git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7383 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/comm.cpp

@@ -66,6 +66,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
   MPI_Comm_size(world,&nprocs);
 
   user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
+  coregrid[0] = coregrid[1] = coregrid[2] = 1;
   gridflag = ONELEVEL;
   mapflag = CART;
   customfile = NULL;
@@ -153,10 +154,16 @@ void Comm::set_proc_grid()
 
   if (recv_from_partition >= 0) {
     MPI_Status status;
-    if (me == 0) MPI_Recv(other_procgrid,3,MPI_INT,
+    if (me == 0) {
+      MPI_Recv(other_procgrid,3,MPI_INT,
 	       universe->root_proc[recv_from_partition],0,
 	       universe->uworld,&status);
+      MPI_Recv(other_coregrid,3,MPI_INT,
+	       universe->root_proc[recv_from_partition],0,
+	       universe->uworld,&status);
+    }
     MPI_Bcast(other_procgrid,3,MPI_INT,0,world);
+    MPI_Bcast(other_coregrid,3,MPI_INT,0,world);
   }
 
   // create ProcMap class to create 3d grid and map procs to it
@@ -168,12 +175,12 @@ void Comm::set_proc_grid()
 
   if (gridflag == ONELEVEL) {
     pmap->onelevel_grid(nprocs,user_procgrid,procgrid,
-			otherflag,other_style,other_procgrid);
+			otherflag,other_style,other_procgrid,other_coregrid);
 
   } else if (gridflag == TWOLEVEL) {
     pmap->twolevel_grid(nprocs,user_procgrid,procgrid,
 			ncores,user_coregrid,coregrid,
-			otherflag,other_style,other_procgrid);
+			otherflag,other_style,other_procgrid,other_coregrid);
 
   } else if (gridflag == NUMA) {
     pmap->numa_grid(nprocs,user_procgrid,procgrid,coregrid);
@@ -215,8 +222,6 @@ void Comm::set_proc_grid()
     else if (mapflag == XYZ)
       pmap->xyz_map(xyz,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
     
-    // printf("AAA %d: %d %d: %d %d: %d %d\n",);
-
   } else if (gridflag == NUMA) {
     pmap->numa_map(0,coregrid,myloc,procneigh,grid2proc);
 
@@ -258,9 +263,14 @@ void Comm::set_proc_grid()
   // send my 3d proc grid to another partition if requested
 
   if (send_to_partition >= 0) {
-    if (me == 0) MPI_Send(procgrid,3,MPI_INT,
+    if (me == 0) {
+      MPI_Send(procgrid,3,MPI_INT,
 	       universe->root_proc[send_to_partition],0,
 	       universe->uworld);
+      MPI_Send(coregrid,3,MPI_INT,
+	       universe->root_proc[send_to_partition],0,
+	       universe->uworld);
+    }
   }
 }
 

src/comm.h

@@ -92,6 +92,7 @@ class Comm : protected Pointers {
   int otherflag;                    // 1 if this partition dependent on another
   int other_style;                  // style of dependency
   int other_procgrid[3];            // proc layout of another partition
+  int other_coregrid[3];            // core layout of another partition
   int ncores;                       // # of cores per node
   int coregrid[3];                  // 3d grid of cores within a node
   int user_coregrid[3];             // user request for cores in each dim

src/dump_custom.cpp

@@ -120,8 +120,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   format_default[0] = '\0';
 
   for (int i = 0; i < size_one; i++) {
-    if (vtype[i] == INT) format_default = strcat(format_default,"%d ");
+    if (vtype[i] == INT) strcat(format_default,"%d ");
-    else if (vtype[i] == DOUBLE) format_default = strcat(format_default,"%g ");
+    else if (vtype[i] == DOUBLE) strcat(format_default,"%g ");
     else if (vtype[i] == STRING) strcat(format_default,"%s ");
     vformat[i] = NULL;
   }
@@ -1306,14 +1306,16 @@ int DumpCustom::modify_param(int narg, char **arg)
     if (strcmp(arg[1],"none") == 0) iregion = -1;
     else {
       iregion = domain->find_region(arg[1]);
-      if (iregion == -1) error->all(FLERR,"Dump_modify region ID does not exist");
+      if (iregion == -1) 
+	error->all(FLERR,"Dump_modify region ID does not exist");
       int n = strlen(arg[1]) + 1;
       idregion = new char[n];
       strcpy(idregion,arg[1]);
     }
     return 2;
+  }
 
-  } else if (strcmp(arg[0],"element") == 0) {
+  if (strcmp(arg[0],"element") == 0) {
     if (narg < ntypes+1)
       error->all(FLERR,"Dump modify element names do not match atom types");
 
