cleanup up rendezvous diagnostic output (a278df58) · Commits · 郑智淋 / lammps

src/RIGID/fix_rigid_small.cpp

+16 −3

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@
		#include "modify.h"
		#include "group.h"
		#include "comm.h"
		#include "neighbor.h"
		#include "force.h"
		#include "input.h"
		#include "output.h"
		@@ -44,6 +45,8 @@ using namespace LAMMPS_NS;
		using namespace FixConst;
		using namespace MathConst;

		#define RVOUS 1 // 0 for irregular, 1 for all2all

		#define MAXLINE 1024
		#define CHUNK 1024
		#define ATTRIBUTE_PERBODY 20
		@@ -585,12 +588,22 @@ void FixRigidSmall::init()
		if (rflag && (modify->fmask[i] & POST_FORCE) &&
		!modify->fix[i]->rigid_flag) {
		char str[128];
		snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
		snprintf(str,128,"Fix %s alters forces after fix rigid",
		modify->fix[i]->id);
		error->warning(FLERR,str);
		}
		}
		}

		// error if maxextent > comm->cutghost
		// NOTE: could just warn if an override flag set
		// NOTE: this could fail for comm multi mode if user sets a wrong cutoff
		// for atom types in rigid bodies - need a more careful test

		double cutghost = MAX(neighbor->cutneighmax,comm->cutghostuser);
		if (maxextent > cutghost)
		error->all(FLERR,"Rigid body extent > ghost cutoff - use comm_modify cutoff");

		// error if npt,nph fix comes before rigid fix

		for (i = 0; i < modify->nfix; i++) {
		@@ -1576,10 +1589,10 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
		// func = compute bbox of each body, find atom closest to geometric center

		char *buf;
		int nreturn = comm->rendezvous(1,ncount,(char *) inbuf,sizeof(InRvous),
		int nreturn = comm->rendezvous(RVOUS,ncount,(char *) inbuf,sizeof(InRvous),
		0,proclist,
		rendezvous_body,0,buf,sizeof(OutRvous),
		(void *) this);
		(void *) this,1);
		OutRvous outbuf = (OutRvous ) buf;

		memory->destroy(proclist);

src/RIGID/fix_shake.cpp

+6 −4

Original line number	Diff line number	Diff line
		@@ -39,6 +39,8 @@ using namespace LAMMPS_NS;
		using namespace FixConst;
		using namespace MathConst;

		#define RVOUS 1 // 0 for irregular, 1 for all2all

		#define BIG 1.0e20
		#define MASSDELTA 0.1

		@@ -1068,7 +1070,7 @@ void FixShake::atom_owners()
		// each proc assigned every 1/Pth atom

		char *buf;
		comm->rendezvous(1,nlocal,(char *) idbuf,sizeof(IDRvous),
		comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),
		0,proclist,
		rendezvous_ids,0,buf,0,(void *) this,1);

		@@ -1174,7 +1176,7 @@ void FixShake::partner_info(int npartner, tagint *partner_tag,
		// receives all data needed to populate un-owned partner 4 values

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PartnerInfo),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PartnerInfo),
		0,proclist,
		rendezvous_partners_info,
		0,buf,sizeof(PartnerInfo),
		@@ -1263,7 +1265,7 @@ void FixShake::nshake_info(int npartner, tagint *partner_tag,
		// receives all data needed to populate un-owned partner nshake

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(NShakeInfo),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(NShakeInfo),
		0,proclist,
		rendezvous_nshake,0,buf,sizeof(NShakeInfo),
		(void *) this,1);
		@@ -1356,7 +1358,7 @@ void FixShake::shake_info(int npartner, tagint *partner_tag,
		// receives all data needed to populate un-owned shake info

