Commit 1f17e8eb authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

remove need for static class member variables in Dump and Irregular 

The dump and irregular classes were using qsort() from the C-library
for sorting lists through custom comparison functions, which required
access to additional data, which was passed via static class variables,
i.e. globals. This collides with having multiple LAMMPS instances in
the same address space.

the calls to qsort() are replaced with a custom merge sort, which passes
a void pointer to the comparison functions, which can contain any kind
of desired information, e.g. a class handle or a list
parent 286d4f27

src/dump.cpp

+35 −48
Original line number Diff line number Diff line
@@ -30,9 +30,7 @@ 


using namespace LAMMPS_NS;



// allocate space for static class variable



Dump *Dump::dumpptr;

#include "mergesort.h"



#define BIG 1.0e20

#define EPSILON 1.0e-6
@@ -690,11 +688,10 @@ void Dump::sort() 
  }



  if (!reorderflag) {

    dumpptr = this;

    for (i = 0; i < nme; i++) index[i] = i;

    if (sortcol == 0) qsort(index,nme,sizeof(int),idcompare);

    else if (sortorder == ASCEND) qsort(index,nme,sizeof(int),bufcompare);

    else qsort(index,nme,sizeof(int),bufcompare_reverse);

    if (sortcol==0) merge_sort(index,nme,(void *)this,idcompare);

    else if (sortorder==ASCEND) merge_sort(index,nme,(void *)this,bufcompare);

    else merge_sort(index,nme,(void *)this,bufcompare_reverse);

  }



  // reset buf size and maxbuf to largest of any post-sort nme values
@@ -718,62 +715,52 @@ void Dump::sort() 


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

   compare two atom IDs

   called via qsort() in sort() method

   is a static method so access data via dumpptr

   called via merge_sort() in sort() method

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



int Dump::idcompare(const void *pi, const void *pj)

{

  tagint *idsort = dumpptr->idsort;



  int i = *((int *) pi);

  int j = *((int *) pj);



int Dump::idcompare(const int i, const int j, void *ptr) {

  tagint *idsort = ((Dump *)ptr)->idsort;

  if (idsort[i] < idsort[j]) return -1;

  if (idsort[i] > idsort[j]) return 1;

  return 0;

  else if (idsort[i] > idsort[j]) return 1;

  else return 0;

}



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

   compare two buffer values with size_one stride

   called via qsort() in sort() method

   is a static method so access data via dumpptr

   called via merge_sort() in sort() method

   sort in ASCENDing order

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



int Dump::bufcompare(const void *pi, const void *pj)

{

  double *bufsort = dumpptr->bufsort;

  int size_one = dumpptr->size_one;

  int sortcolm1 = dumpptr->sortcolm1;

int Dump::bufcompare(const int i, const int j, void *ptr) {

  Dump *dptr = (Dump *) ptr;

  double *bufsort     = dptr->bufsort;

  const int size_one  = dptr->size_one;

  const int sortcolm1 = dptr->sortcolm1;



  int i = *((int *) pi)*size_one + sortcolm1;

  int j = *((int *) pj)*size_one + sortcolm1;

  const int ii=i*size_one + sortcolm1;

  const int jj=j*size_one + sortcolm1;

        

  if (bufsort[i] < bufsort[j]) return -1;

  if (bufsort[i] > bufsort[j]) return 1;

  return 0;

  if (bufsort[ii] < bufsort[jj]) return -1;

  else if (bufsort[ii] > bufsort[jj]) return 1;

  else return 0;

}



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

   compare two buffer values with size_one stride

   called via qsort() in sort() method

   is a static method so access data via dumpptr

   called via merge_sort() in sort() method

   sort in DESCENDing order

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



int Dump::bufcompare_reverse(const void *pi, const void *pj)

{

  double *bufsort = dumpptr->bufsort;

  int size_one = dumpptr->size_one;

  int sortcolm1 = dumpptr->sortcolm1;

int Dump::bufcompare_reverse(const int i, const int j, void *ptr) {

  Dump *dptr = (Dump *) ptr;

  double *bufsort     = dptr->bufsort;

  const int size_one  = dptr->size_one;

  const int sortcolm1 = dptr->sortcolm1;



  int i = *((int *) pi)*size_one + sortcolm1;

  int j = *((int *) pj)*size_one + sortcolm1;

  const int ii=i*size_one + sortcolm1;

  const int jj=j*size_one + sortcolm1;

