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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11036 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-11-21 20:47:55 +00:00
parent c223829854
commit 378ab5cce1
10 changed files with 373 additions and 42 deletions
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113
src/dump.cpp
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@ -71,6 +71,8 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
clearstep = 0;
sort_flag = 0;
append_flag = 0;
buffer_allow = 0;
buffer_flag = 0;
padflag = 0;
maxbuf = maxids = maxsort = maxproc = 0;
@ -78,6 +80,9 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
ids = idsort = index = proclist = NULL;
irregular = NULL;
maxsbuf = 0;
sbuf = NULL;
// parse filename for special syntax
// if contains '%', write one file per proc and replace % with proc-ID
// if contains '*', write one file per timestep and replace * with timestep
@ -141,6 +146,8 @@ Dump::~Dump()
memory->destroy(proclist);
delete irregular;
memory->destroy(sbuf);
if (multiproc) MPI_Comm_free(&clustercomm);
// XTC style sets fp to NULL since it closes file in its destructor
@ -301,11 +308,9 @@ void Dump::write()
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()
// sort buf as needed
// insure buf is sized for packing and communicating
// use nmax to insure filewriter proc can receive info from others
// limit nmax*size_one to int since used as arg in MPI calls
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
@ -314,41 +319,90 @@ void Dump::write()
memory->destroy(buf);
memory->create(buf,maxbuf*size_one,"dump:buf");
}
// insure ids buffer is sized for sorting
if (sort_flag && sortcol == 0 && nmax > maxids) {
maxids = nmax;
memory->destroy(ids);
memory->create(ids,maxids,"dump:ids");
}
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (sort_flag && sortcol == 0) pack(ids);
else pack(NULL);
if (sort_flag) sort();
// if buffering, convert doubles into strings
// insure sbuf is sized for communicating
if (buffer_flag) {
nsme = convert_string(nme,buf);
int nsmin,nsmax;
MPI_Allreduce(&nsme,&nsmin,1,MPI_INT,MPI_MIN,world);
if (nsmin < 0) error->all(FLERR,"Too much buffered per-proc info for dump");
if (multiproc != nprocs)
MPI_Allreduce(&nsme,&nsmax,1,MPI_INT,MPI_MAX,world);
else nsmax = nsme;
if (nsmax > maxsbuf) {
maxsbuf = nsmax;
memory->grow(sbuf,maxsbuf,"dump:sbuf");
}
}
// filewriter = 1 = this proc writes to file
// ping each proc in my cluster, receive its data, write data 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
int tmp,nlines;
int tmp,nlines,nchars;
MPI_Status status;
MPI_Request request;
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);
// comm and output buf of doubles
if (buffer_flag == 0) {
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);
}
// comm and output sbuf = one big string of formatted values per proc
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,fileproc,0,world);
if (filewriter) {
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(sbuf,maxsbuf,MPI_CHAR,me+iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,me+iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_CHAR,&nchars);
} else nchars = nsme;
write_data(nchars,(double *) sbuf);
}
if (flush_flag) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(sbuf,nsme,MPI_CHAR,fileproc,0,world);
}
}
// if file per timestep, close file if I am filewriter
@ -659,6 +713,16 @@ void Dump::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) append_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"buffer") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) buffer_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) buffer_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
if (buffer_flag && buffer_allow == 0)
error->all(FLERR,"Dump_modify buffer yes not allowed for this style");
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
int idump;
@ -677,6 +741,7 @@ void Dump::modify_params(int narg, char **arg)
}
output->every_dump[idump] = n;
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) first_flag = 1;
@ -719,6 +784,7 @@ void Dump::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) flush_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
delete [] format_user;
@ -768,6 +834,7 @@ void Dump::modify_params(int narg, char **arg)
padflag = force->inumeric(FLERR,arg[iarg+1]);
if (padflag < 0) error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
@ -787,6 +854,7 @@ void Dump::modify_params(int narg, char **arg)
sortcolm1 = sortcol - 1;
}
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all(FLERR,"Illegal dump_modify command");
@ -802,6 +870,7 @@ void Dump::modify_params(int narg, char **arg)
bigint Dump::memory_usage()
{
bigint bytes = memory->usage(buf,size_one*maxbuf);
bytes += memory->usage(sbuf,maxsbuf);
if (sort_flag) {
if (sortcol == 0) bytes += memory->usage(ids,maxids);
bytes += memory->usage(bufsort,size_one*maxsort);