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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11100 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-12-06 23:19:33 +00:00
parent f41d6124fb
commit a4c075eacf
5 changed files with 115 additions and 52 deletions
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12
src/output.cpp
View File

@ -762,13 +762,13 @@ void Output::create_restart(int narg, char **arg)
error->all(FLERR,"Both restart files must have '%' or neither");
}
int mpiio;
if (strstr(arg[1],".mpi")) mpiio = 1;
else mpiio = 0;
int mpiioflag;
if (strstr(arg[1],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (nfile == 2) {
if (mpiio && !strstr(arg[2],".mpi"))
if (mpiioflag && !strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
if (!mpiio && strstr(arg[2],".mpi"))
if (!mpiioflag && strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
}
@ -777,7 +777,7 @@ void Output::create_restart(int narg, char **arg)
delete restart;
restart = new WriteRestart(lmp);
int iarg = nfile+1;
restart->multiproc_options(multiproc,mpiio,narg-iarg,&arg[iarg]);
restart->multiproc_options(multiproc,mpiioflag,narg-iarg,&arg[iarg]);
}
/* ----------------------------------------------------------------------

69
src/read_restart.cpp
View File

@ -35,6 +35,7 @@
#include "improper.h"
#include "special.h"
#include "universe.h"
#include "mpiio.h"
#include "memory.h"
#include "error.h"
@ -96,13 +97,20 @@ void ReadRestart::command(int narg, char **arg)
if (strchr(arg[0],'%')) multiproc = 1;
else multiproc = 0;
if (strstr(arg[0],".mpi")) mpiio = 1;
else mpiio = 0;
if (strstr(arg[0],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiio)
if (multiproc && mpiioflag)
error->all(FLERR,
"Read restart MPI-IO output not allowed with '%' in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
if (!mpiio->mpiio_exists)
error->all(FLERR,"Reading from MPI-IO filename when "
"MPIIO package is not installed");
}
// open single restart file or base file for multiproc case
if (me == 0) {
@ -170,19 +178,37 @@ void ReadRestart::command(int narg, char **arg)
if (me == 0) fclose(fp);
// single file:
// nprocs_file = # of chunks in file
// proc 0 reads a chunk and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
AtomVec *avec = atom->avec;
int maxbuf = 0;
double *buf = NULL;
int m;
if (multiproc == 0) {
// MPI-IO input from single file
if (mpiioflag) {
// add calls to RestartMPIIO class
// reopen header file
// perform reads
// allow for different # of procs reading than wrote the file
// mpiio->open(file);
// mpiio->read();
// mpiio->close();
// then process atom info as
//m = 0;
//while (m < n) m += avec->unpack_restart(&buf[m]);
}
// input of single native file
// nprocs_file = # of chunks in file
// proc 0 reads a chunk and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
else if (multiproc == 0) {
int triclinic = domain->triclinic;
double *x,lamda[3];
@ -225,13 +251,14 @@ void ReadRestart::command(int narg, char **arg)
}
if (me == 0) fclose(fp);
}
// multiple files with procs <= files
// input of multiple native files with procs <= files
// # of files = multiproc_file
// each proc reads a subset of files, striding by nprocs
// each proc keeps all atoms in all perproc chunks in its files
} else if (nprocs <= multiproc_file) {
else if (nprocs <= multiproc_file) {
char *procfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
@ -275,15 +302,16 @@ void ReadRestart::command(int narg, char **arg)
}
delete [] procfile;
}
// multiple files with procs > files
// input of multiple native files with procs > files
// # of files = multiproc_file
// cluster procs based on # of files
// 1st proc in each cluster reads per-proc chunks from file
// sends chunks round-robin to other procs in its cluster
// each proc keeps all atoms in its perproc chunks in file
} else {
else {
// nclusterprocs = # of procs in my cluster that read from one file
// filewriter = 1 if this proc reads file, else 0
@ -382,10 +410,10 @@ void ReadRestart::command(int narg, char **arg)
delete [] file;
memory->destroy(buf);
// for multiproc files:
// for multiproc or MPI-IO files:
// perform irregular comm to migrate atoms to correct procs
if (multiproc) {
if (multiproc || mpiioflag) {
// create a temporary fix to hold and migrate extra atom info
// necessary b/c irregular will migrate atoms
@ -899,13 +927,16 @@ void ReadRestart::file_layout()
error->all(FLERR,"Restart file is a multi-proc file");
} else if (flag = MPIIO) {
int mpiio_file = read_int();
if (mpiio == 0 && mpiio_file)
int mpiioflag_file = read_int();
if (mpiioflag == 0 && mpiioflag_file)
error->all(FLERR,"Restart file is a MPI-IO file");
if (mpiio && mpiio_file == 0)
if (mpiioflag && mpiioflag_file == 0)
error->all(FLERR,"Restart file is not a MPI-IO file");
}
// NOTE: could add reading of MPI-IO specific fields to header here
// e.g. read vector of PERPROCSIZE values
flag = read_int();
}
}

