fix buffer overflow in writing triclinic headers with MPI-I/O
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, Sandia National Laboratories
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@ -16,16 +15,17 @@
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Contributing author: Paul Coffman (IBM)
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------------------------------------------------------------------------- */
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#include "omp_compat.h"
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#include "dump_atom_mpiio.h"
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#include <cmath>
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#include <cstring>
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#include "domain.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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#include "memory.h"
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#include "update.h"
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#include <cmath>
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#include <cstring>
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#include "omp_compat.h"
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#if defined(_OPENMP)
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#include <omp.h>
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#endif
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@ -38,24 +38,23 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg) :
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DumpAtom(lmp, narg, arg) {}
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DumpAtomMPIIO::DumpAtomMPIIO(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg) {}
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/* ---------------------------------------------------------------------- */
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DumpAtomMPIIO::~DumpAtomMPIIO()
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{
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if (multifile == 0) MPI_File_close(&mpifh);
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if (multifile == 0) MPI_File_close(&mpifh);
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}
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/* ---------------------------------------------------------------------- */
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void DumpAtomMPIIO::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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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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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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@ -67,61 +66,56 @@ void DumpAtomMPIIO::openfile()
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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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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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if (padflag == 0) {
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sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", 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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if (maxfiles > 0) {
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if (numfiles < maxfiles) {
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nameslist[numfiles] = new char[strlen(filecurrent)+1];
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strcpy(nameslist[numfiles],filecurrent);
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nameslist[numfiles] = new char[strlen(filecurrent) + 1];
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strcpy(nameslist[numfiles], filecurrent);
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++numfiles;
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} else {
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remove(nameslist[fileidx]);
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delete[] nameslist[fileidx];
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nameslist[fileidx] = new char[strlen(filecurrent)+1];
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strcpy(nameslist[fileidx],filecurrent);
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nameslist[fileidx] = new char[strlen(filecurrent) + 1];
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strcpy(nameslist[fileidx], filecurrent);
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fileidx = (fileidx + 1) % maxfiles;
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}
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}
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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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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,
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MPI_INFO_NULL, &mpifh);
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if (err != MPI_SUCCESS)
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error->one(FLERR, "Cannot open dump file {}: {}", filecurrent, utils::getsyserror());
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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_Comm_rank(world, &myrank);
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if (myrank == 0) 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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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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} else { // replace open
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int err =
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MPI_File_open(world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &mpifh);
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if (err != MPI_SUCCESS)
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error->one(FLERR, "Cannot open dump file {}: {}", filecurrent, utils::getsyserror());
