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/*
Copyright (C) 2008-2022 Michele Martone
This file is part of librsb.
librsb is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
librsb is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public
License along with librsb; see the file COPYING.
If not, see <http://www.gnu.org/licenses/>.
*/
/* @cond INNERDOC */
/*!
* @file
* @author Michele Martone
* @brief
* This source file contains parallel sorting functions.
* */
#include "rsb_common.h"
#define RSB_DO_WANT_PSORT_VERBOSE 0 /* set this to >0 to print parallel sort statistics */
#define RSB_DO_WANT_PSORT_TIMING (RSB_DO_WANT_PSORT_VERBOSE+0) /* set this to 1 to print some statistics */
#define RSB_DO_WANT_PSORT_FASTER_BUT_RISKY 0 /* FIXME: STILL UNFINISHED */
#define RSB_WANT_SORT_PARALLEL_BUT_SLOW 1
#define RSB_IS_ENOUGH_NNZ_FOR_PARALLEL_SORT(NNZ) ((NNZ)>=RSB__ENOUGH_NNZ_FOR_PARALLEL_SORT)
RSB_INTERNALS_COMMON_HEAD_DECLS
rsb_err_t rsb__util_sort_row_major_parallel(void *VA, rsb_coo_idx_t * IA, rsb_coo_idx_t * JA, rsb_nnz_idx_t nnz, rsb_coo_idx_t nr, rsb_coo_idx_t nc, rsb_type_t typecode, rsb_flags_t flags)
{
/**
* \ingroup gr_util
* TODO: should describe somewhere our technique: this is a mixed counting sort + merge sort.
*
* FIXME: it is known that very small matrices (e.g.: 2x2 from `make tests`) are not handled, here.
* require RSB_IS_ENOUGH_NNZ_FOR_PARALLEL_SORT(nnz).
*/
rsb_err_t errval = RSB_ERR_NO_ERROR;
int cfi;
const size_t el_size = RSB_SIZEOF(typecode);
const float cfa[] = {2}; // will use threads count as a reference
// const float cfa[] = {1}; // will use cache size as a reference
// const float cfa[] = {-1}; // will use as much memory as possible
const long wet = rsb_get_num_threads(); /* want executing threads */
if( nr > RSB_MAX_MATRIX_DIM || nc > RSB_MAX_MATRIX_DIM || nnz > RSB_MAX_MATRIX_NNZ )
{
errval = RSB_ERR_LIMITS;
RSB_PERR_GOTO(err,RSB_ERRM_ES);
}
if(!RSB_IS_ENOUGH_NNZ_FOR_PARALLEL_SORT(nnz))
{
//errval = RSB_ERR_BADARGS;
//RSB_PERR_GOTO(err,RSB_ERRM_ES);
return rsb__util_sort_row_major_inner(VA, IA, JA, nnz, nr, nc, typecode , flags);
}
if(!IA || !JA || !VA)
{
errval = RSB_ERR_BADARGS;
RSB_PERR_GOTO(err,RSB_ERRM_ES);
}
for(cfi=0;cfi<sizeof(cfa)/sizeof(float);++cfi)
{
void *W = NULL;
rsb_char_t *IW = NULL;
size_t ti;
long cs,tc,tcs;
rsb_nnz_idx_t cnnz = 0;
size_t bnnz = 0;
size_t wb = 0;
const size_t fsm = rsb__sys_free_system_memory();
const long ns=2*sizeof(rsb_coo_idx_t)+el_size;
const long bs=nnz*ns;
#if RSB_DO_WANT_PSORT_TIMING
rsb_time_t dt,st,mt,tt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
// compute how many bytes are necessary for an element
// compute how many bytes are necessary for the whole processing
if(cfa[cfi]>1)
tcs=bs+(wet*ns);
else if(cfa[cfi]>0)
tcs = rsb__get_lastlevel_c_size()*cfa[cfi]*wet;/* FIXME: '*wet' is a hack just for benchmark-related issues */
else
tcs=fsm/2; /* could be 0 */
if(tcs<1)
tcs=bs; /* could happen, for an interfacing problem */
else
if(fsm>0)
{
tcs = RSB_MIN(fsm,tcs);
}
// prepare a buffer
W = rsb__malloc(tcs);
cs=tcs/wet;
//RSB_INFO("cache is %d bytes\n",cs);
// compute nnz count fitting in the buffer
cnnz=cs/ns;
// compute total count of necessary passes
//tc=(bs+cs-1)/cs;
tc=(nnz+(cnnz-1))/(cnnz);
wb = RSB_DO_REQUIRE_BYTES_FOR_INDEX_BASED_SORT(cnnz,nr,nc,1,1);
IW = rsb__malloc(wb*wet);
if(!IW || !W)
{
errval = RSB_ERR_ENOMEM;
RSB_PERR_GOTO(erri,RSB_ERRM_ES);
}
//RSB_INFO("there are %d nnz (%d bytes), %d times the cache (%z bytes), %d nnz per cache\n",nnz,bs,tc,cs,cnnz);
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
st=-dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
// this phase is potentially parallel, and is the slower one.