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(ShakeInfo),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(ShakeInfo),
		0,proclist,
		rendezvous_shake,0,buf,sizeof(ShakeInfo),
		(void *) this,1);

src/comm.cpp

+42 −121

Original line number	Diff line number	Diff line
		@@ -796,7 +796,7 @@ rendezvous_irregular(int n, char inbuf, int insize, int inorder, int procs,
		"rendezvous:inbuf");
		irregular->exchange_data(inbuf,insize,inbuf_rvous);

		bigint irregular1_bytes = 0; //irregular->irregular_bytes;
		bigint irregular1_bytes = irregular->memory_usage();
		irregular->destroy_data();
		delete irregular;

		@@ -826,7 +826,7 @@ rendezvous_irregular(int n, char inbuf, int insize, int inorder, int procs,
		"rendezvous:outbuf");
		irregular->exchange_data(outbuf_rvous,outsize,outbuf);

		bigint irregular2_bytes = 0; //irregular->irregular_bytes;
		bigint irregular2_bytes = irregular->memory_usage();
		irregular->destroy_data();
		delete irregular;

		@@ -834,90 +834,11 @@ rendezvous_irregular(int n, char inbuf, int insize, int inorder, int procs,
		memory->sfree(outbuf_rvous);

		// return number of output datums
		// last arg to stats() = memory for procs_rvous + irregular comm

		if (!statflag) return nout;

		// memory info for caller and rendezvous decompositions

		bigint size_in_all,size_in_max,size_in_min;
		bigint size_out_all,size_out_max,size_out_min;
		bigint size_inrvous_all,size_inrvous_max,size_inrvous_min;
		bigint size_outrvous_all,size_outrvous_max,size_outrvous_min;

		bigint size = (bigint) n*insize;
		MPI_Allreduce(&size,&size_in_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		MPI_Allreduce(&size,&size_in_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_in_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		size = (bigint) nout*outsize;
		MPI_Allreduce(&size,&size_out_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		MPI_Allreduce(&size,&size_out_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_out_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		size = (bigint) nrvous*insize;
		MPI_Allreduce(&size,&size_inrvous_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		MPI_Allreduce(&size,&size_inrvous_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_inrvous_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		size = (bigint) nrvous_out*insize;
		MPI_Allreduce(&size,&size_outrvous_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		MPI_Allreduce(&size,&size_outrvous_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_outrvous_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		int mbytes = 1024*1024;

		if (me == 0) {
		if (screen) {
		fprintf(screen,"Rendezvous balance and memory info:\n");
		fprintf(screen," input datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_in_all/insize,1.0*size_in_all/nprocs/insize,
		size_in_max/insize,size_in_min/insize);
		fprintf(screen," input data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		1.0size_in_all/mbytes,1.0size_in_all/nprocs/mbytes,
		1.0size_in_max/mbytes,1.0size_in_min/mbytes);
		fprintf(screen," output datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_out_all/outsize,1.0*size_out_all/nprocs/outsize,
		size_out_max/outsize,size_out_min/outsize);
		fprintf(screen," output data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		1.0size_out_all/mbytes,1.0size_out_all/nprocs/mbytes,
		1.0size_out_max/mbytes,1.0size_out_min/mbytes);
		fprintf(screen," input rvous datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_inrvous_all/insize,1.0*size_inrvous_all/nprocs/insize,
		size_inrvous_max/insize,size_inrvous_min/insize);
		fprintf(screen," input rvous data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		1.0size_inrvous_all/mbytes,1.0size_inrvous_all/nprocs/mbytes,
		1.0size_inrvous_max/mbytes,1.0size_inrvous_min/mbytes);
		fprintf(screen," output rvous datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_outrvous_all/outsize,1.0*size_outrvous_all/nprocs/outsize,
		size_outrvous_max/outsize,size_outrvous_min/outsize);
		fprintf(screen," output rvous data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		1.0size_outrvous_all/mbytes,1.0size_outrvous_all/nprocs/mbytes,
		1.0size_outrvous_max/mbytes,1.0size_outrvous_min/mbytes);
		}
		}

