git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11316 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
675
src/MPIIO/dump_custom_mpiio.cpp
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675
src/MPIIO/dump_custom_mpiio.cpp
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@ -0,0 +1,675 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Paul Coffman (IBM)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "dump_custom_mpiio.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "region.h"
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#include "group.h"
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#include "input.h"
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#include "variable.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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#include <stdlib.h>
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#if defined(_OPENMP)
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#include <omp.h>
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#endif
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using namespace LAMMPS_NS;
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#define MAX_TEXT_HEADER_SIZE 4096
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#define DUMP_BUF_CHUNK_SIZE 16384
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#define DUMP_BUF_INCREMENT_SIZE 4096
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enum{ID,MOL,TYPE,ELEMENT,MASS,
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X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
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XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
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IX,IY,IZ,
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VX,VY,VZ,FX,FY,FZ,
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Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
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OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
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TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
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COMPUTE,FIX,VARIABLE};
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enum{LT,LE,GT,GE,EQ,NEQ};
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enum{INT,DOUBLE,STRING}; // same as in DumpCFG
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/* ---------------------------------------------------------------------- */
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DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg) :
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DumpCustom(lmp, narg, arg)
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{
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}
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/* ---------------------------------------------------------------------- */
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DumpCustomMPIIO::~DumpCustomMPIIO()
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{
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if (multifile == 0) MPI_File_close(&mpifh);
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::openfile()
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{
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if (singlefile_opened) { // single file already opened, so just return after resetting filesize
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mpifo = currentFileSize;
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MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
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currentFileSize = mpifo+headerSize+sumFileSize;
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return;
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}
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if (multifile == 0) singlefile_opened = 1;
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// if one file per timestep, replace '*' with current timestep
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filecurrent = filename;
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if (multifile) {
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char *filestar = filecurrent;
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filecurrent = new char[strlen(filestar) + 16];
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char *ptr = strchr(filestar,'*');
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*ptr = '\0';
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if (padflag == 0)
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sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
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filestar,update->ntimestep,ptr+1);
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else {
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char bif[8],pad[16];
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strcpy(bif,BIGINT_FORMAT);
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sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);
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sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
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}
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*ptr = '*';
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}
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if (append_flag) { // append open
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int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
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if (err != MPI_SUCCESS) {
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char str[128];
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sprintf(str,"Cannot open dump file %s",filecurrent);
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error->one(FLERR,str);
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}
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int myrank;
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MPI_Comm_rank(world,&myrank);
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if (myrank == 0)
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MPI_File_get_size(mpifh,&mpifo);
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MPI_Bcast(&mpifo, 1, MPI_LMP_BIGINT, 0, world);
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MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
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currentFileSize = mpifo+headerSize+sumFileSize;
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}
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else { // replace open
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int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
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if (err != MPI_SUCCESS) {
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char str[128];
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sprintf(str,"Cannot open dump file %s",filecurrent);
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error->one(FLERR,str);
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}
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mpifo = 0;
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MPI_File_set_size(mpifh,(MPI_Offset) (headerSize+sumFileSize));
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currentFileSize = (headerSize+sumFileSize);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::write()
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{
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if (domain->triclinic == 0) {
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boxxlo = domain->boxlo[0];
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boxxhi = domain->boxhi[0];
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boxylo = domain->boxlo[1];
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boxyhi = domain->boxhi[1];
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boxzlo = domain->boxlo[2];
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boxzhi = domain->boxhi[2];
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} else {
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boxxlo = domain->boxlo_bound[0];
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boxxhi = domain->boxhi_bound[0];
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boxylo = domain->boxlo_bound[1];
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boxyhi = domain->boxhi_bound[1];
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boxzlo = domain->boxlo_bound[2];
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boxzhi = domain->boxhi_bound[2];
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boxxy = domain->xy;
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boxxz = domain->xz;
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boxyz = domain->yz;
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}
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// nme = # of dump lines this proc contributes to dump
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nme = count();
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// ntotal = total # of dump lines in snapshot
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// nmax = max # of dump lines on any proc