@@ -1330,8 +1332,9 @@ int DumpCustom::modify_param(int narg, char **arg)
       strcpy(typenames[itype],arg[itype]);
     }
     return ntypes+1;
+  }
 
-  } else if (strcmp(arg[0],"thresh") == 0) {
+  if (strcmp(arg[0],"thresh") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
     if (strcmp(arg[1],"none") == 0) {
       if (nthresh) {
@@ -1462,13 +1465,16 @@ int DumpCustom::modify_param(int narg, char **arg)
       if (n < 0) error->all(FLERR,"Could not find dump modify compute ID");
 
       if (modify->compute[n]->peratom_flag == 0)
-	error->all(FLERR,"Dump modify compute ID does not compute per-atom info");
+	error->all(FLERR,
+		   "Dump modify compute ID does not compute per-atom info");
       if (argindex[nfield+nthresh] == 0 && 
 	  modify->compute[n]->size_peratom_cols > 0)
-	error->all(FLERR,"Dump modify compute ID does not compute per-atom vector");
+	error->all(FLERR,
+		   "Dump modify compute ID does not compute per-atom vector");
       if (argindex[nfield+nthresh] > 0 && 
 	  modify->compute[n]->size_peratom_cols == 0)
-	error->all(FLERR,"Dump modify compute ID does not compute per-atom array");
+	error->all(FLERR,
+		   "Dump modify compute ID does not compute per-atom array");
       if (argindex[nfield+nthresh] > 0 && 
 	  argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols)
 	error->all(FLERR,"Dump modify compute ID vector is not large enough");

src/input.cpp

@@ -1327,7 +1327,9 @@ void Input::suffix()
 void Input::thermo()
 {
   if (narg != 1) error->all(FLERR,"Illegal thermo command");
-  output->thermo_every = atoi(arg[0]);
+  int n = atoi(arg[0]);
+  if (n < 0) error->all(FLERR,"Illegal thermo command");
+  output->thermo_every = n;
 }
 
 /* ---------------------------------------------------------------------- */

src/output.cpp

@@ -38,9 +38,6 @@ using namespace LAMMPS_NS;
 
 #define DELTA 1
 
-#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
-#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
-
 /* ----------------------------------------------------------------------
    initialize all output 
 ------------------------------------------------------------------------- */
@@ -187,7 +184,7 @@ void Output::setup(int flag)
 	if (writeflag) modify->addstep_compute(next_dump[idump]);
 	else modify->addstep_compute_all(next_dump[idump]);
       }
-      if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
+      if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
       else next_dump_any = next_dump[0];
     }
   } else next_dump_any = update->laststep + 1;
@@ -218,7 +215,7 @@ void Output::setup(int flag)
 
   if (thermo_every) {
     next_thermo = (ntimestep/thermo_every)*thermo_every + thermo_every;
-    next_thermo = MYMIN(next_thermo,update->laststep);
+    next_thermo = MIN(next_thermo,update->laststep);
   } else if (var_thermo) {
     next_thermo = static_cast<int> 
       (input->variable->compute_equal(ivar_thermo));
@@ -230,8 +227,8 @@ void Output::setup(int flag)
 
   // next = next timestep any output will be done
 
-  next = MYMIN(next_dump_any,next_restart);
+  next = MIN(next_dump_any,next_restart);
-  next = MYMIN(next,next_thermo);
+  next = MIN(next,next_thermo);
 }
 
 /* ----------------------------------------------------------------------
@@ -265,7 +262,7 @@ void Output::write(bigint ntimestep)
 	}
         if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
       }
-      if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
+      if (idump) next_dump_any = MIN(next_dump_any,next_dump[idump]);
       else next_dump_any = next_dump[0];
     }
   }
@@ -311,14 +308,14 @@ void Output::write(bigint ntimestep)
       if (next_thermo <= ntimestep)
 	error->all(FLERR,"Thermo every variable returned a bad timestep");
     } else next_thermo = update->laststep;
-    next_thermo = MYMIN(next_thermo,update->laststep);
+    next_thermo = MIN(next_thermo,update->laststep);
     modify->addstep_compute(next_thermo);
   }
 
   // next = next timestep any output will be done
 
-  next = MYMIN(next_dump_any,next_restart);
+  next = MIN(next_dump_any,next_restart);
-  next = MYMIN(next,next_thermo);
+  next = MIN(next,next_thermo);
 }
 
