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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9725 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-04-02 15:11:27 +00:00
parent 9b0265211d
commit 9b753bd19f
2 changed files with 145 additions and 66 deletions
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199
src/dump.cpp
View File

@ -90,19 +90,25 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
compressed = 0;
binary = 0;
multifile = 0;
multiproc = 0;
nclusterprocs = nprocs;
filewriter = 0;
if (me == 0) filewriter = 1;
fileproc = 0;
multiname = NULL;
char *ptr;
if (ptr = strchr(filename,'%')) {
multiproc = 1;
char *extend = new char[strlen(filename) + 16];
nclusterprocs = 1;
filewriter = 1;
fileproc = me;
MPI_Comm_split(world,me,0,&dumpcomm);
multiname = new char[strlen(filename) + 16];
*ptr = '\0';
sprintf(extend,"%s%d%s",filename,me,ptr+1);
delete [] filename;
n = strlen(extend) + 1;
filename = new char[n];
strcpy(filename,extend);
delete [] extend;
sprintf(multiname,"%s%d%s",filename,me,ptr+1);
*ptr = '%';
}
if (strchr(filename,'*')) multifile = 1;
@ -120,6 +126,7 @@ Dump::~Dump()
delete [] id;
delete [] style;
delete [] filename;
delete [] multiname;
delete [] format;
delete [] format_default;
@ -133,15 +140,15 @@ Dump::~Dump()
memory->destroy(proclist);
delete irregular;
if (multiproc) MPI_Comm_free(&dumpcomm);
// XTC style sets fp to NULL since it closes file in its destructor
if (multifile == 0 && fp != NULL) {
if (compressed) {
if (multiproc) pclose(fp);
else if (me == 0) pclose(fp);
if (filewriter) pclose(fp);
} else {
if (multiproc) fclose(fp);
else if (me == 0) fclose(fp);
if (filewriter) fclose(fp);
}
}
}
@ -167,6 +174,8 @@ void Dump::init()
}
if (sort_flag) {
if (multiproc > 1)
error->all(FLERR,"Cannot dump sort when multiple procs write the dump file");
if (sortcol == 0 && atom->tag_enable == 0)
error->all(FLERR,"Cannot dump sort on atom IDs with no atom IDs defined");
if (sortcol && sortcol > size_one)
@ -266,27 +275,30 @@ void Dump::write()
boxyz = domain->yz;
}
// nme = # of dump lines this proc will contribute to dump
// nme = # of dump lines this proc contributes to dump
nme = count();
bigint bnme = nme;
// ntotal = total # of dump lines
// 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;
if (multiproc) nmax = nme;
else {
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
}
if (multiproc != nprocs) MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
else nmax = nme;
// write timestep header
// for multiproc, nheader = # of lines in this file via Allreduce on dumpcomm
if (multiproc) write_header(bnme);
else write_header(ntotal);
bigint nheader = ntotal;
if (multiproc)
MPI_Allreduce(&bnme,&nheader,1,MPI_LMP_BIGINT,MPI_SUM,dumpcomm);
// insure proc 0 can receive everyone's info
if (filewriter) write_header(nheader);
// 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()
@ -309,46 +321,40 @@ void Dump::write()
else pack(NULL);
if (sort_flag) sort();
// multiproc = 1 = each proc writes own data to own file
// multiproc = 0 = all procs write to one file thru proc 0
// proc 0 pings each proc, receives it's data, writes to file
// all other procs wait for ping, send their data to proc 0
// filewriter = 1 = this proc writes to file
// ping each proc in my cluster, receive its data, write data to file
// else wait for ping from fileproc, send my data to fileproc
if (multiproc) write_data(nme,buf);
else {
int tmp,nlines;
MPI_Status status;
MPI_Request request;
int tmp,nlines;
MPI_Status status;
MPI_Request request;
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
if (flush_flag) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,0,0,world);
if (filewriter) {
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
if (flush_flag) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,fileproc,0,world);
}
// if file per timestep, close file
// if file per timestep, close file if I am filewriter
if (multifile) {
if (compressed) {
if (multiproc) pclose(fp);
else if (me == 0) pclose(fp);
if (filewriter) pclose(fp);
} else {
if (multiproc) fclose(fp);
else if (me == 0) fclose(fp);
if (filewriter) fclose(fp);
}
}
}
@ -368,27 +374,29 @@ void Dump::openfile()
// if one file per timestep, replace '*' with current timestep
char *filecurrent;
if (multifile == 0) filecurrent = filename;
else {
filecurrent = new char[strlen(filename) + 16];
char *ptr = strchr(filename,'*');
char *filecurrent = filename;
if (multiproc) filecurrent = multiname;
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",
filename,update->ntimestep,ptr+1);
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,filename,update->ntimestep,ptr+1);
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
}
// open one file on proc 0 or file on every proc
// each proc with filewriter = 1 opens a file
if (me == 0 || multiproc) {
if (filewriter) {
if (compressed) {
#ifdef LAMMPS_GZIP
char gzip[128];
@ -552,8 +560,7 @@ void Dump::sort()
// this insures proc 0 can receive everyone's info
int nmax;
if (multiproc) nmax = nme;
else MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
if (nmax > maxbuf) {
maxbuf = nmax;
@ -669,6 +676,36 @@ void Dump::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) first_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify fileper "
"without % in dump file name");
int nper = atoi(arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal dump_modify command");
multiproc = nprocs/nper;
if (nprocs % nper) multiproc++;
fileproc = me/nper * nper;
int fileprocnext = MIN(fileproc+nper,nprocs);
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
int icluster = fileproc/nper;
MPI_Comm_free(&dumpcomm);
MPI_Comm_split(world,icluster,0,&dumpcomm);
delete [] multiname;
multiname = new char[strlen(filename) + 16];
char *ptr = strchr(filename,'%');
*ptr = '\0';
sprintf(multiname,"%s%d%s",filename,icluster,ptr+1);
*ptr = '%';
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) flush_flag = 1;
@ -685,6 +722,40 @@ void Dump::modify_params(int narg, char **arg)
strcpy(format_user,arg[iarg+1]);
}
iarg += 2;
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify nfile "
"without % in dump file name");
int nfile = atoi(arg[iarg+1]);
if (nfile <= 0) error->all(FLERR,"Illegal dump_modify command");
nfile = MIN(nfile,nprocs);
multiproc = nfile;
int icluster = static_cast<int> ((bigint) me * nfile/nprocs);
fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
nclusterprocs = fileprocnext - fileproc;
if (me == fileproc) filewriter = 1;
else filewriter = 0;
MPI_Comm_free(&dumpcomm);
MPI_Comm_split(world,icluster,0,&dumpcomm);
delete [] multiname;
multiname = new char[strlen(filename) + 16];
char *ptr = strchr(filename,'%');
*ptr = '\0';
sprintf(multiname,"%s%d%s",filename,icluster,ptr+1);
*ptr = '%';
iarg += 2;
} else if (strcmp(arg[iarg],"pad") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
padflag = atoi(arg[iarg+1]);