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int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | 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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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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@ -156,10 +150,10 @@ void DumpAtomMPIIO::write()
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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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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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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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@ -175,64 +169,70 @@ void DumpAtomMPIIO::write()
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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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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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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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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(nullptr);
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if (sort_flag && sortcol == 0)
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pack(ids);
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else
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pack(nullptr);
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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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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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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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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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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 DumpAtomMPIIO::init_style()
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{
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if (image_flag == 0) size_one = 5;
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else size_one = 8;
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if (image_flag == 0)
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size_one = 5;
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else
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size_one = 8;
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// format = copy of default or user-specified line format
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// default depends on image flags
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delete [] format;
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delete[] format;
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if (format_line_user) {
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int n = strlen(format_line_user) + 2;
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format = new char[n];
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strcpy(format,format_line_user);
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strcat(format,"\n");
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strcpy(format, format_line_user);
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strcat(format, "\n");
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} else {
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char *str;
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if (image_flag == 0) str = (char *) TAGINT_FORMAT " %d %g %g %g";
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else str = (char *) TAGINT_FORMAT " %d %g %g %g %d %d %d";
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if (image_flag == 0)
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str = (char *) TAGINT_FORMAT " %d %g %g %g";
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else
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str = (char *) TAGINT_FORMAT " %d %g %g %g %d %d %d";
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int n = strlen(str) + 2;
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format = new char[n];
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strcpy(format,str);
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strcat(format,"\n");
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strcpy(format, str);
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strcat(format, "\n");
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}
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// setup boundary string
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@ -274,10 +274,14 @@ void DumpAtomMPIIO::init_style()
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else if (scale_flag == 0 && image_flag == 1)
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pack_choice = &DumpAtomMPIIO::pack_noscale_image;
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if (binary) write_choice = &DumpAtomMPIIO::write_binary;
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else if (buffer_flag == 1) write_choice = &DumpAtomMPIIO::write_string;
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else if (image_flag == 0) write_choice = &DumpAtomMPIIO::write_lines_noimage;
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else if (image_flag == 1) write_choice = &DumpAtomMPIIO::write_lines_image;
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if (binary)
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write_choice = &DumpAtomMPIIO::write_binary;
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else if (buffer_flag == 1)
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write_choice = &DumpAtomMPIIO::write_string;
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else if (image_flag == 0)
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write_choice = &DumpAtomMPIIO::write_lines_noimage;
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else if (image_flag == 1)
