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

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This commit is contained in:
sjplimp
2014-01-25 16:11:46 +00:00
parent d94ff39c8f
commit 8ef19992c2
8 changed files with 28 additions and 54 deletions
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4
src/MPIIO/dump_atom_mpiio.cpp
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@ -38,9 +38,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg) :
DumpAtom(lmp, narg, arg)
{
}
DumpAtom(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */

6
src/MPIIO/dump_atom_mpiio.h
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@ -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

10
src/MPIIO/dump_custom_mpiio.cpp
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@ -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;

9
src/MPIIO/dump_custom_mpiio.h
View File

@ -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 *);
};
}

9
src/MPIIO/dump_xyz_mpiio.cpp
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@ -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)

6
src/MPIIO/dump_xyz_mpiio.h
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@ -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

16
src/MPIIO/restart_mpiio.cpp
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@ -82,12 +82,12 @@ void RestartMPIIO::openForWrite(char *filename)
void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
{
MPI_Status mpiStatus;
long incPrefix = 0;
long longSendSize = (long) send_size;
MPI_Scan(&longSendSize,&incPrefix,1,MPI_LONG,MPI_SUM,world);
bigint incPrefix = 0;
bigint bigintSendSize = (bigint) send_size;
MPI_Scan(&bigintSendSize,&incPrefix,1,MPI_LMP_BIGINT,MPI_SUM,world);
long largestIncPrefix = incPrefix;
MPI_Bcast(&largestIncPrefix, 1, MPI_LONG, (nprocs-1), world);
bigint largestIncPrefix = incPrefix;
MPI_Bcast(&largestIncPrefix, 1, MPI_LMP_BIGINT, (nprocs-1), world);
int err = MPI_File_set_size(mpifh,
(headerOffset+(largestIncPrefix*sizeof(double))));
@ -102,7 +102,7 @@ void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
}
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];
@ -124,12 +124,12 @@ void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf)
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;

2
src/MPIIO/restart_mpiio.h
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@ -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();
};