// NOTE:before parallelization, one should avoid allocations during sort, or serialize in them in some way!
#pragma omp parallel for schedule(static,1) shared(IA,JA,VA) reduction(|:errval) RSB_NTC
for(ti=0;ti<tc;++ti)
{
const size_t fnnz=ti*cnnz;
const rsb_nnz_idx_t bnnz=(ti==tc-1)?(nnz-fnnz):cnnz;
// RSB_INFO("s:%d..%d (bnnz=%d)\n",fnnz,fnnz+bnnz-1,bnnz);
errval = rsb__util_sort_row_major_buffered(((rsb_byte_t*)VA)+el_size*fnnz,IA+fnnz,JA+fnnz,bnnz,nr,nc,typecode,flags,IW+wb*ti,wb);
//assert(!rsb__util_is_sorted_coo_as_row_major(IA+fnnz,JA+fnnz,bnnz,typecode,NULL,flags));
RSB_PS_ASSERT(!rsb__util_is_sorted_coo_as_row_major(IA+fnnz,JA+fnnz,bnnz,typecode,NULL,flags));
}
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
st+=dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
if(RSB_SOME_ERROR(errval))
{
RSB_PERR_GOTO(err,RSB_ERRM_ES)
}
// this phase is potentially parallel, too
for(bnnz=cnnz;bnnz<nnz;)
{
// size_t fnnz;
rsb_nnz_idx_t fi, fn = ((nnz-bnnz)+(2*bnnz-1))/(2*bnnz);
#pragma omp parallel for schedule(static,1) shared(IA,JA,VA) RSB_NTC
// for(fnnz=0;fnnz<nnz-bnnz;fnnz+=2*bnnz)
for(fi=0;fi<fn;++fi)
{
#if RSB_WANT_OMP_RECURSIVE_KERNELS
rsb_char_t * lW=((rsb_char_t*)W)+cs*omp_get_thread_num();
#else /* RSB_WANT_OMP_RECURSIVE_KERNELS */
rsb_char_t * lW=((rsb_char_t*)W)+cs*0;
#endif /* RSB_WANT_OMP_RECURSIVE_KERNELS */
const size_t fnnz=fi*2*bnnz;
const size_t lnnz=(fnnz+2*bnnz>nnz)?(nnz-(fnnz+bnnz)):bnnz;
void *fVA=RSB_VA_OFFSET_POINTER(VA,el_size,fnnz);
void *fIA=IA+fnnz;
void *fJA=JA+fnnz;
#if RSB_PS_ASSERT
void *bVA=RSB_VA_OFFSET_POINTER(VA,el_size,(fnnz+bnnz));
void *bIA=IA+fnnz+bnnz;
void *bJA=JA+fnnz+bnnz;
#endif /* RSB_PS_ASSERT */
//RSB_INFO("nr:%d..%d %d..%d (%d) (bnnz=%d) (lnnz=%d)\n",fnnz,fnnz+bnnz-1,fnnz+bnnz,fnnz+bnnz+lnnz-1,cs,bnnz,lnnz);
// RSB_INFO("sentinel:%x %d %d\n",IA+fnnz+bnnz+lnnz,IA[fnnz+bnnz+lnnz],JA[fnnz+bnnz+lnnz]);
RSB_PS_ASSERT(!rsb__util_is_sorted_coo_as_row_major(fIA,fJA,bnnz,typecode,NULL,flags));
RSB_PS_ASSERT(!rsb__util_is_sorted_coo_as_row_major(bIA,bJA,lnnz,typecode,NULL,flags));
rsb__do_util_merge_sorted_subarrays_in_place(fVA,fIA,fJA,lW,bnnz,lnnz,cs,flags,typecode);
// RSB_INFO("sentinel:%x %d %d\n",IA+fnnz+bnnz+lnnz,IA[fnnz+bnnz+lnnz],JA[fnnz+bnnz+lnnz]);
RSB_PS_ASSERT(!rsb__util_is_sorted_coo_as_row_major(fIA,fJA,bnnz,typecode,NULL,flags));
RSB_PS_ASSERT(!rsb__util_is_sorted_coo_as_row_major(fIA,fJA,bnnz+lnnz,typecode,NULL,flags));
}
#pragma omp barrier
bnnz *= 2;
