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dump_xyz_mpiio.cpp
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Sat, Jun 29, 10:43

dump_xyz_mpiio.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "dump_xyz_mpiio.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
#include <stdlib.h>
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
#define MAX_TEXT_HEADER_SIZE 4096
#define DUMP_BUF_CHUNK_SIZE 16384
#define DUMP_BUF_INCREMENT_SIZE 4096
enum{ID,MOL,TYPE,ELEMENT,MASS,
X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE,STRING}; // same as in DumpCFG
/* ---------------------------------------------------------------------- */
DumpXYZMPIIO::DumpXYZMPIIO(LAMMPS *lmp, int narg, char **arg) :
DumpXYZ(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
DumpXYZMPIIO::~DumpXYZMPIIO()
{
if (multifile == 0) MPI_File_close(&mpifh);
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::openfile()
{
if (singlefile_opened) { // single file already opened, so just return after resetting filesize
mpifo = currentFileSize;
MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
currentFileSize = mpifo+headerSize+sumFileSize;
return;
}
if (multifile == 0) singlefile_opened = 1;
// if one file per timestep, replace '*' with current timestep
filecurrent = filename;
if (multifile) {
char *filestar = filecurrent;
filecurrent = new char[strlen(filestar) + 16];
char *ptr = strchr(filestar,'*');
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filestar,update->ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
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) {
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)
MPI_File_get_size(mpifh,&mpifo);
MPI_Bcast(&mpifo, 1, MPI_LMP_BIGINT, 0, world);
MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
currentFileSize = mpifo+headerSize+sumFileSize;
}
else { // replace open
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
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);
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::write()
{
if (domain->triclinic == 0) {
boxxlo = domain->boxlo[0];
boxxhi = domain->boxhi[0];
boxylo = domain->boxlo[1];
boxyhi = domain->boxhi[1];
boxzlo = domain->boxlo[2];
boxzhi = domain->boxhi[2];
} else {
boxxlo = domain->boxlo_bound[0];
boxxhi = domain->boxhi_bound[0];
boxylo = domain->boxlo_bound[1];
boxyhi = domain->boxhi_bound[1];
boxzlo = domain->boxlo_bound[2];
boxzhi = domain->boxhi_bound[2];
boxxy = domain->xy;
boxxz = domain->xz;
boxyz = domain->yz;
}
// nme = # of dump lines this proc contributes to dump
nme = count();
// ntotal = total # of dump lines in snapshot
// nmax = max # of dump lines on any proc
bigint bnme = nme;
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
int nmax;
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
// write timestep header
// for multiproc,
// nheader = # of lines in this file via Allreduce on clustercomm
bigint nheader = ntotal;
// insure filewriter proc can receive everyone's info
// limit nmax*size_one to int since used as arg in MPI_Rsend() below
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
error->all(FLERR,"Too much per-proc info for dump");
maxbuf = nmax;
memory->destroy(buf);
memory->create(buf,(maxbuf*size_one),"dump:buf");
}
if (sort_flag && sortcol == 0 && nmax > maxids) {
maxids = nmax;
memory->destroy(ids);
memory->create(ids,maxids,"dump:ids");
}
if (sort_flag && sortcol == 0) pack(ids);
else pack(NULL);
if (sort_flag) sort();
// determine how much data needs to be written for setting the file size and prepocess it prior to writing
performEstimate = 1;
write_header(nheader);
write_data(nme,buf);
MPI_Bcast(&sumFileSize, 1, MPI_LMP_BIGINT, (nprocs-1), world);
openfile();
performEstimate = 0;
write_header(nheader); // actually write the header - mpifo now points to end of header info
// now actually write the data
performEstimate = 0;
write_data(nme,buf);
if (multifile) MPI_File_close(&mpifh);
if (multifile) delete [] filecurrent;
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::init_style()
{
// format = copy of default or user-specified line format
delete [] format;
char *str;
if (format_line_user) str = format_line_user;
else str = format_default;
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
strcat(format,"\n");
// initialize typenames array to be backward compatible by default