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write_choice = &DumpAtomMPIIO::write_lines_image;
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}
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/* ---------------------------------------------------------------------- */
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@ -293,48 +297,47 @@ void DumpAtomMPIIO::header_binary(bigint ndump)
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{
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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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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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memcpy(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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memcpy(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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memcpy(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(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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} else { // write data
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if (me == 0)
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MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,MPI_STATUS_IGNORE);
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MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_BYTE, MPI_STATUS_IGNORE);
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mpifo += headerSize;
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free(headerBuffer);
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}
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@ -346,59 +349,58 @@ void DumpAtomMPIIO::header_binary_triclinic(bigint ndump)
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{
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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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headerBuffer = (char *) malloc((2 * sizeof(bigint)) + (9 * sizeof(int)) + (9 * sizeof(double)));
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headerSize = 0;
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memcpy(&((char*)headerBuffer)[headerSize],&update->ntimestep,sizeof(bigint));
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memcpy(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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memcpy(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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memcpy(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(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(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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memcpy(headerBuffer + headerSize, &boxzhi, sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxxy,sizeof(double));
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memcpy(headerBuffer + headerSize, &boxxy, sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxxz,sizeof(double));
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memcpy(headerBuffer + headerSize, &boxxz, sizeof(double));
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headerSize += sizeof(double);
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memcpy(&((char*)headerBuffer)[headerSize],&boxyz,sizeof(double));
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memcpy(headerBuffer + headerSize, &boxyz, 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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memcpy(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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memcpy(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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} else { // write data
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if (me == 0)
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MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,MPI_STATUS_IGNORE);
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MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_BYTE, MPI_STATUS_IGNORE);
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mpifo += headerSize;
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free(headerBuffer);
|
||||
}
|
||||
@ -410,25 +412,21 @@ void DumpAtomMPIIO::header_item(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
auto itemtxt = fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
|
||||
itemtxt += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
|
||||
itemtxt += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
|
||||
itemtxt += fmt::format("{} {}\n{} {}\n{} {}\n", boxxlo, boxxhi, boxylo, boxyhi, boxzlo, boxzhi);
|
||||
itemtxt += fmt::format("ITEM: ATOMS {}\n", columns);
|
||||
|
||||
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
|
||||
headerSize = itemtxt.size();
|
||||
headerBuffer = utils::strdup(itemtxt);
|
||||
|
||||
} else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_CHAR, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
delete[] headerBuffer;
|
||||
}
|
||||
}
|
||||
|
||||
@ -438,25 +436,22 @@ void DumpAtomMPIIO::header_item_triclinic(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
auto itemtxt = fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
|
||||
itemtxt += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
|
||||
itemtxt += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
|
||||
itemtxt += fmt::format("{} {} {}\n{} {} {}\n{} {} {}\n", boxxlo, boxxhi, boxxy, boxylo, boxyhi,
|
||||
boxxz, boxzlo, boxzhi, boxyz);
|
||||
itemtxt += fmt::format("ITEM: ATOMS {}\n", columns);
|
||||
|
||||
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
|
||||
headerSize = itemtxt.size();
|
||||
headerBuffer = utils::strdup(itemtxt);
|
||||
|
||||
} else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_CHAR, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
delete[] headerBuffer;
|
||||
}
|
||||
}
|
||||
|
||||
@ -464,8 +459,7 @@ void DumpAtomMPIIO::header_item_triclinic(bigint ndump)
|
||||
|