12
src/dump.h
View File

@ -14,6 +14,7 @@
#ifndef LMP_DUMP_H
#define LMP_DUMP_H
#include "mpi.h"
#include "stdio.h"
#include "pointers.h"
@ -55,7 +56,14 @@ class Dump : protected Pointers {
int compressed; // 1 if dump file is written compressed, 0 no
int binary; // 1 if dump file is written binary, 0 no
int multifile; // 0 = one big file, 1 = one file per timestep
int multiproc; // 0 = proc 0 writes for all, 1 = one file/proc
int multiproc; // 0 = proc 0 writes for all,
// else # of procs writing files
int nclusterprocs; // # of procs in my cluster that write to one file
int filewriter; // 1 if this proc writes a file, else 0
int fileproc; // ID of proc in my cluster who writes to file
char *multiname; // dump filename with % converted to cluster ID
MPI_Comm dumpcomm;
int header_flag; // 0 = item, 2 = xyz
int flush_flag; // 0 if no flush, 1 if flush every dump
@ -80,7 +88,7 @@ class Dump : protected Pointers {
double boxzlo,boxzhi;
double boxxy,boxxz,boxyz;
bigint ntotal; // # of per-atom lines in snapshot
bigint ntotal; // total # of per-atom lines in snapshot
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
int nme_reorder; // # of atoms I must own in snapshot