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bigint bnme = nme;
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MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
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int nmax;
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MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
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// write timestep header
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// for multiproc,
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// nheader = # of lines in this file via Allreduce on clustercomm
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bigint nheader = ntotal;
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// insure filewriter proc can receive everyone's info
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// limit nmax*size_one to int since used as arg in MPI_Rsend() below
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// pack my data into buf
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// if sorting on IDs also request ID list from pack()
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// sort buf as needed
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if (nmax > maxbuf) {
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if ((bigint) nmax * size_one > MAXSMALLINT)
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error->all(FLERR,"Too much per-proc info for dump");
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maxbuf = nmax;
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memory->destroy(buf);
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memory->create(buf,(maxbuf*size_one),"dump:buf");
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}
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if (sort_flag && sortcol == 0 && nmax > maxids) {
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maxids = nmax;
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memory->destroy(ids);
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memory->create(ids,maxids,"dump:ids");
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}
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if (sort_flag && sortcol == 0) pack(ids);
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else pack(NULL);
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if (sort_flag) sort();
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// determine how much data needs to be written for setting the file size and prepocess it prior to writing
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performEstimate = 1;
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write_header(nheader);
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write_data(nme,buf);
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MPI_Bcast(&sumFileSize, 1, MPI_LMP_BIGINT, (nprocs-1), world);
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openfile();
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performEstimate = 0;
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write_header(nheader); // mpifo now points to end of header info
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// now actually write the data
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performEstimate = 0;
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write_data(nme,buf);
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if (multifile) MPI_File_close(&mpifh);
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if (multifile) delete [] filecurrent;
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::init_style()
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{
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delete [] format;
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char *str;
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if (format_user) str = format_user;
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else str = format_default;
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int n = strlen(str) + 1;
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format = new char[n];
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strcpy(format,str);
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// default for element names = C
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if (typenames == NULL) {
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typenames = new char*[ntypes+1];
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for (int itype = 1; itype <= ntypes; itype++) {
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typenames[itype] = new char[2];
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strcpy(typenames[itype],"C");
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}
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}
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// tokenize the format string and add space at end of each format element
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char *ptr;
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for (int i = 0; i < size_one; i++) {
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if (i == 0) ptr = strtok(format," \0");
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else ptr = strtok(NULL," \0");
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if (ptr == NULL) error->all(FLERR,"Dump_modify format string is too short");
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delete [] vformat[i];
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vformat[i] = new char[strlen(ptr) + 2];
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strcpy(vformat[i],ptr);
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vformat[i] = strcat(vformat[i]," ");
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}
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// setup boundary string
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domain->boundary_string(boundstr);
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// setup function ptrs
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if (binary && domain->triclinic == 0)
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header_choice = &DumpCustomMPIIO::header_binary;
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else if (binary && domain->triclinic == 1)
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header_choice = &DumpCustomMPIIO::header_binary_triclinic;
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else if (!binary && domain->triclinic == 0)
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header_choice = &DumpCustomMPIIO::header_item;
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else if (!binary && domain->triclinic == 1)
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header_choice = &DumpCustomMPIIO::header_item_triclinic;
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if (binary) write_choice = &DumpCustomMPIIO::write_binary;
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else write_choice = &DumpCustomMPIIO::write_string;
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// find current ptr for each compute,fix,variable
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// check that fix frequency is acceptable
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int icompute;
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for (int i = 0; i < ncompute; i++) {
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icompute = modify->find_compute(id_compute[i]);
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if (icompute < 0) error->all(FLERR,"Could not find dump custom compute ID");
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compute[i] = modify->compute[icompute];
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}
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int ifix;
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for (int i = 0; i < nfix; i++) {
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ifix = modify->find_fix(id_fix[i]);
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if (ifix < 0) error->all(FLERR,"Could not find dump custom fix ID");
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fix[i] = modify->fix[ifix];
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if (nevery % modify->fix[ifix]->peratom_freq)
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error->all(FLERR,"Dump custom and fix not computed at compatible times");
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}
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int ivariable;
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for (int i = 0; i < nvariable; i++) {
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ivariable = input->variable->find(id_variable[i]);
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if (ivariable < 0)
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error->all(FLERR,"Could not find dump custom variable name");
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variable[i] = ivariable;
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}
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// set index and check validity of region
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if (iregion >= 0) {
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for dump custom does not exist");
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::write_header(bigint ndump)
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{
