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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11289 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-22 15:31:45 +00:00
parent ad30cd374c
commit 7932bcc79b
19 changed files with 599 additions and 38 deletions
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94
src/read_restart.cpp
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@ -98,7 +98,7 @@ void ReadRestart::command(int narg, char **arg)
if (strchr(arg[0],'%')) multiproc = 1;
else multiproc = 0;
if (strstr(arg[0],".mpi")) mpiioflag = 1;
if (strstr(arg[0],".mpiio")) mpiioflag = 1;
else mpiioflag = 0;
if (multiproc && mpiioflag)
@ -190,19 +190,13 @@ void ReadRestart::command(int narg, char **arg)
// 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->openForRead(file);
memory->create(buf,assignedChunkSize,"read_restart:buf");
mpiio->read((headerOffset+assignedChunkOffset),assignedChunkSize,buf);
mpiio->close();
// mpiio->open(file);
// mpiio->read();
// mpiio->close();
// then process atom info as
//m = 0;
//while (m < n) m += avec->unpack_restart(&buf[m]);
m = 0;
while (m < assignedChunkSize) m += avec->unpack_restart(&buf[m]);
}
// input of single native file
@ -937,13 +931,81 @@ void ReadRestart::file_layout()
error->all(FLERR,"Restart file is a MPI-IO file");
if (mpiioflag && mpiioflag_file == 0)
error->all(FLERR,"Restart file is not a MPI-IO file");
if (mpiioflag) {
long *nproc_chunk_offsets;
memory->create(nproc_chunk_offsets,nprocs,
"write_restart:nproc_chunk_offsets");
long *nproc_chunk_sizes;
memory->create(nproc_chunk_sizes,nprocs,
"write_restart:nproc_chunk_sizes");
// on rank 0 read in the chunk sizes that were written out
// then consolidate them and compute offsets relative to the
// end of the header info to fit the current partition size
// if the number of ranks that did the writing is different
if (me == 0) {
int *all_written_send_sizes;
memory->create(all_written_send_sizes,nprocs_file,
"write_restart:all_written_send_sizes");
int *nproc_chunk_number;
memory->create(nproc_chunk_number,nprocs,
"write_restart:nproc_chunk_number");
fread(all_written_send_sizes,sizeof(int),nprocs_file,fp);
int init_chunk_number = nprocs_file/nprocs;
int num_extra_chunks = nprocs_file - (nprocs*init_chunk_number);
for (int i = 0; i < nprocs; i++) {
if (i < num_extra_chunks)
nproc_chunk_number[i] = init_chunk_number+1;
else
nproc_chunk_number[i] = init_chunk_number;
}
int all_written_send_sizes_index = 0;
long current_offset = 0;
for (int i=0;i<nprocs;i++) {
nproc_chunk_offsets[i] = current_offset;
nproc_chunk_sizes[i] = 0;
for (int j=0;j<nproc_chunk_number[i];j++) {
nproc_chunk_sizes[i] +=
all_written_send_sizes[all_written_send_sizes_index];
current_offset +=
(all_written_send_sizes[all_written_send_sizes_index] *
sizeof(double));
all_written_send_sizes_index++;
}
}
memory->destroy(all_written_send_sizes);
memory->destroy(nproc_chunk_number);
}
// scatter chunk sizes and offsets to all procs
MPI_Scatter(nproc_chunk_sizes, 1, MPI_LONG,
&assignedChunkSize , 1, MPI_LONG, 0,world);
MPI_Scatter(nproc_chunk_offsets, 1, MPI_LONG,
&assignedChunkOffset , 1, MPI_LONG, 0,world);
memory->destroy(nproc_chunk_sizes);
memory->destroy(nproc_chunk_offsets);
}
}
// NOTE: could add reading of MPI-IO specific fields to header here
// e.g. read vector of PERPROCSIZE values
flag = read_int();
}
// if MPI-IO file, broadcast the end of the header offste
// this allows all ranks to compute offset to their data
if (mpiioflag) {
if (me == 0) headerOffset = ftell(fp);
MPI_Bcast(&headerOffset,1,MPI_LONG,0,world);
}
}
// ----------------------------------------------------------------------