		/*
		bigint rvous_bytes = 0;
		rvous_bytes += n*insize; // inbuf
		rvous_bytes += nout*outsize; // outbuf
		rvous_bytes += nrvous*insize; // inbuf_rvous
		rvous_bytes += nrvous_out*outsize; // outbuf_rvous
		rvous_bytes += nrvous_out*sizeof(int); // procs_rvous
		rvous_bytes += MAX(irregular1_bytes,irregular2_bytes); // max of 2 comms
		*/

		if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
		(bigint) nrvous_out*sizeof(int) +
		MAX(irregular1_bytes,irregular2_bytes));
		return nout;
		}

		@@ -1121,15 +1042,28 @@ rendezvous_all2all(int n, char inbuf, int insize, int inorder, int procs,
		memory->destroy(rdispls);

		// return number of output datums
		// last arg to stats() = mem for procs_rvous + per-proc vecs + reordering ops

		if (!statflag) return nout;
		if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
		(bigint) nrvous_out*sizeof(int) +
		4nprocssizeof(int) +
		MAX(all2all1_bytes,all2all2_bytes));
		return nout;
		}

		// memory info for caller and rendezvous decompositions
		/* ----------------------------------------------------------------------
		print balance and memory info for rendezvous operation
		useful for debugging
		------------------------------------------------------------------------- */

		void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out,
		int insize, int outsize, bigint commsize)
		{
		bigint size_in_all,size_in_max,size_in_min;
		bigint size_out_all,size_out_max,size_out_min;
		bigint size_inrvous_all,size_inrvous_max,size_inrvous_min;
		bigint size_outrvous_all,size_outrvous_max,size_outrvous_min;
		bigint size_comm_all,size_comm_max,size_comm_min;

		bigint size = (bigint) n*insize;
		MPI_Allreduce(&size,&size_in_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		@@ -1151,62 +1085,49 @@ rendezvous_all2all(int n, char inbuf, int insize, int inorder, int procs,
		MPI_Allreduce(&size,&size_outrvous_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_outrvous_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		size = commsize;
		MPI_Allreduce(&size,&size_comm_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
		MPI_Allreduce(&size,&size_comm_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
		MPI_Allreduce(&size,&size_comm_min,1,MPI_LMP_BIGINT,MPI_MIN,world);

		int mbytes = 1024*1024;

		if (me == 0) {
		if (screen) {
		fprintf(screen,"Rendezvous balance and memory info:\n");
		fprintf(screen," input datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		fprintf(screen,"Rendezvous balance and memory info: (tot,ave,max,min) \n");
		fprintf(screen," input datum count: "
		BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_in_all/insize,1.0*size_in_all/nprocs/insize,
		size_in_max/insize,size_in_min/insize);
		fprintf(screen," input data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		fprintf(screen," input data (MB): %g %g %g %g\n",
		1.0size_in_all/mbytes,1.0size_in_all/nprocs/mbytes,
		1.0size_in_max/mbytes,1.0size_in_min/mbytes);
		fprintf(screen," output datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		fprintf(screen," output datum count: "
		BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_out_all/outsize,1.0*size_out_all/nprocs/outsize,
		size_out_max/outsize,size_out_min/outsize);
		fprintf(screen," output data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		fprintf(screen," output data (MB): %g %g %g %g\n",
		1.0size_out_all/mbytes,1.0size_out_all/nprocs/mbytes,
		1.0size_out_max/mbytes,1.0size_out_min/mbytes);
		fprintf(screen," input rvous datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		fprintf(screen," input rvous datum count: "
		BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_inrvous_all/insize,1.0*size_inrvous_all/nprocs/insize,
		size_inrvous_max/insize,size_inrvous_min/insize);
		fprintf(screen," input rvous data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		fprintf(screen," input rvous data (MB): %g %g %g %g\n",
		1.0size_inrvous_all/mbytes,1.0size_inrvous_all/nprocs/mbytes,
		1.0size_inrvous_max/mbytes,1.0size_inrvous_min/mbytes);
		fprintf(screen," output rvous datum count "
		"(tot,ave,max,min): " BIGINT_FORMAT " %g "
		BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		fprintf(screen," output rvous datum count: "
		BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
		size_outrvous_all/outsize,1.0*size_outrvous_all/nprocs/outsize,
		size_outrvous_max/outsize,size_outrvous_min/outsize);
		fprintf(screen," output rvous data (MB) "
		"(tot,ave,max,min): %g %g %g %g\n",
		fprintf(screen," output rvous data (MB): %g %g %g %g\n",
		1.0size_outrvous_all/mbytes,1.0size_outrvous_all/nprocs/mbytes,
		1.0size_outrvous_max/mbytes,1.0size_outrvous_min/mbytes);
		fprintf(screen," rvous comm (MB): %g %g %g %g\n",
		1.0size_comm_all/mbytes,1.0size_comm_all/nprocs/mbytes,
		1.0size_comm_max/mbytes,1.0size_comm_min/mbytes);
		}
		}