        

  if (bufsort[i] > bufsort[j]) return -1;

  if (bufsort[i] < bufsort[j]) return 1;

  return 0;

  if (bufsort[ii] < bufsort[jj]) return 1;

  else if (bufsort[ii] > bufsort[jj]) return -1;

  else return 0;

}



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

src/dump.h

+3 −7
Original line number Diff line number Diff line
@@ -33,10 +33,6 @@ class Dump : protected Pointers { 
  int comm_forward;          // size of forward communication (0 if none)

  int comm_reverse;          // size of reverse communication (0 if none)



  // static variable across all Dump objects



  static Dump *dumpptr;         // holds a ptr to Dump currently being used



  Dump(class LAMMPS *, int, char **);

  virtual ~Dump();

  void init();
@@ -134,9 +130,9 @@ class Dump : protected Pointers { 
  void pbc_allocate();

    

  void sort();

  static int idcompare(const void *, const void *);

  static int bufcompare(const void *, const void *);

  static int bufcompare_reverse(const void *, const void *);

  static int idcompare(const int, const int, void *);

  static int bufcompare(const int, const int, void *);

  static int bufcompare_reverse(const int, const int, void *);

};



}

src/irregular.cpp

+9 −13
Original line number Diff line number Diff line
@@ -21,13 +21,13 @@ 
#include "comm.h"

#include "memory.h"



#include "mergesort.h"



using namespace LAMMPS_NS;



// allocate space for static class variable

// prototype for non-class function



int *Irregular::proc_recv_copy;

int compare_standalone(const void *, const void *);

static int compare_standalone(const int, const int, void *);



enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};    // several files
@@ -423,8 +423,7 @@ int Irregular::create_atom(int n, int *sizes, int *proclist, int sortflag) 
    int *length_recv_ordered = new int[nrecv_proc];



    for (i = 0; i < nrecv_proc; i++) order[i] = i;

    proc_recv_copy = proc_recv;

    qsort(order,nrecv_proc,sizeof(int),compare_standalone);

    merge_sort(order,nrecv_proc,(void *)proc_recv,compare_standalone);



    int j;

    for (i = 0; i < nrecv_proc; i++) {
@@ -451,15 +450,13 @@ int Irregular::create_atom(int n, int *sizes, int *proclist, int sortflag) 
}



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

   comparison function invoked by qsort()

   accesses static class member proc_recv_copy, set before call to qsort()

   comparison function invoked by merge_sort()

   void pointer contains proc_recv list;

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



int compare_standalone(const void *iptr, const void *jptr)

int compare_standalone(const int i, const int j, void *ptr)

{

  int i = *((int *) iptr);

  int j = *((int *) jptr);

  int *proc_recv = Irregular::proc_recv_copy;

  int *proc_recv = (int *) ptr;

  if (proc_recv[i] < proc_recv[j]) return -1;

  if (proc_recv[i] > proc_recv[j]) return 1;

  return 0;
@@ -671,8 +668,7 @@ int Irregular::create_data(int n, int *proclist, int sortflag) 
    int *num_recv_ordered = new int[nrecv_proc];



    for (i = 0; i < nrecv_proc; i++) order[i] = i;

    proc_recv_copy = proc_recv;

    qsort(order,nrecv_proc,sizeof(int),compare_standalone);

    merge_sort(order,nrecv_proc,(void *)proc_recv,compare_standalone);



    int j;

    for (i = 0; i < nrecv_proc; i++) {

src/irregular.h

+0 −4
Original line number Diff line number Diff line
@@ -21,10 +21,6 @@ namespace LAMMPS_NS { 
class Irregular : protected Pointers {

 public:



  // static variable across all Irregular objects, for qsort callback



  static int *proc_recv_copy;



  Irregular(class LAMMPS *);

  ~Irregular();

  void migrate_atoms(int sortflag = 0, int preassign = 0,

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