// a 32-bit int can be maximally 10 digits plus sign
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = new char[12];
sprintf(typenames[itype],"%d",itype);
}
}
// setup function ptr
write_choice = &DumpXYZMPIIO::write_string;
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::write_header(bigint n)
{
if (performEstimate) {
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
headerSize = 0;
headerSize += sprintf(((char*)&((char*)headerBuffer)[headerSize]),BIGINT_FORMAT "\n",n);
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep);
}
else { // write data
if (me == 0)
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,MPI_STATUS_IGNORE);
mpifo += headerSize;
free(headerBuffer);
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::write_data(int n, double *mybuf)
{
(this->*write_choice)(n,mybuf);
}
/* ---------------------------------------------------------------------- */
void DumpXYZMPIIO::write_string(int n, double *mybuf)
{
if (performEstimate) {
#if defined(_OPENMP)
int nthreads = omp_get_max_threads();
if (nthreads > 1)
nsme = convert_string_omp(n,mybuf);
else
nsme = convert_string(n,mybuf);
#else
nsme = convert_string(n,mybuf);
#endif
bigint incPrefix = 0;
bigint bigintNsme = (bigint) nsme;
MPI_Scan(&bigintNsme,&incPrefix,1,MPI_LMP_BIGINT,MPI_SUM,world);
sumFileSize = (incPrefix*sizeof(char));
offsetFromHeader = ((incPrefix-bigintNsme)*sizeof(char));
}
else { // write data
MPI_File_write_at_all(mpifh,mpifo+offsetFromHeader,sbuf,nsme,MPI_CHAR,MPI_STATUS_IGNORE);
if (flush_flag)
MPI_File_sync(mpifh);
}
}
#if defined(_OPENMP)
/* ----------------------------------------------------------------------
multithreaded version - convert mybuf of doubles to one big formatted string in sbuf
return -1 if strlen exceeds an int, since used as arg in MPI calls in Dump
------------------------------------------------------------------------- */
int DumpXYZMPIIO::convert_string_omp(int n, double *mybuf)
{
char **mpifh_buffer_line_per_thread;
int mpifhStringCount;
int *mpifhStringCountPerThread, *bufOffset, *bufRange, *bufLength;
mpifhStringCount = 0;
int nthreads = omp_get_max_threads();
if (nthreads > n) { // call serial version
convert_string(n,mybuf);
}
else {
memory->create(mpifhStringCountPerThread,nthreads,"dump:mpifhStringCountPerThread");
mpifh_buffer_line_per_thread = (char **) malloc(nthreads*sizeof(char*));
memory->create(bufOffset,nthreads,"dump:bufOffset");
memory->create(bufRange,nthreads,"dump:bufRange");
memory->create(bufLength,nthreads,"dump:bufLength");
int i=0;
for (i=0;i<(nthreads-1);i++) {
mpifhStringCountPerThread[i] = 0;
bufOffset[i] = (int) (i*(int)(floor((double)n/(double)nthreads))*size_one);
bufRange[i] = (int)(floor((double)n/(double)nthreads));
bufLength[i] = DUMP_BUF_CHUNK_SIZE;
mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char));
mpifh_buffer_line_per_thread[i][0] = '\0';
}
mpifhStringCountPerThread[i] = 0;
bufOffset[i] = (int) (i*(int)(floor((double)n/(double)nthreads))*size_one);
bufRange[i] = n-(i*(int)(floor((double)n/(double)nthreads)));
bufLength[i] = DUMP_BUF_CHUNK_SIZE;
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(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
{
int tid = omp_get_thread_num();
int m=0;
for (int i = 0; i < bufRange[tid]; i++) {
if ((bufLength[tid] - mpifhStringCountPerThread[tid]) < DUMP_BUF_INCREMENT_SIZE) {
mpifh_buffer_line_per_thread[tid] = (char *) realloc(mpifh_buffer_line_per_thread[tid],(mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char));
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> (mybuf[bufOffset[tid]+m+1])],mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
m += size_one;
}
}
#pragma omp barrier
mpifhStringCount = 0;
for (i=0;i<nthreads;i++) {
mpifhStringCount += mpifhStringCountPerThread[i];
}
memory->destroy(bufOffset);
memory->destroy(bufRange);
memory->destroy(bufLength);
if (mpifhStringCount > 0) {
if (mpifhStringCount > maxsbuf) {
if (mpifhStringCount > MAXSMALLINT) return -1;
maxsbuf = mpifhStringCount;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
sbuf[0] = '\0';
}
for (int i=0;i<nthreads;i++) {
strcat(sbuf,mpifh_buffer_line_per_thread[i]);
free(mpifh_buffer_line_per_thread[i]);
}
memory->destroy(mpifhStringCountPerThread);
free(mpifh_buffer_line_per_thread);
}
return mpifhStringCount;
}
#endif

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