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(this->*header_choice)(ndump);
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::header_binary(bigint ndump)
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{
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MPI_Status mpiStatus;
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if (performEstimate) {
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headerBuffer = (char *) malloc((2*sizeof(bigint)) + (9*sizeof(int)) + (6*sizeof(double)));
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headerSize = 0;
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memcpy(&((char*)headerBuffer)[headerSize],&update->ntimestep,sizeof(bigint));
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headerSize += sizeof(bigint);
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memcpy(&((char*)headerBuffer)[headerSize],&ndump,sizeof(bigint));
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headerSize += sizeof(bigint);
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memcpy(&((char*)headerBuffer)[headerSize],&domain->triclinic,sizeof(int));
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headerSize += sizeof(int);
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memcpy(&((char*)headerBuffer)[headerSize],&domain->boundary[0][0],6*sizeof(int));
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headerSize += 6*sizeof(int);
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memcpy(&((char*)headerBuffer)[headerSize],&boxxlo,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxxhi,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxylo,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxyhi,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxzlo,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxzhi,sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&size_one,sizeof(int));
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headerSize += sizeof(int);
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memcpy(&((char*)headerBuffer)[headerSize],&nprocs,sizeof(int));
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headerSize += sizeof(int);
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}
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else { // write data
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if (me == 0)
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MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,&mpiStatus);
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mpifo += headerSize;
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free(headerBuffer);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpCustomMPIIO::header_binary_triclinic(bigint ndump)
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{
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MPI_Status mpiStatus;
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if (performEstimate) {
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headerBuffer = (char *) malloc((2*sizeof(bigint)) + (9*sizeof(int)) + (6*sizeof(double)));
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headerSize = 0;
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memcpy(&((char*)headerBuffer)[headerSize],&update->ntimestep,sizeof(bigint));
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headerSize += sizeof(bigint);
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||||
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||||
memcpy(&((char*)headerBuffer)[headerSize],&ndump,sizeof(bigint));
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headerSize += sizeof(bigint);
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||||
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memcpy(&((char*)headerBuffer)[headerSize],&domain->triclinic,sizeof(int));
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headerSize += sizeof(int);
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||||
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||||
memcpy(&((char*)headerBuffer)[headerSize],&domain->boundary[0][0],6*sizeof(int));
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||||
headerSize += 6*sizeof(int);
|
||||
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||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxlo,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
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||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxhi,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxylo,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxyhi,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzlo,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzhi,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxy,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxz,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxyz,sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
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||||
memcpy(&((char*)headerBuffer)[headerSize],&size_one,sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&nprocs,sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
}
|
||||
else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,&mpiStatus);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomMPIIO::header_item(bigint ndump)
|
||||
{
|
||||
MPI_Status mpiStatus;
|
||||
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
|
||||
headerSize = 0;
|
||||
headerSize += sprintf(((char*)&((char*)headerBuffer)[headerSize]),"ITEM: TIMESTEP\n");
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],BIGINT_FORMAT "\n",update->ntimestep);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: NUMBER OF ATOMS\n");
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],BIGINT_FORMAT "\n",ndump);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: BOX BOUNDS %s\n",boundstr);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g\n",boxxlo,boxxhi);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g\n",boxylo,boxyhi);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g\n",boxzlo,boxzhi);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: ATOMS %s\n",columns);
|
||||
}
|
||||
else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,&mpiStatus);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomMPIIO::header_item_triclinic(bigint ndump)
|
||||
{
|
||||
MPI_Status mpiStatus;
|
||||
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
|
||||
headerSize = 0;
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: TIMESTEP\n");
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],BIGINT_FORMAT "\n",update->ntimestep);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: NUMBER OF ATOMS\n");
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],BIGINT_FORMAT "\n",ndump);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g %g\n",boxxlo,boxxhi,boxxy);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g %g\n",boxylo,boxyhi,boxxz);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"%g %g %g\n",boxzlo,boxzhi,boxyz);
|
||||
headerSize += sprintf(&((char*)headerBuffer)[headerSize],"ITEM: ATOMS %s\n",columns);
|
||||
}
|
||||
else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,&mpiStatus);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomMPIIO::write_data(int n, double *mybuf)
|
||||
{
|
||||
|
||||
(this->*write_choice)(n,mybuf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomMPIIO::write_binary(int n, double *mybuf)
|
||||
{
|
||||
|
||||
MPI_Status mpiStatus;
|
||||
n *= size_one;
|
||||
|
||||
if (performEstimate) {
|
||||
|
||||
bigint incPrefix = 0;
|
||||
bigint bigintNme = (bigint) nme;
|
||||
MPI_Scan(&bigintNme,&incPrefix,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
sumFileSize = (incPrefix*size_one*sizeof(double)) + (nprocs * sizeof(int));
|
||||
offsetFromHeader = ((incPrefix-bigintNme)*size_one*sizeof(double)) + (me * sizeof(int));
|
||||
}
|
||||
else {
|
||||
int byteBufSize = (n*sizeof(double)) + sizeof(int);
|
||||
|
||||
char *bufWithSize;
|
||||
memory->create(bufWithSize,byteBufSize,"dump:bufWithSize");
|
||||
memcpy(bufWithSize,(char*)(&n),sizeof(int));
|
||||
memcpy(&((char*)bufWithSize)[sizeof(int)],mybuf,(n*sizeof(double)));
|
||||
MPI_File_write_at_all(mpifh,mpifo+offsetFromHeader,bufWithSize,byteBufSize,MPI_BYTE,&mpiStatus);
|
||||
memory->destroy(bufWithSize);
|
||||
|
||||
if (flush_flag)
|
||||
MPI_File_sync(mpifh);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustomMPIIO::write_string(int n, double *mybuf)
|
||||
{
|
||||
MPI_Status mpiStatus;
|
||||
|
||||
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 {
|
||||
MPI_File_write_at_all(mpifh,mpifo+offsetFromHeader,sbuf,nsme,MPI_CHAR,&mpiStatus);
|
||||
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 DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
|
||||
{
|
||||
MPI_Status mpiStatus;
|
||||
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)
|
||||
{
|
||||
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);
|
||||
}
|
||||
for (int j = 0; j < size_one; j++) {
|
||||
|
||||
if (vtype[j] == INT)
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
|
||||
else if (vtype[j] == DOUBLE)
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
|
||||
else if (vtype[j] == STRING)
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
|
||||
m ++;
|
||||
}
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
#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
|
||||
Reference in New Issue
Block a user