 /* ----------------------------------------------------------------------
@@ -369,7 +366,8 @@ void Output::add_dump(int narg, char **arg)
   // error checks
 
   for (int idump = 0; idump < ndump; idump++)
-    if (strcmp(arg[0],dump[idump]->id) == 0) error->all(FLERR,"Reuse of dump ID");
+    if (strcmp(arg[0],dump[idump]->id) == 0) 
+      error->all(FLERR,"Reuse of dump ID");
   int igroup = group->find(arg[1]);
   if (igroup == -1) error->all(FLERR,"Could not find dump group ID");
   if (atoi(arg[3]) <= 0) error->all(FLERR,"Invalid dump frequency");

src/procmap.cpp

@@ -41,7 +41,7 @@ ProcMap::ProcMap(LAMMPS *lmp) : Pointers(lmp) {}
 
 void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
 			    int otherflag, int other_style,
-			    int *other_procgrid)
+			    int *other_procgrid, int *other_coregrid)
 {
   int **factors;
 
@@ -56,7 +56,8 @@ void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
   if (domain->dimension == 2) npossible = cull_2d(npossible,factors,3);
   npossible = cull_user(npossible,factors,3,user_procgrid);
   if (otherflag) npossible = cull_other(npossible,factors,3,
-					other_style,other_procgrid);
+					other_style,other_procgrid,
+					other_coregrid);
 
   // user/other constraints make failure possible
 
@@ -79,7 +80,7 @@ void ProcMap::onelevel_grid(int nprocs, int *user_procgrid, int *procgrid,
 void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid,
 			    int ncores, int *user_coregrid, int *coregrid,
 			    int otherflag, int other_style, 
-			    int *other_procgrid)
+			    int *other_procgrid, int *other_coregrid)
 {
   int **nfactors,**cfactors,**factors;
 
@@ -116,7 +117,8 @@ void ProcMap::twolevel_grid(int nprocs, int *user_procgrid, int *procgrid,
 
   npossible = cull_user(npossible,factors,4,user_procgrid);
   if (otherflag) npossible = cull_other(npossible,factors,4,
-					other_style,other_procgrid);
+					other_style,other_procgrid,
+					other_coregrid);
 
   // user/other constraints make failure possible
 
@@ -796,19 +798,21 @@ int ProcMap::cull_user(int n, int **factors, int m, int *user_factors)
 
 /* ----------------------------------------------------------------------
    remove any factors that do not match settings from other partition
-   MULTIPLE = other Px,Py,Pz must be multiple of my Px,Py,Pz
+   MULTIPLE = other Nx,Ny,Nz must be multiple of my Px,Py,Pz
+              where Nx,Ny,Nz = node grid = procgrid/coregrid
 ------------------------------------------------------------------------- */
 
 int ProcMap::cull_other(int n, int **factors, int m, 
-			int other_style, int *other_grid)
+			int other_style, int *other_procgrid,
+			int *other_coregrid)
 {
   int i = 0;
   while (i < n) {
     if (other_style == MULTIPLE) {
       int flag = 0;
-      if (other_grid[0] % factors[i][0]) flag = 1;
+      if ((other_procgrid[0]/other_coregrid[0]) % factors[i][0]) flag = 1;
-      if (other_grid[1] % factors[i][1]) flag = 1;
+      if ((other_procgrid[1]/other_coregrid[1]) % factors[i][1]) flag = 1;
-      if (other_grid[2] % factors[i][2]) flag = 1;
+      if ((other_procgrid[2]/other_coregrid[2]) % factors[i][2]) flag = 1;
       if (flag) {
 	for (int j = 0; j < m; j++) factors[i][j] = factors[n-1][j];
 	n--;

src/procmap.h

@@ -22,8 +22,9 @@ class ProcMap : protected Pointers {
  public:
   ProcMap(class LAMMPS *);
   ~ProcMap() {}
-  void onelevel_grid(int, int *, int *, int, int, int *);
+  void onelevel_grid(int, int *, int *, int, int, int *, int *);
-  void twolevel_grid(int, int *, int *, int, int *, int *, int, int, int *);
+  void twolevel_grid(int, int *, int *, int, int *, int *, int, int, 
+		     int *, int *);
   void numa_grid(int, int *, int *, int *);
   void custom_grid(char *, int, int *, int *);
   void cart_map(int, int *, int *, int [3][2], int ***);
@@ -46,7 +47,7 @@ class ProcMap : protected Pointers {
   int combine_factors(int, int **, int, int **, int **);
   int cull_2d(int, int **, int);
   int cull_user(int, int **, int, int *);
-  int cull_other(int, int **, int, int, int *);
+  int cull_other(int, int **, int, int, int *, int *);
   int best_factors(int, int **, int *, int, int, int);
   void grid_shift(int, int, int &, int &);
 };