -72,7 +72,7 @@ void RestartMPIIO::openForWrite(char *filename)
 }
 
 /* ----------------------------------------------------------------------
-   determine the absolute offset for the data to be written with 
+   determine the absolute offset for the data to be written with
      MPI_Scan of the send sizes
    compute the file size based off the MPI_Scan send size value on the last rank
    set the filesize with ftruncate via MPI_File_set_size
@@ -82,13 +82,13 @@ void RestartMPIIO::openForWrite(char *filename)
 void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
 {
   MPI_Status mpiStatus;
-  long incPrefix = 0;
+  bigint incPrefix = 0;
-  long longSendSize = (long) send_size;
+  bigint bigintSendSize = (bigint) send_size;
-  MPI_Scan(&longSendSize,&incPrefix,1,MPI_LONG,MPI_SUM,world);
+  MPI_Scan(&bigintSendSize,&incPrefix,1,MPI_LMP_BIGINT,MPI_SUM,world);
-  
+
-  long largestIncPrefix = incPrefix;
+  bigint largestIncPrefix = incPrefix;
-  MPI_Bcast(&largestIncPrefix, 1, MPI_LONG, (nprocs-1), world);
+  MPI_Bcast(&largestIncPrefix, 1, MPI_LMP_BIGINT, (nprocs-1), world);
-  
+
   int err = MPI_File_set_size(mpifh,
                               (headerOffset+(largestIncPrefix*sizeof(double))));
   if (err != MPI_SUCCESS) {
@@ -100,9 +100,9 @@ void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
             mpiErrorString);
     error->one(FLERR,str);
   }
-  
+
-  err = MPI_File_write_at_all(mpifh,headerOffset + 
+  err = MPI_File_write_at_all(mpifh,headerOffset +
-                              ((incPrefix-longSendSize)*sizeof(double)),
+                              ((incPrefix-bigintSendSize)*sizeof(double)),
                               buf,send_size,MPI_DOUBLE,&mpiStatus);
   if (err != MPI_SUCCESS) {
     char str[MPI_MAX_ERROR_STRING+128];
@@ -118,24 +118,24 @@ void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
 /* ----------------------------------------------------------------------
    read the data into buf via collective MPI-IO by calling MPI_File_read_at_all
    with the chunkOffset and chunkSize provided
-   if the consolidated chunksize is greater than INT_MAX 
+   if the consolidated chunksize is greater than INT_MAX
      can only happen in extreme situation of reading restart file on
      much fewer ranks than written and with relatively large data sizes
    follow the collective IO call with rank independant IO to read remaining data
 ------------------------------------------------------------------------- */
 
-void RestartMPIIO::read(MPI_Offset chunkOffset, long chunkSize, double *buf)
+void RestartMPIIO::read(MPI_Offset chunkOffset, bigint chunkSize, double *buf)
 {
   MPI_Status mpiStatus;
 
   int intChunkSize;
-  long remainingSize = 0;
+  bigint remainingSize = 0;
   if (chunkSize > INT_MAX) {
     intChunkSize = INT_MAX;
     remainingSize = chunkSize - INT_MAX;
   }
   else intChunkSize = (int) chunkSize;
-  
+
   int err = MPI_File_read_at_all(mpifh,chunkOffset,buf,intChunkSize,
                                  MPI_DOUBLE,&mpiStatus);
   if (err != MPI_SUCCESS) {
@@ -147,7 +147,7 @@ void RestartMPIIO::read(MPI_Offset chunkOffset, long chunkSize, double *buf)
             mpiErrorString);
     error->one(FLERR,str);
   }
-  
+
   MPI_Offset currentOffset = chunkOffset+intChunkSize;
   MPI_Offset bufOffset = intChunkSize;
   while (remainingSize > 0) {

src/MPIIO/restart_mpiio.h

@@ -31,7 +31,7 @@ class RestartMPIIO  : protected Pointers {
   void openForRead(char *);
   void openForWrite(char *);
   void write(MPI_Offset, int, double *);
-  void read(MPI_Offset, long, double *);
+  void read(MPI_Offset, bigint, double *);
   void close();
 };