||||
void DumpAtomMPIIO::write_data(int n, double *mybuf)
|
||||
{
|
||||
|
||||
(this->*write_choice)(n,mybuf);
|
||||
(this->*write_choice)(n, mybuf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -478,22 +472,21 @@ void DumpAtomMPIIO::write_binary(int n, double *mybuf)
|
||||
|
||||
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);
|
||||
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,MPI_STATUS_IGNORE);
|
||||
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,
|
||||
MPI_STATUS_IGNORE);
|
||||
memory->destroy(bufWithSize);
|
||||
|
||||
if (flush_flag)
|
||||
MPI_File_sync(mpifh);
|
||||
if (flush_flag) MPI_File_sync(mpifh);
|
||||
}
|
||||
}
|
||||
|
||||
@ -506,23 +499,21 @@ void DumpAtomMPIIO::write_string(int n, double *mybuf)
|
||||
#if defined(_OPENMP)
|
||||
int nthreads = omp_get_max_threads();
|
||||
if (nthreads > 1)
|
||||
nsme = convert_string_omp(n,mybuf);
|
||||
nsme = convert_string_omp(n, mybuf);
|
||||
else {
|
||||
nsme = convert_string(n,mybuf);
|
||||
nsme = convert_string(n, mybuf);
|
||||
}
|
||||
#else
|
||||
nsme = convert_string(n,mybuf);
|
||||
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,MPI_STATUS_IGNORE);
|
||||
if (flush_flag)
|
||||
MPI_File_sync(mpifh);
|
||||
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, MPI_STATUS_IGNORE);
|
||||
if (flush_flag) MPI_File_sync(mpifh);
|
||||
}
|
||||
}
|
||||
|
||||
@ -531,9 +522,9 @@ void DumpAtomMPIIO::write_string(int n, double *mybuf)
|
||||
int DumpAtomMPIIO::convert_string(int n, double *mybuf)
|
||||
{
|
||||
if (image_flag == 0)
|
||||
return convert_noimage(n,mybuf);
|
||||
return convert_noimage(n, mybuf);
|
||||
else
|
||||
return convert_image(n,mybuf);
|
||||
return convert_image(n, mybuf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -543,9 +534,9 @@ int DumpAtomMPIIO::convert_string(int n, double *mybuf)
|
||||
int DumpAtomMPIIO::convert_string_omp(int n, double *mybuf)
|
||||
{
|
||||
if (image_flag == 0)
|
||||
return convert_noimage_omp(n,mybuf);
|
||||
return convert_noimage_omp(n, mybuf);
|
||||
else
|
||||
return convert_image_omp(n,mybuf);
|
||||
return convert_image_omp(n, mybuf);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -562,55 +553,63 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
|
||||
mpifhStringCount = 0;
|
||||
|
||||
int nthreads = omp_get_max_threads();
|
||||
if (nthreads > n) { // call serial version
|
||||
convert_string(n,mybuf);
|
||||
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");
|
||||
} 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++) {
|
||||
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));
|
||||
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)));
|
||||
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 LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, \
|
||||
mpifhStringCountPerThread, \
|
||||
mpifh_buffer_line_per_thread, mybuf)
|
||||
{
|
||||
int tid = omp_get_thread_num();
|
||||
int m=0;
|
||||
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);
|
||||
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);
|
||||
}
|
||||
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4],static_cast<int> (mybuf[bufOffset[tid]+m+5]),static_cast<int> (mybuf[bufOffset[tid]+m+6]),static_cast<int> (mybuf[bufOffset[tid]+m+7]));
|
||||
mpifhStringCountPerThread[tid] +=
|
||||
sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]), format,
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m]),
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m + 1]), mybuf[bufOffset[tid] + m + 2],
|
||||
mybuf[bufOffset[tid] + m + 3], mybuf[bufOffset[tid] + m + 4],
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m + 5]),
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m + 6]),
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m + 7]));
|
||||
m += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
#pragma omp barrier
|
||||
mpifhStringCount = 0;
|
||||
for (i=0;i<nthreads;i++) {
|
||||
mpifhStringCount += mpifhStringCountPerThread[i];
|
||||
}
|
||||
for (i = 0; i < nthreads; i++) { mpifhStringCount += mpifhStringCountPerThread[i]; }
|
||||
|
||||
memory->destroy(bufOffset);
|
||||
memory->destroy(bufRange);
|
||||
@ -619,21 +618,19 @@ int DumpAtomMPIIO::convert_image_omp(int n, double *mybuf)
|
||||
if (mpifhStringCount > 0) {
|
||||
if (mpifhStringCount > maxsbuf) {
|
||||
if (mpifhStringCount > MAXSMALLINT) return -1;
|
||||
maxsbuf = mpifhStringCount+1;
|
||||
memory->grow(sbuf,maxsbuf,"dump:sbuf");
|
||||
maxsbuf = mpifhStringCount + 1;
|
||||
memory->grow(sbuf, maxsbuf, "dump:sbuf");
|
||||
}
|
||||
sbuf[0] = '\0';
|
||||
}
|
||||
|
||||
|
||||
for (int i=0;i<nthreads;i++) {
|
||||
strcat(sbuf,mpifh_buffer_line_per_thread[i]);
|
||||
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;
|
||||
}
|
||||
@ -652,55 +649,60 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
|
||||
mpifhStringCount = 0;
|
||||
|
||||
int nthreads = omp_get_max_threads();
|
||||
if (nthreads > n) { // call serial version
|
||||
convert_string(n,mybuf);
|
||||
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");
|
||||
} 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++) {
|
||||
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));
|
||||
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)));
|
||||
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 LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, \
|
||||
mpifhStringCountPerThread, \
|
||||
mpifh_buffer_line_per_thread, mybuf)
|
||||
{
|
||||
int tid = omp_get_thread_num();
|
||||
int m=0;
|
||||
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);
|
||||
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);
|
||||
}
|
||||
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),format,static_cast<int> (mybuf[bufOffset[tid]+m]),static_cast<int> (mybuf[bufOffset[tid]+m+1]),mybuf[bufOffset[tid]+m+2],mybuf[bufOffset[tid]+m+3],mybuf[bufOffset[tid]+m+4]);
|
||||
mpifhStringCountPerThread[tid] +=
|
||||
sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]), format,
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m]),
|
||||