}
#if RSB_DO_WANT_PSORT_TIMING
mt = - dt;
dt = rsb_time();
mt += dt;
tt = mt + st;
RSB_INFO("using %zd partitions, (sort=%.5lg+merge=%.5lg)=%.5lg, on %d threads\n",(size_t)tc,st,mt,tt,wet);
#endif /* RSB_DO_WANT_PSORT_TIMING */
// assert(!rsb__util_is_sorted_coo_as_row_major(IA,JA,nnz,typecode,NULL,flags));
// if(rsb__util_is_sorted_coo_as_row_major(IA,JA,nnz,typecode,NULL,flags))
// RSB_PERR_GOTO(err,RSB_ERRM_EM);
erri:
RSB_CONDITIONAL_FREE(W);
RSB_CONDITIONAL_FREE(IW);
}
err:
RSB_DO_ERR_RETURN(errval)
}
rsb_err_t rsb__util_sort_row_major_bucket_based_parallel(void * RSB_RESTRICT VA, rsb_coo_idx_t * RSB_RESTRICT IA, rsb_coo_idx_t * RSB_RESTRICT JA, const rsb_nnz_idx_t nnz, const rsb_coo_idx_t nr, const rsb_coo_idx_t nc, const rsb_type_t typecode , const rsb_flags_t flags /*, void * WA, size_t wb */)
{
/**
\ingroup gr_internals
Tolerate duplicates
So tolerate e.g. nr*nc<nnz, arising in sparse matrices' sum.
*/
rsb_nnz_idx_t psc = RSB_PSORT_CHUNK;
rsb_err_t errval = RSB_ERR_NO_ERROR;
rsb_nnz_idx_t mnzpr = 0;
rsb_nnz_idx_t *PA = NULL;
void *WA = NULL;
rsb_coo_idx_t *iWA = NULL;
rsb_coo_idx_t *jWA = NULL;
rsb_coo_idx_t *nWA = NULL;
void *vWA = NULL;
rsb_nnz_idx_t n = 0;
size_t el_size = RSB_SIZEOF(typecode);
//struct rsb_mtx_partitioning_info_t pinfop;
/* const long wet = rsb_get_num_threads();*/ /* want executing threads */
const long wet = rsb__set_num_threads(RSB_THREADS_GET_MAX_SYS); /* want executing threads; FIXME: it seems there is a severe bug with the definition of RSB_NTC */
#if RSB_DO_WANT_PSORT_TIMING
rsb_time_t dt,pt,st,mt,ct;
rsb_time_t tt = - rsb_time();
#endif /* RSB_DO_WANT_PSORT_TIMING */
const rsb_int_t ei = RSB_DO_FLAG_HAS(flags,RSB_FLAG_FORTRAN_INDICES_INTERFACE) ? 1 : 0;
/* Follows a workaround for possible overflows encountered when compiling with gcc versions through 11.2.0 and running
$ ./rsbench --limits-testing
A stand-alone reproducer for the bug:
// # gcc -Wall -Wextra -pedantic -fopenmp -std=c11 -O0 overflow.c
#include <stdlib.h> // abort
#include <limits.h> // INT_MAX
#include <omp.h> // compile with -fopenmp
int main ()
{
const int chunk_size = 1000;
const int n = INT_MAX - 100; // 2147483547
int l = 0;
#pragma omp parallel for schedule (static,chunk_size) num_threads (1)
for (int i = 0; i < n; ++i)
{
l = i;
if(i < 0)
abort ();
}
if ( l != n-1 )
abort ();
return 0;
}
The workaround consists of maximizing chunk size, and seems not necessary with clang-11.0.1 or icc-19.0.5.281.