		/*
		bigint rvous_bytes = 0;
		rvous_bytes += n*insize; // inbuf
		rvous_bytes += nout*outsize; // outbuf
		rvous_bytes += nrvous*insize; // inbuf_rvous
		rvous_bytes += nrvous_out*outsize; // outbuf_rvous
		rvous_bytes += nrvous_out*sizeof(int); // procs_rvous
		rvous_bytes += 4nprocssizeof(int); // all2all vectors
		rvous_bytes += MAX(all2all1_bytes,all2all2_bytes); // reorder ops
		*/

		return nout;
		}

		/* ----------------------------------------------------------------------

src/comm.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -153,6 +153,7 @@ class Comm : protected Pointers {
		int rendezvous_all2all(int, char , int, int, int ,
		int ()(int, char , int &, int &, char &, void *),
		int, char &, int, void , int);
		void rendezvous_stats(int, int, int, int, int, int, bigint);

		public:
		enum{MULTIPLE};

src/special.cpp

+8 −6

Original line number	Diff line number	Diff line
		@@ -27,6 +27,8 @@

		using namespace LAMMPS_NS;

		#define RVOUS 1 // 0 for irregular, 1 for all2all

		/* ---------------------------------------------------------------------- */

		Special::Special(LAMMPS *lmp) : Pointers(lmp)
		@@ -185,7 +187,7 @@ void Special::atom_owners()
		// perform rendezvous operation

		char *buf;
		comm->rendezvous(1,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist,
		comm->rendezvous(RVOUS,nlocal,(char *) idbuf,sizeof(IDRvous),0,proclist,
		rendezvous_ids,0,buf,0,(void *) this,1);

		memory->destroy(proclist);
		@@ -241,7 +243,7 @@ void Special::onetwo_build_newton()
		// perform rendezvous operation

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PairRvous),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
		0,proclist,
		rendezvous_pairs,0,buf,sizeof(PairRvous),
		(void *) this,1);
		@@ -376,7 +378,7 @@ void Special::onethree_build()
		// perform rendezvous operation

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PairRvous),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
		0,proclist,
		rendezvous_pairs,0,buf,sizeof(PairRvous),
		(void *) this,1);
		@@ -481,7 +483,7 @@ void Special::onefour_build()
		// perform rendezvous operation

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PairRvous),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
		0,proclist,
		rendezvous_pairs,0,buf,sizeof(PairRvous),
		(void *) this,1);
		@@ -904,7 +906,7 @@ void Special::angle_trim()
		// perform rendezvous operation

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PairRvous),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
		0,proclist,
		rendezvous_pairs,0,buf,sizeof(PairRvous),
		(void *) this,1);
		@@ -1123,7 +1125,7 @@ void Special::dihedral_trim()
		// perform rendezvous operation

		char *buf;
		int nreturn = comm->rendezvous(1,nsend,(char *) inbuf,sizeof(PairRvous),
		int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
		0,proclist,
		rendezvous_pairs,0,buf,sizeof(PairRvous),
		(void *) this,1);

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