static_cast<int>(mybuf[bufOffset[tid] + m + 1]), mybuf[bufOffset[tid] + m + 2],
|
||||
mybuf[bufOffset[tid] + m + 3], mybuf[bufOffset[tid] + m + 4]);
|
||||
m += size_one;
|
||||
}
|
||||
}
|
||||
|
||||
#pragma omp barrier
|
||||
mpifhStringCount = 0;
|
||||
for (i=0;i<nthreads;i++) {
|
||||
mpifhStringCount += mpifhStringCountPerThread[i];
|
||||
}
|
||||
for (i = 0; i < nthreads; i++) { mpifhStringCount += mpifhStringCountPerThread[i]; }
|
||||
|
||||
memory->destroy(bufOffset);
|
||||
memory->destroy(bufRange);
|
||||
@ -709,21 +711,19 @@ int DumpAtomMPIIO::convert_noimage_omp(int n, double *mybuf)
|
||||
if (mpifhStringCount > 0) {
|
||||
if (mpifhStringCount > maxsbuf) {
|
||||
if (mpifhStringCount > MAXSMALLINT) return -1;
|
||||
maxsbuf = mpifhStringCount+1;
|
||||
memory->grow(sbuf,maxsbuf,"dump:sbuf");
|
||||
maxsbuf = mpifhStringCount + 1;
|
||||
memory->grow(sbuf, maxsbuf, "dump:sbuf");
|
||||
}
|
||||
sbuf[0] = '\0';
|
||||
}
|
||||
|
||||
|
||||
for (int i=0;i<nthreads;i++) {
|
||||
strcat(sbuf,mpifh_buffer_line_per_thread[i]);
|
||||
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;
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
@ -16,20 +15,21 @@
|
||||
Contributing author: Paul Coffman (IBM)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "omp_compat.h"
|
||||
#include "dump_custom_mpiio.h"
|
||||
#include <cmath>
|
||||
|
||||
#include <cstring>
|
||||
#include "domain.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "input.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
#include "omp_compat.h"
|
||||
#if defined(_OPENMP)
|
||||
#include <omp.h>
|
||||
#endif
|
||||
@ -40,21 +40,20 @@ using namespace LAMMPS_NS;
|
||||
#define DUMP_BUF_CHUNK_SIZE 16384
|
||||
#define DUMP_BUF_INCREMENT_SIZE 4096
|
||||
|
||||
enum{ID,MOL,TYPE,ELEMENT,MASS,
|
||||
X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,
|
||||
XSU,YSU,ZSU,XSUTRI,YSUTRI,ZSUTRI,
|
||||
IX,IY,IZ,
|
||||
VX,VY,VZ,FX,FY,FZ,
|
||||
Q,MUX,MUY,MUZ,MU,RADIUS,DIAMETER,
|
||||
OMEGAX,OMEGAY,OMEGAZ,ANGMOMX,ANGMOMY,ANGMOMZ,
|
||||
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
|
||||
COMPUTE,FIX,VARIABLE};
|
||||
enum{LT,LE,GT,GE,EQ,NEQ};
|
||||
|
||||
// clang-format off
|
||||
enum{ ID, MOL, TYPE, ELEMENT, MASS,
|
||||
X, Y, Z, XS, YS, ZS, XSTRI, YSTRI, ZSTRI, XU, YU, ZU, XUTRI, YUTRI, ZUTRI,
|
||||
XSU, YSU, ZSU, XSUTRI, YSUTRI, ZSUTRI,
|
||||
IX, IY, IZ, VX, VY, VZ, FX, FY, FZ,
|
||||
Q, MUX, MUY, MUZ, MU, RADIUS, DIAMETER,
|
||||
OMEGAX, OMEGAY, OMEGAZ, ANGMOMX, ANGMOMY, ANGMOMZ,
|
||||
TQX, TQY, TQZ, SPIN, ERADIUS, ERVEL, ERFORCE,
|
||||
COMPUTE, FIX, VARIABLE };
|
||||
enum{ LT, LE, GT, GE, EQ, NEQ };
|
||||
// clang-format on
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg) :
|
||||
DumpCustom(lmp, narg, arg) {}
|
||||
DumpCustomMPIIO::DumpCustomMPIIO(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -67,10 +66,10 @@ DumpCustomMPIIO::~DumpCustomMPIIO()
|
||||
|
||||
void DumpCustomMPIIO::openfile()
|
||||
{
|
||||
if (singlefile_opened) { // single file already opened, so just return after resetting filesize
|
||||
if (singlefile_opened) { // single file already opened, so just return after resetting filesize
|
||||
mpifo = currentFileSize;
|
||||
MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
|
||||
currentFileSize = mpifo+headerSize+sumFileSize;
|
||||
MPI_File_set_size(mpifh, mpifo + headerSize + sumFileSize);
|
||||
currentFileSize = mpifo + headerSize + sumFileSize;
|
||||
return;
|
||||
}
|
||||
if (multifile == 0) singlefile_opened = 1;
|
||||
@ -82,62 +81,56 @@ void DumpCustomMPIIO::openfile()
|
||||
if (multifile) {
|
||||
char *filestar = filecurrent;
|
||||
filecurrent = new char[strlen(filestar) + 16];
|
||||
char *ptr = strchr(filestar,'*');
|
||||
char *ptr = strchr(filestar, '*');
|
||||
*ptr = '\0';
|
||||
if (padflag == 0)
|
||||
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
|
||||
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,filestar,update->ntimestep,ptr+1);
|
||||
if (padflag == 0) {
|
||||
sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", 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, filestar, update->ntimestep, ptr + 1);
|
||||
}
|
||||
*ptr = '*';
|
||||
if (maxfiles > 0) {
|
||||
if (numfiles < maxfiles) {
|
||||
nameslist[numfiles] = new char[strlen(filecurrent)+1];
|
||||
strcpy(nameslist[numfiles],filecurrent);
|
||||
nameslist[numfiles] = new char[strlen(filecurrent) + 1];
|
||||
strcpy(nameslist[numfiles], filecurrent);
|
||||
++numfiles;
|
||||
} else {
|
||||
remove(nameslist[fileidx]);
|
||||
delete[] nameslist[fileidx];
|
||||
nameslist[fileidx] = new char[strlen(filecurrent)+1];
|
||||
strcpy(nameslist[fileidx],filecurrent);
|
||||
nameslist[fileidx] = new char[strlen(filecurrent) + 1];
|
||||
strcpy(nameslist[fileidx], filecurrent);
|
||||
fileidx = (fileidx + 1) % maxfiles;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (append_flag) { // append open
|
||||
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
|
||||
if (err != MPI_SUCCESS) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open dump file %s",filecurrent);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
if (append_flag) { // append open
|
||||
int err = MPI_File_open(world, filecurrent, MPI_MODE_CREATE | MPI_MODE_APPEND | MPI_MODE_WRONLY,
|
||||
MPI_INFO_NULL, &mpifh);
|
||||
if (err != MPI_SUCCESS)
|
||||
error->one(FLERR, "Cannot open dump file {}: {}", filecurrent, utils::getsyserror());
|
||||
|
||||
int myrank;
|
||||
MPI_Comm_rank(world,&myrank);
|
||||
if (myrank == 0)
|
||||
MPI_File_get_size(mpifh,&mpifo);
|
||||
MPI_Comm_rank(world, &myrank);
|
||||
if (myrank == 0) MPI_File_get_size(mpifh, &mpifo);
|
||||
MPI_Bcast(&mpifo, 1, MPI_LMP_BIGINT, 0, world);
|
||||
MPI_File_set_size(mpifh,mpifo+headerSize+sumFileSize);
|
||||
currentFileSize = mpifo+headerSize+sumFileSize;
|
||||
MPI_File_set_size(mpifh, mpifo + headerSize + sumFileSize);
|
||||
currentFileSize = mpifo + headerSize + sumFileSize;
|
||||
|
||||
}
|
||||
else { // replace open
|
||||
} else { // replace open
|
||||
|
||||
int err =
|
||||
MPI_File_open(world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &mpifh);