More information about the bug on the gcc bug tracker [https://gcc.gnu.org/bugzilla/show_bug.cgi?id=102461] and
on the GNU Octave tracker [https://savannah.gnu.org/bugs/?60042].
*/
if(RSB_INVALID_COO_COUNT(psc+nr))
psc = RSB_MAX(1,( RSB_MAX_VALUE_FOR_TYPE(rsb_nnz_idx_t) - nr ) / wet);
if(wet==0)
{
/* see RSB_CHECK_LIB_INIT_CHECK */
errval = RSB_ERR_GENERIC_ERROR;
RSB_PERR_GOTO(ret,"%s\n","No threads detected! Are you sure to have initialized the library?\n"); /* RSB_ERRM_FLI */
}
if(RSB_MATRIX_UNSUPPORTED_TYPE(typecode))
{
errval = RSB_ERR_UNSUPPORTED_TYPE;
RSB_PERR_GOTO(ret,"\n");
}
if(nnz<2)
goto ret;
if( nr > RSB_MAX_MATRIX_DIM || nc > RSB_MAX_MATRIX_DIM || nnz > RSB_MAX_MATRIX_NNZ )
{
errval = RSB_ERR_LIMITS;
RSB_PERR_GOTO(ret,RSB_ERRM_ES);
}
if(RSB_MUL_OVERFLOW(sizeof(rsb_nnz_idx_t),(nr+2),size_t,rsb_non_overflowing_t)
|| RSB_MUL_OVERFLOW(sizeof(rsb_nnz_idx_t)*2+el_size,(nnz),size_t,rsb_non_overflowing_t))
{
errval = RSB_ERR_LIMITS;
RSB_PERR_GOTO(err,"sorry, allocating that much memory would cause overflows\n");
}
PA = rsb__calloc(sizeof(rsb_nnz_idx_t)*(nr+2));
// WA = rsb__calloc(RSB_MAX(sizeof(rsb_coo_idx_t),el_size)*(nnz+1));
// WA = rsb__calloc((2+3*sizeof(rsb_coo_idx_t)+el_size)*nnz);
// WA = rsb__calloc((2*sizeof(rsb_coo_idx_t)+el_size)*nnz);
WA = rsb__calloc_parallel((sizeof(rsb_coo_idx_t)*2+el_size)*nnz); // NEW 20101201
if(!PA || !WA)
{
errval = RSB_ERR_ENOMEM;
RSB_PERR_GOTO(err,"after calloc, pa=%p, wa=%p\n",PA,WA);
}
iWA=((rsb_coo_idx_t*) WA);
jWA=((rsb_coo_idx_t*)iWA)+nnz;
vWA=((rsb_coo_idx_t*)jWA)+nnz;
// nWA=((rsb_char_t*)vWA)+(el_size*nnz);
/* saving one head element with a trick */
++PA;
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
mt=-dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
#if RSB_DO_WANT_PSORT_FASTER_BUT_RISKY
# if 1
/* FIXME: unfinished and incorrect code */
#pragma omp parallel for schedule(static,psc) shared(PA,IA) RSB_NTC
for(n=0;n<nnz;++n)
PA[IA[n]+1-ei]++;
# else
/* actually, this code is VERY SLOW :) */
#pragma omp parallel reduction(|:errval) shared(PA,IA)
{
rsb_nnz_idx_t n;
rsb_thr_t th_id = omp_get_thread_num();
rsb_thr_t tn = omp_get_num_threads();
for(n=0;RSB_LIKELY(n<nnz);++n)
if(IA[n]%tn==th_id)
PA[IA[n]+1-ei]++;
}
#pragma omp barrier
#endif
#else /* RSB_DO_WANT_PSORT_FASTER_BUT_RISKY */
/* setting PA[i] to contain the count of elements on row i */
for(n=0;RSB_LIKELY(n<nnz);++n)