4
src/read_restart.h
View File

@ -35,10 +35,12 @@ class ReadRestart : protected Pointers {
FILE *fp;
int nfix_restart_global,nfix_restart_peratom;
int mpiio; // 1 for MPIIO output, else 0
int multiproc; // 0 = proc 0 writes for all
// else # of procs writing files
int mpiioflag; // 1 for MPIIO output, else 0
class RestartMPIIO *mpiio; // MPIIO for restart file input
void file_search(char *, char *);
void header(int);
void type_arrays();

78
src/write_restart.cpp
View File

@ -34,6 +34,7 @@
#include "comm.h"
#include "output.h"
#include "thermo.h"
#include "mpiio.h"
#include "memory.h"
#include "error.h"
@ -96,17 +97,24 @@ void WriteRestart::command(int narg, char **arg)
if (strchr(arg[0],'%')) multiproc = nprocs;
else multiproc = 0;
if (strstr(arg[0],".mpi")) mpiio = 1;
else mpiio = 0;
if (strstr(arg[0],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiio)
if (multiproc && mpiioflag)
error->all(FLERR,
"Write restart MPI-IO output not allowed with '%' in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
if (!mpiio->mpiio_exists)
error->all(FLERR,"Writing to MPI-IO filename when "
"MPIIO package is not installed");
}
// setup output style and process optional args
// also called by Output class for periodic restart files
multiproc_options(multiproc,mpiio,narg-1,&arg[1]);
multiproc_options(multiproc,mpiioflag,narg-1,&arg[1]);
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
@ -136,11 +144,11 @@ void WriteRestart::command(int narg, char **arg)
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void WriteRestart::multiproc_options(int multiproc_caller, int mpiio_caller,
void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
int narg, char **arg)
{
multiproc = multiproc_caller;
mpiio = mpiio_caller;
mpiioflag = mpiioflag_caller;
// defaults for multiproc file writing
@ -363,33 +371,50 @@ void WriteRestart::write(char *file)
}
}
// MPI-IO output to single file
if (mpiioflag) {
// add calls to RestartMPIIO class
// reopen header file in append mode
// perform writes
// mpiio->open(file);
// mpiio->write(send_size,buf);
// mpiio->close();
}
// output of one or more native files
// 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
int tmp,recv_size;
MPI_Status status;
MPI_Request request;
else {
int tmp,recv_size;
MPI_Status status;
MPI_Request request;
if (filewriter) {
write_int(PROCSPERFILE,nclusterprocs);
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,max_size,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,&recv_size);
} else recv_size = send_size;
if (filewriter) {
write_int(PROCSPERFILE,nclusterprocs);
for (int iproc = 0; iproc < nclusterprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,max_size,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,&recv_size);
} else recv_size = send_size;
write_double_vec(PERPROC,recv_size,buf);
}
fclose(fp);
write_double_vec(PERPROC,recv_size,buf);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,send_size,MPI_DOUBLE,fileproc,0,world);
}
fclose(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,&status);
MPI_Rsend(buf,send_size,MPI_DOUBLE,fileproc,0,world);
}
// clean up
memory->destroy(buf);
// invoke any fixes that write their own restart file
@ -528,9 +553,12 @@ void WriteRestart::file_layout(int send_size)
{
if (me == 0) {
write_int(MULTIPROC,multiproc);
write_int(MPIIO,mpiio);
write_int(MPIIO,mpiioflag);
}
// NOTE: could add MPI-IO specific fields to header here
// e.g. gather send_size across all procs and call write_int_vec()
// -1 flag signals end of file layout info
if (me == 0) {

4
src/write_restart.h
View File

@ -37,7 +37,6 @@ class WriteRestart : protected Pointers {
FILE *fp;
bigint natoms; // natoms (sum of nlocal) to write into file
int mpiio; // 1 for MPIIO output, else 0
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
@ -45,6 +44,9 @@ class WriteRestart : protected Pointers {
int fileproc; // ID of proc in my cluster who writes to file
int icluster; // which cluster I am in
int mpiioflag; // 1 for MPIIO output, else 0
class RestartMPIIO *mpiio; // MPIIO for restart file output
void header();
void type_arrays();
void force_fields();