|
||||
if (err != MPI_SUCCESS)
|
||||
error->one(FLERR, "Cannot open dump file {}: {}", filecurrent, utils::getsyserror());
|
||||
|
||||
int err = MPI_File_open( world, filecurrent, MPI_MODE_CREATE | MPI_MODE_WRONLY , MPI_INFO_NULL, &mpifh);
|
||||
if (err != MPI_SUCCESS) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open dump file %s",filecurrent);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
mpifo = 0;
|
||||
|
||||
MPI_File_set_size(mpifh,(MPI_Offset) (headerSize+sumFileSize));
|
||||
currentFileSize = (headerSize+sumFileSize);
|
||||
|
||||
MPI_File_set_size(mpifh, (MPI_Offset)(headerSize + sumFileSize));
|
||||
currentFileSize = (headerSize + sumFileSize);
|
||||
}
|
||||
}
|
||||
|
||||
@ -172,10 +165,10 @@ void DumpCustomMPIIO::write()
|
||||
// nmax = max # of dump lines on any proc
|
||||
|
||||
bigint bnme = nme;
|
||||
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
MPI_Allreduce(&bnme, &ntotal, 1, MPI_LMP_BIGINT, MPI_SUM, world);
|
||||
|
||||
int nmax;
|
||||
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
|
||||
MPI_Allreduce(&nme, &nmax, 1, MPI_INT, MPI_MAX, world);
|
||||
|
||||
// write timestep header
|
||||
// for multiproc,
|
||||
@ -191,38 +184,40 @@ void DumpCustomMPIIO::write()
|
||||
|
||||
if (nmax > maxbuf) {
|
||||
if ((bigint) nmax * size_one > MAXSMALLINT)
|
||||
error->all(FLERR,"Too much per-proc info for dump");
|
||||
error->all(FLERR, "Too much per-proc info for dump");
|
||||
maxbuf = nmax;
|
||||
memory->destroy(buf);
|
||||
memory->create(buf,(maxbuf*size_one),"dump:buf");
|
||||
memory->create(buf, (maxbuf * size_one), "dump:buf");
|
||||
}
|
||||
if (sort_flag && sortcol == 0 && nmax > maxids) {
|
||||
maxids = nmax;
|
||||
memory->destroy(ids);
|
||||
memory->create(ids,maxids,"dump:ids");
|
||||
memory->create(ids, maxids, "dump:ids");
|
||||
}
|
||||
|
||||
if (sort_flag && sortcol == 0) pack(ids);
|
||||
else pack(nullptr);
|
||||
if (sort_flag && sortcol == 0)
|
||||
pack(ids);
|
||||
else
|
||||
pack(nullptr);
|
||||
if (sort_flag) sort();
|
||||
|
||||
// determine how much data needs to be written for setting the file size and prepocess it prior to writing
|
||||
performEstimate = 1;
|
||||
write_header(nheader);
|
||||
write_data(nme,buf);
|
||||
MPI_Bcast(&sumFileSize, 1, MPI_LMP_BIGINT, (nprocs-1), world);
|
||||
write_data(nme, buf);
|
||||
MPI_Bcast(&sumFileSize, 1, MPI_LMP_BIGINT, (nprocs - 1), world);
|
||||
|
||||
openfile();
|
||||
|
||||
performEstimate = 0;
|
||||
write_header(nheader); // mpifo now points to end of header info
|
||||
write_header(nheader); // mpifo now points to end of header info
|
||||
|
||||
// now actually write the data
|
||||
performEstimate = 0;
|
||||
write_data(nme,buf);
|
||||
write_data(nme, buf);
|
||||
|
||||
if (multifile) MPI_File_close(&mpifh);
|
||||
if (multifile) delete [] filecurrent;
|
||||
if (multifile) MPI_File_close(&mpifh);
|
||||
if (multifile) delete[] filecurrent;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -231,14 +226,16 @@ void DumpCustomMPIIO::init_style()
|
||||
{
|
||||
// format = copy of default or user-specified line format
|
||||
|
||||
delete [] format;
|
||||
delete[] format;
|
||||
char *str;
|
||||
if (format_line_user) str = format_line_user;
|
||||
else str = format_default;
|
||||
if (format_line_user)
|
||||
str = format_line_user;
|
||||
else
|
||||
str = format_default;
|
||||
|
||||
int n = strlen(str) + 1;
|
||||
format = new char[n];
|
||||
strcpy(format,str);
|
||||
strcpy(format, str);
|
||||
|
||||
// tokenize the format string and add space at end of each format element
|
||||
// if user-specified int/float format exists, use it instead
|
||||
@ -247,29 +244,31 @@ void DumpCustomMPIIO::init_style()
|
||||
|
||||
char *ptr;
|
||||
for (int i = 0; i < size_one; i++) {
|
||||
if (i == 0) ptr = strtok(format," \0");
|
||||
else ptr = strtok(nullptr," \0");
|
||||
if (ptr == nullptr) error->all(FLERR,"Dump_modify format line is too short");
|
||||
delete [] vformat[i];
|
||||
if (i == 0)
|
||||
ptr = strtok(format, " \0");
|
||||
else
|
||||
ptr = strtok(nullptr, " \0");
|
||||
if (ptr == nullptr) error->all(FLERR, "Dump_modify format line is too short");
|
||||
delete[] vformat[i];
|
||||
|
||||
if (format_column_user[i]) {
|
||||
vformat[i] = new char[strlen(format_column_user[i]) + 2];
|
||||
strcpy(vformat[i],format_column_user[i]);
|
||||
strcpy(vformat[i], format_column_user[i]);
|
||||
} else if (vtype[i] == Dump::INT && format_int_user) {
|
||||
vformat[i] = new char[strlen(format_int_user) + 2];
|
||||
strcpy(vformat[i],format_int_user);
|
||||
strcpy(vformat[i], format_int_user);
|
||||
} else if (vtype[i] == Dump::DOUBLE && format_float_user) {
|
||||
vformat[i] = new char[strlen(format_float_user) + 2];
|
||||
strcpy(vformat[i],format_float_user);
|
||||
strcpy(vformat[i], format_float_user);
|
||||
} else if (vtype[i] == Dump::BIGINT && format_bigint_user) {
|
||||
vformat[i] = new char[strlen(format_bigint_user) + 2];
|
||||
strcpy(vformat[i],format_bigint_user);
|
||||
strcpy(vformat[i], format_bigint_user);
|
||||
} else {
|
||||
vformat[i] = new char[strlen(ptr) + 2];
|
||||
strcpy(vformat[i],ptr);
|
||||
strcpy(vformat[i], ptr);
|
||||
}
|
||||
|
||||
vformat[i] = strcat(vformat[i]," ");
|
||||
vformat[i] = strcat(vformat[i], " ");
|
||||
}
|
||||
|
||||
// setup boundary string
|
||||
@ -287,8 +286,10 @@ void DumpCustomMPIIO::init_style()
|
||||
else if (!binary && domain->triclinic == 1)
|
||||
header_choice = &DumpCustomMPIIO::header_item_triclinic;
|
||||
|
||||
if (binary) write_choice = &DumpCustomMPIIO::write_binary;
|
||||
else write_choice = &DumpCustomMPIIO::write_string;
|
||||
if (binary)
|
||||
write_choice = &DumpCustomMPIIO::write_binary;
|
||||
else
|
||||
write_choice = &DumpCustomMPIIO::write_string;
|
||||
|
||||
// find current ptr for each compute,fix,variable
|
||||
// check that fix frequency is acceptable
|
||||
@ -296,24 +297,23 @@ void DumpCustomMPIIO::init_style()
|
||||
int icompute;
|
||||
for (int i = 0; i < ncompute; i++) {
|
||||
icompute = modify->find_compute(id_compute[i]);