{
RSB_ASSERT(IA[n]>=0);
RSB_ASSERT(IA[n]<=nr);
PA[IA[n]+1-ei]++;
#if RSB_DO_WANT_PSORT_VERBOSE>1
RSB_INFO("PA[nr] = %d\n",PA[nr]);
RSB_INFO("IA[%d] = %d PA[%d] = %d\n",n,IA[n],IA[n]+1-ei,PA[IA[n]+1-ei]);
#endif /* RSB_DO_WANT_PSORT_VERBOSE */
}
#endif /* RSB_DO_WANT_PSORT_FASTER_BUT_RISKY */
/* setting PA[i] to contain the count of elements before row i */
for(n=0;RSB_LIKELY(n<nr);++n)
{
PA[n+1] += PA[n];
#if RSB_DO_WANT_PSORT_VERBOSE>1
RSB_INFO("PA[%d] = %d\n",n,PA[n]);
#endif /* RSB_DO_WANT_PSORT_VERBOSE */
}
#if RSB_DO_WANT_PSORT_VERBOSE>1
RSB_INFO("PA[%d] = %d\n",n,PA[n]);
#endif /* RSB_DO_WANT_PSORT_VERBOSE */
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
mt+=dt;
pt=-dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
/* shuffling elements on the basis of their row
* FIXME : this is the slowest part of this code
* its performance is largely dependent on cache lenghts and latencies.. */
/* FIXME : parallelization of this is challenging */
rsb__util_do_scatter_rows(vWA,iWA,jWA,VA,IA,JA,PA-ei,nnz,typecode);
--PA; /* PA has been modified. */
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
pt+=dt;
st=-dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
// RSB_COA_MEMCPY(IA,iWA,0,0,nnz);
// RSB_COA_MEMCPY(JA,jWA,0,0,nnz);
// RSB_A_MEMCPY(VA,vWA,0,0,nnz,el_size);
// SB_COA_MEMCPY_parallel(IA,iWA,0,0,nnz);
// RSB_COA_MEMCPY_parallel(JA,jWA,0,0,nnz);
// RSB_A_MEMCPY_parallel(VA,vWA,0,0,nnz,el_size);
/* restore the row pointers with a trick */
RSB_ASSERT(PA[nr+1-ei]==nnz);
/* TODO: parallelization of this ? FIXME: is this necessary ? */
for(n=0;n<nr;++n)
mnzpr = RSB_MAX(mnzpr,PA[n+1]-PA[n]);
nWA = rsb__malloc(sizeof(rsb_nnz_idx_t)*(mnzpr+2)*wet);/* rsb__malloc is evil inside openmp */
if(!nWA) { RSB_DO_ERROR_CUMULATE(errval,RSB_ERR_ENOMEM);RSB_PERR_GOTO(err,RSB_ERRM_ES); }
psc = RSB_MIN(psc,nr);
/* the rows are ready to be sorted (FIXME: this is slow, and could be optimized very much) */
// #pragma omp parallel for reduction(|:errval)
// #pragma omp parallel for
// #pragma omp parallel for schedule(static,10)
// #pragma omp parallel for schedule(static,1)
// #pragma omp parallel for schedule(static,psc) shared(iWA,jWA,vWA,nWA,PA) num_threads(wet)
#pragma omp parallel for schedule(static,psc) shared(iWA,jWA,vWA,nWA,PA) RSB_NTC
for(n=0;n<nr;++n)
{
rsb_nnz_idx_t nnz1,nnz0;
#if 1
#if RSB_WANT_OMP_RECURSIVE_KERNELS
