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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11631 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-03-13 17:34:00 +00:00
parent d2bbbcef02
commit be64063802
3 changed files with 47 additions and 27 deletions
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26
src/MPIIO/dump_atom_mpiio.cpp
View File

@ -82,8 +82,11 @@ void DumpAtomMPIIO::openfile()
if (append_flag) { // append open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
int myrank;
MPI_Comm_rank(world,&myrank);
if (myrank == 0)
@ -96,8 +99,11 @@ void DumpAtomMPIIO::openfile()
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
mpifo = 0;
MPI_File_set_size(mpifh,(MPI_Offset) (headerSize+sumFileSize));
@ -546,7 +552,7 @@ int DumpAtomMPIIO::convert_string_omp(int n, double *mybuf)
int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
{
double *localbuf = mybuf;
MPI_Status mpiStatus;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -581,7 +587,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
{
int tid = omp_get_thread_num();
int m=0;
@ -593,7 +599,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (localbuf[bufOffset[tid]+m]),static_cast<int> (localbuf[bufOffset[tid]+m+1]),localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4],static_cast<int> (localbuf[bufOffset[tid]+m+5]),static_cast<int> (localbuf[bufOffset[tid]+m+6]),static_cast<int> (localbuf[bufOffset[tid]+m+7]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4],static_cast<int> (mybuf[bufOffset[tid]+m+5]),static_cast<int> (mybuf[bufOffset[tid]+m+6]),static_cast<int> (mybuf[bufOffset[tid]+m+7]));
m += size_one;
}
}
@ -637,7 +643,7 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
{
double *localbuf = mybuf;
MPI_Status mpiStatus;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -672,7 +678,7 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
{
int tid = omp_get_thread_num();
int m=0;
@ -684,7 +690,7 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (localbuf[bufOffset[tid]+m]),static_cast<int> (localbuf[bufOffset[tid]+m+1]),localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
m += size_one;
}
}

25
src/MPIIO/dump_custom_mpiio.cpp
View File

@ -103,8 +103,11 @@ void DumpCustomMPIIO::openfile()
if (append_flag) { // append open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
int myrank;
MPI_Comm_rank(world,&myrank);
if (myrank == 0)
@ -117,12 +120,16 @@ void DumpCustomMPIIO::openfile()
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
mpifo = 0;
MPI_File_set_size(mpifh,(MPI_Offset) (headerSize+sumFileSize));
currentFileSize = (headerSize+sumFileSize);
}
}
@ -566,7 +573,7 @@ void DumpCustomMPIIO::write_string(int n, double *mybuf)
int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
{
double *localbuf = mybuf;
MPI_Status mpiStatus;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -601,7 +608,7 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
{
int tid = omp_get_thread_num();
int m=0;
@ -615,11 +622,11 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
for (int j = 0; j < size_one; j++) {
if (vtype[j] == INT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (localbuf[bufOffset[tid]+m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
else if (vtype[j] == DOUBLE)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],localbuf[bufOffset[tid]+m]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
else if (vtype[j] == STRING)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) localbuf[bufOffset[tid]+m]]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
m ++;
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");

21
src/MPIIO/dump_xyz_mpiio.cpp
View File

@ -103,8 +103,11 @@ void DumpXYZMPIIO::openfile()
if (append_flag) { // append open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
int myrank;
MPI_Comm_rank(world,&myrank);
if (myrank == 0)
@ -116,12 +119,16 @@ void DumpXYZMPIIO::openfile()
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
if (err != MPI_SUCCESS)
error->one(FLERR,"Cannot open dump file");
if (err != MPI_SUCCESS) {
char str[128];
sprintf(str,"Cannot open dump file %s",filecurrent);
error->one(FLERR,str);
}
mpifo = 0;
MPI_File_set_size(mpifh,(MPI_Offset) (headerSize+sumFileSize));
currentFileSize = (headerSize+sumFileSize);
}
}
@ -308,7 +315,7 @@ void DumpXYZMPIIO::write_string(int n, double *mybuf)
int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
{
double *localbuf = mybuf;
MPI_Status mpiStatus;
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
@ -343,7 +350,7 @@ int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
#pragma omp parallel default(none) shared(localbuf,bufLength,bufOffset,bufRange,mpifhStringCountPerThread,mpifh_buffer_line_per_thread)
#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
{
int tid = omp_get_thread_num();
int m=0;
@ -355,7 +362,7 @@ int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,typenames[static_cast<int> (localbuf[bufOffset[tid]+m+1])],localbuf[bufOffset[tid]+m+2],localbuf[bufOffset[tid]+m+3],localbuf[bufOffset[tid]+m+4]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,typenames[static_cast<int> (mybuf[bufOffset[tid]+m+1])],mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
m += size_one;
}