|
||||
if (icompute < 0) error->all(FLERR,"Could not find dump custom compute ID");
|
||||
if (icompute < 0) error->all(FLERR, "Could not find dump custom compute ID");
|
||||
compute[i] = modify->compute[icompute];
|
||||
}
|
||||
|
||||
int ifix;
|
||||
for (int i = 0; i < nfix; i++) {
|
||||
ifix = modify->find_fix(id_fix[i]);
|
||||
if (ifix < 0) error->all(FLERR,"Could not find dump custom fix ID");
|
||||
if (ifix < 0) error->all(FLERR, "Could not find dump custom fix ID");
|
||||
fix[i] = modify->fix[ifix];
|
||||
if (nevery % modify->fix[ifix]->peratom_freq)
|
||||
error->all(FLERR,"Dump custom and fix not computed at compatible times");
|
||||
error->all(FLERR, "Dump custom and fix not computed at compatible times");
|
||||
}
|
||||
|
||||
int ivariable;
|
||||
for (int i = 0; i < nvariable; i++) {
|
||||
ivariable = input->variable->find(id_variable[i]);
|
||||
if (ivariable < 0)
|
||||
error->all(FLERR,"Could not find dump custom variable name");
|
||||
if (ivariable < 0) error->all(FLERR, "Could not find dump custom variable name");
|
||||
variable[i] = ivariable;
|
||||
}
|
||||
|
||||
@ -321,8 +321,7 @@ void DumpCustomMPIIO::init_style()
|
||||
|
||||
if (iregion >= 0) {
|
||||
iregion = domain->find_region(idregion);
|
||||
if (iregion == -1)
|
||||
error->all(FLERR,"Region ID for dump custom does not exist");
|
||||
if (iregion == -1) error->all(FLERR, "Region ID for dump custom does not exist");
|
||||
}
|
||||
}
|
||||
|
||||
@ -339,48 +338,47 @@ void DumpCustomMPIIO::header_binary(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc((2*sizeof(bigint)) + (9*sizeof(int)) + (6*sizeof(double)));
|
||||
headerBuffer = (char *) malloc((2 * sizeof(bigint)) + (9 * sizeof(int)) + (6 * sizeof(double)));
|
||||
|
||||
headerSize = 0;
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&update->ntimestep,sizeof(bigint));
|
||||
memcpy(headerBuffer + headerSize, &update->ntimestep, sizeof(bigint));
|
||||
headerSize += sizeof(bigint);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&ndump,sizeof(bigint));
|
||||
memcpy(headerBuffer + headerSize, &ndump, sizeof(bigint));
|
||||
headerSize += sizeof(bigint);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&domain->triclinic,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &domain->triclinic, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&domain->boundary[0][0],6*sizeof(int));
|
||||
headerSize += 6*sizeof(int);
|
||||
memcpy(headerBuffer + headerSize, &domain->boundary[0][0], 6 * sizeof(int));
|
||||
headerSize += 6 * sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxlo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxlo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxylo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxylo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxyhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxyhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzlo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxzlo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxzhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&size_one,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &size_one, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&nprocs,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &nprocs, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
}
|
||||
else { // write data
|
||||
} else { // write data
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_BYTE, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
}
|
||||
@ -392,59 +390,58 @@ void DumpCustomMPIIO::header_binary_triclinic(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc((2*sizeof(bigint)) + (9*sizeof(int)) + (6*sizeof(double)));
|
||||
headerBuffer = (char *) malloc((2 * sizeof(bigint)) + (9 * sizeof(int)) + (9 * sizeof(double)));
|
||||
|
||||
headerSize = 0;
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&update->ntimestep,sizeof(bigint));
|
||||
memcpy(headerBuffer + headerSize, &update->ntimestep, sizeof(bigint));
|
||||
headerSize += sizeof(bigint);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&ndump,sizeof(bigint));
|
||||
memcpy(headerBuffer + headerSize, &ndump, sizeof(bigint));
|
||||
headerSize += sizeof(bigint);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&domain->triclinic,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &domain->triclinic, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&domain->boundary[0][0],6*sizeof(int));
|
||||
headerSize += 6*sizeof(int);
|
||||
memcpy(headerBuffer + headerSize, &domain->boundary[0][0], 6 * sizeof(int));
|
||||
headerSize += 6 * sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxlo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxlo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxylo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxylo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxyhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxyhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzlo,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxzlo, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxzhi,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxzhi, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxy,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxy, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxxz,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxxz, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&boxyz,sizeof(double));
|
||||
memcpy(headerBuffer + headerSize, &boxyz, sizeof(double));
|
||||
headerSize += sizeof(double);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&size_one,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &size_one, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
memcpy(&((char*)headerBuffer)[headerSize],&nprocs,sizeof(int));
|
||||
memcpy(headerBuffer + headerSize, &nprocs, sizeof(int));
|
||||
headerSize += sizeof(int);
|
||||
|
||||
}
|
||||
else { // write data
|
||||
} else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_BYTE,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_BYTE, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