rsb_thread_t th_id = omp_get_thread_num();
#else /* RSB_WANT_OMP_RECURSIVE_KERNELS */
rsb_thread_t th_id=0;
#endif /* RSB_WANT_OMP_RECURSIVE_KERNELS */
rsb_nnz_idx_t tnoff=th_id*(mnzpr+2);
nnz1=PA[n+1];
nnz0=PA[n];
#if RSB_DO_WANT_PSORT_VERBOSE
RSB_INFO("psort row %d/%d: nonzeros [%d .. %d/%d] on thread %d\n",(int)n,nr,(int)nnz0,(int)nnz1,(int)nnz,(int)th_id);
#endif /* RSB_DO_WANT_PSORT_VERBOSE */
if(nnz1-nnz0<2)
continue;/* skip empty line. TODO: could implement with macro sorting algorithms for few nnz */
if(!RSB_SOME_ERROR(rsb__do_msort_up(nnz1-nnz0,jWA+nnz0,nWA+tnoff)))
rsb__ip_reord(nnz1-nnz0,RSB_VA_OFFSET_POINTER(vWA,el_size,nnz0),iWA+nnz0,jWA+nnz0,nWA+tnoff,typecode);
#else
nnz1=PA[n+1];
nnz0=PA[n];
rsb__do_util_sortcoo(vWA+nnz0,iWA+nnz0,jWA+nnz0,nr,nc,nnz1-nnz0,typecode,NULL,flags,NULL,0);
#endif
}
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
st+=dt;
ct=-dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
RSB_COA_MEMCPY_parallel(IA,iWA,0,0,nnz);
RSB_COA_MEMCPY_parallel(JA,jWA,0,0,nnz);
RSB_A_MEMCPY_parallel(VA,vWA,0,0,nnz,el_size);
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
ct+=dt;
#endif /* RSB_DO_WANT_PSORT_TIMING */
err:
RSB_CONDITIONAL_FREE(PA);
RSB_CONDITIONAL_FREE(WA);
RSB_CONDITIONAL_FREE(nWA);
#if RSB_DO_WANT_PSORT_TIMING
dt = rsb_time();
tt+=dt;
RSB_INFO("tt:%lg pt:%lg st:%lg mt:%lg ct:%lg\n",tt,pt,st,mt,ct);
#endif /* RSB_DO_WANT_PSORT_TIMING */
ret:
RSB_DO_ERR_RETURN(errval)
}
rsb_err_t rsb__util_sort_row_major_inner(void * RSB_RESTRICT VA, rsb_coo_idx_t * RSB_RESTRICT IA, rsb_coo_idx_t * RSB_RESTRICT JA, const rsb_nnz_idx_t nnz, const rsb_coo_idx_t nr, const rsb_coo_idx_t nc, const rsb_type_t typecode , const rsb_flags_t flags /*, void * WA, size_t wb */)
{
rsb_err_t errval = RSB_ERR_NO_ERROR;
if( nr == 0 || nc == 0 )
goto ret;
#if RSB_WANT_SORT_PARALLEL_BUT_SLOW
if( rsb_global_session_handle.asm_sort_method > 0 && RSB_IS_ENOUGH_NNZ_FOR_PARALLEL_SORT(nnz) )
/* parallel and scaling but slow */
errval = rsb__util_sort_row_major_parallel(VA,IA,JA,nnz,nr,nc,typecode,flags);
else
#else /* RSB_WANT_SORT_PARALLEL_BUT_SLOW */
#endif /* RSB_WANT_SORT_PARALLEL_BUT_SLOW */
/* not so parallel nor scaling but fast */
errval = rsb__util_sort_row_major_bucket_based_parallel(VA,IA,JA,nnz,nr,nc,typecode,flags);
ret:
return errval;
}
/* @endcond */
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