}
|
||||
@ -456,25 +453,21 @@ void DumpCustomMPIIO::header_item(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
auto itemtxt = fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
|
||||
itemtxt += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
|
||||
itemtxt += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
|
||||
itemtxt += fmt::format("{} {}\n{} {}\n{} {}\n", boxxlo, boxxhi, boxylo, boxyhi, boxzlo, boxzhi);
|
||||
itemtxt += fmt::format("ITEM: ATOMS {}\n", columns);
|
||||
|
||||
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
|
||||
headerSize = itemtxt.size();
|
||||
headerBuffer = utils::strdup(itemtxt);
|
||||
|
||||
} else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_CHAR, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
delete[] headerBuffer;
|
||||
}
|
||||
}
|
||||
|
||||
@ -484,25 +477,22 @@ void DumpCustomMPIIO::header_item_triclinic(bigint ndump)
|
||||
{
|
||||
if (performEstimate) {
|
||||
|
||||
headerBuffer = (char *) malloc(MAX_TEXT_HEADER_SIZE);
|
||||
auto itemtxt = fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
|
||||
itemtxt += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
|
||||
itemtxt += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
|
||||
itemtxt += fmt::format("{} {} {}\n{} {} {}\n{} {} {}\n", boxxlo, boxxhi, boxxy, boxylo, boxyhi,
|
||||
boxxz, boxzlo, boxzhi, boxyz);
|
||||
itemtxt += fmt::format("ITEM: ATOMS {}\n", columns);
|
||||
|
||||
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
|
||||
headerSize = itemtxt.size();
|
||||
headerBuffer = utils::strdup(itemtxt);
|
||||
|
||||
} else { // write data
|
||||
|
||||
if (me == 0)
|
||||
MPI_File_write_at(mpifh,mpifo,headerBuffer,headerSize,MPI_CHAR,MPI_STATUS_IGNORE);
|
||||
MPI_File_write_at(mpifh, mpifo, headerBuffer, headerSize, MPI_CHAR, MPI_STATUS_IGNORE);
|
||||
mpifo += headerSize;
|
||||
free(headerBuffer);
|
||||
delete[] headerBuffer;
|
||||
}
|
||||
}
|
||||
|
||||
@ -510,7 +500,7 @@ void DumpCustomMPIIO::header_item_triclinic(bigint ndump)
|
||||
|
||||
void DumpCustomMPIIO::write_data(int n, double *mybuf)
|
||||
{
|
||||
(this->*write_choice)(n,mybuf);
|
||||
(this->*write_choice)(n, mybuf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -523,22 +513,21 @@ void DumpCustomMPIIO::write_binary(int n, double *mybuf)
|
||||
|
||||
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);
|
||||
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,MPI_STATUS_IGNORE);
|
||||
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,
|
||||
MPI_STATUS_IGNORE);
|
||||
memory->destroy(bufWithSize);
|
||||
|
||||
if (flush_flag)
|
||||
MPI_File_sync(mpifh);
|
||||
if (flush_flag) MPI_File_sync(mpifh);
|
||||
}
|
||||
}
|
||||
|
||||
@ -551,23 +540,20 @@ void DumpCustomMPIIO::write_string(int n, double *mybuf)
|
||||
#if defined(_OPENMP)
|
||||
int nthreads = omp_get_max_threads();
|
||||
if ((nthreads > 1) && !(lmp->kokkos))
|
||||
nsme = convert_string_omp(n,mybuf); // not (yet) compatible with Kokkos
|
||||
nsme = convert_string_omp(n, mybuf); // not (yet) compatible with Kokkos
|
||||
else
|
||||
nsme = convert_string(n,mybuf);
|
||||
nsme = convert_string(n, mybuf);
|
||||
#else
|
||||
|
||||
nsme = convert_string(n,mybuf);
|
||||
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,MPI_STATUS_IGNORE);
|
||||
if (flush_flag)
|
||||
MPI_File_sync(mpifh);
|
||||
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, MPI_STATUS_IGNORE);
|
||||
if (flush_flag) MPI_File_sync(mpifh);
|
||||
}
|
||||
}
|
||||
|
||||
@ -587,64 +573,71 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
|
||||
mpifhStringCount = 0;
|
||||
|
||||
int nthreads = omp_get_max_threads();
|
||||
if (nthreads > n) { // call serial version
|
||||
convert_string(n,mybuf);
|
||||
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");
|
||||
} 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++) {
|
||||
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));
|
||||
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)));
|
||||
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 LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf)
|
||||
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(bufOffset, bufRange, bufLength, \
|
||||
mpifhStringCountPerThread, \
|
||||
mpifh_buffer_line_per_thread, mybuf)
|
||||
{
|
||||
int tid = omp_get_thread_num();
|
||||
int m=0;
|
||||
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);
|
||||
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] == Dump::INT)
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
|
||||
mpifhStringCountPerThread[tid] +=
|
||||
sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),
|
||||
vformat[j], static_cast<int>(mybuf[bufOffset[tid] + m]));
|
||||
else if (vtype[j] == Dump::DOUBLE)
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
|
||||
mpifhStringCountPerThread[tid] +=
|
||||
sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),
|
||||
vformat[j], mybuf[bufOffset[tid] + m]);
|
||||
else if (vtype[j] == Dump::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]]),
|
||||
vformat[j], typenames[(int) mybuf[bufOffset[tid] + m]]);
|
||||
m++;
|
||||
}
|
||||
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
|
||||
|
||||
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];
|
||||
}
|
||||
for (i = 0; i < nthreads; i++) { mpifhStringCount += mpifhStringCountPerThread[i]; }
|
||||
|
||||
memory->destroy(bufOffset);
|
||||
memory->destroy(bufRange);
|
||||
@ -653,21 +646,19 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
|
||||
if (mpifhStringCount > 0) {
|
||||
if (mpifhStringCount > maxsbuf) {
|
||||
if (mpifhStringCount > MAXSMALLINT) return -1;
|
||||
maxsbuf = mpifhStringCount+1;
|
||||
memory->grow(sbuf,maxsbuf,"dump:sbuf");
|
||||
maxsbuf = mpifhStringCount + 1;
|
||||
memory->grow(sbuf, maxsbuf, "dump:sbuf");
|
||||
}
|
||||
sbuf[0] = '\0';
|
||||
}
|
||||
|
||||
|
||||
for (int i=0;i<nthreads;i++) {
|
||||
strcat(sbuf,mpifh_buffer_line_per_thread[i]);
|
||||
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;
|
||||
|
||||
Reference in New Issue
Block a user