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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Utility macros for parallelism.
// ==========================================================================
#ifndef SEQAN_PARALLEL_PARALLEL_SPLITTING_H_
#define SEQAN_PARALLEL_PARALLEL_SPLITTING_H_
namespace seqan {
struct Equidistant_;
typedef Tag<Equidistant_> Equidistant;
/*!
* @class Splitter
* @headerfile <seqan/parallel.h>
* @brief Splits an interval into subintervals.
*
* @signature template <typename TValue, typename TSpec>
* class Splitter;
*
* @tparam TValue Type of the interval boundaries.
* @tparam TSpec Tag to select the way the values are sampled.
*
* This class divides an interval into the disjoint union of subintervals and enumerates its boundaries. It can be used
* to parallelize large for-loops that iterate over a contiguous range of elements. The interval and the number of
* subintervals can be set in the constructor @link Splitter::Splitter @endlink. @link Splitter#length @endlink and
* @link Splitter#resize @endlink can be used to retrieve or change the number of subintervals later. In contrast to
* other containers the Splitter allows one to access one more element than its length would imply to allow to retrieve the
* right boundary of each subinterval (see example code below).
*
* @section Examples
*
* Simple example for equidistant (default) splitting.
*
* @include demos/dox/parallel/splitter_example.cpp
*
* The output is:
*
* @include demos/dox/parallel/splitter_example.cpp.stdout
*/
/*!
* @fn Splitter::Splitter
* @brief Constructor
*
* @signature Splitter::Splitter(beginPos, endPos[, subintervalCount]);
* @signature Splitter::Splitter(beginPos, endPos, parallelTag);
*
* @param[in] beginPos Left interval boundary.
* @param[in] endPos Right interval boundary.
* @param[in] subintervalCount Number of subintervals. @link Splitter#length @endlink and @link Splitter#resize
* @endlink can be used to retrieve or change the number of subintervals later.
* Default: The minimum of interval size and the number of available threads (returned by
* <tt>omp_get_max_threads()</tt>).
* @param[in] parallelTag Tag to generically enable/disable parallelism. If its type is <tt>Parallel</tt>, the
* default number of subintervals is used. If it is <tt>Serial</tt>, only one subinterval
* is used. This tag should be used to write generic parallel algorithms and to switch
* between parallel and serial variants.
*/
/*!
* @class Equidistant Splitter
* @extends Splitter
* @headerfile <seqan/parallel.h>
* @brief Splits an interval into equal-sized subintervals.
*
* @signature template <typename TValue>
* class Splitter<TValue, Equidistant>;
*
* @tparam TValue Type of the interval boundaries.
*
* This @link Splitter @endlink specialization divides an interval into subintervals of (almost) equal length, i.e. two
* subintervals differ by at most 1 in size.
*
* @section Examples
*
* Simple example for equidistant splitting.
*
* @include demos/dox/parallel/splitter_example.cpp
*
* Output:
*
* @code
* [10,14)
* [14,17)
* [17,20)
* @endcode
*/
template <typename TValue, typename TSpec = Equidistant>
class Splitter
{
public:
typedef typename Size<Splitter>::Type TSize;
TValue beginPos;
TSize subintervalCount;
TSize blockLength;
TSize rest;
Splitter(TValue beginPos_, TValue endPos):
beginPos(beginPos_)
{
// we choose the counts automatically and don't want to have empty jobs
_resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads()));
}
Splitter(TValue beginPos_, TValue endPos, Parallel):
beginPos(beginPos_)
{
// we choose the counts automatically and don't want to have empty jobs
_resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads()));
}
Splitter(TValue beginPos_, TValue endPos, Serial):
beginPos(beginPos_)
{
// we produce at most 1 job (or none if interval is empty)
_resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1));
}
Splitter(TValue beginPos_, TValue endPos, TSize subintervalCount):
beginPos(beginPos_)
{
_resize(*this, endPos - beginPos, subintervalCount);
}
TValue operator[] (TSize i) const
{
SEQAN_ASSERT_LEQ_MSG(i, subintervalCount, "Trying to access an element behind the last one!");
return beginPos + blockLength * i + std::min(i, rest);
}
};
/*!
* @mfn Splitter#Size
* @brief Returns the size type for the Splitter.
*
* @signature Size<TSplitter>::Type;
*
* @tparam TSplitter The Splitter to query for its size type.
*/
template <typename TValue, typename TSpec>
struct Size<Splitter<TValue, TSpec> >
{
typedef typename MakeUnsigned<typename Difference<TValue>::Type>::Type Type;
};
/*!
* @mfn Splitter#Value
* @brief Returns the value type for the Splitter.
*
* @signature Value<TSplitter>::Type;
*
* @tparam TSplitter The Splitter to query for its value type.
*/
template <typename TValue, typename TSpec>
struct Value<Splitter<TValue, TSpec> >
{
typedef TValue Type;
};
/*!
* @fn Splitter#length
* @brief Return the number of elements in the splitter.
*
* @signature TSize length(splitter);
*
* @param[in] splitter The Splitter object to query.
*
* @return TSize The number of elements in the Splitter, <tt>TSize</tt> is the size type.
*/
template <typename TValue, typename TSpec>
inline typename Size<Splitter<TValue, TSpec> >::Type
length(Splitter<TValue, TSpec> const &splitter)
{
return splitter.subintervalCount;
}
/*!
* @fn Splitter#resize
* @brief Change the number of elements in the splitter.
*
* @signature void resize(splitter, newCount);
*
* @param[out] splitter The Splitter object to update.
* @param[in] newCount The updated number of elements in the splitter.
*/
template <typename TValue, typename TSpec, typename TSize1, typename TSize2>
inline void
_resize(Splitter<TValue, TSpec> &splitter, TSize1 intervalLen, TSize2 newCount)
{
if (newCount != 0)
{
splitter.blockLength = intervalLen / newCount;
splitter.rest = intervalLen % newCount;
}
else
{
splitter.blockLength = 0;
splitter.rest = intervalLen;
}
splitter.subintervalCount = newCount;
}
template <typename TValue, typename TSpec, typename TSize>
inline typename Size<Splitter<TValue, TSpec> >::Type
resize(Splitter<TValue, TSpec> &splitter, TSize newCount)
{
_resize(splitter, splitter.blockLength * splitter.subintervalCount + splitter.rest, newCount);
return newCount;
}
// --------------------------------------------------------------------------
// Function computeSplitters()
// --------------------------------------------------------------------------
/*!
* @fn computeSplitters
* @headerfile <seqan/parallel.h>
* @brief Compute splitters for a sequence of objects.
*
* @signature void computeSplitters(splitters, size, count);
*
* @param[out] splitters Resulting splitters, will be resized to contain <tt>count + 1</tt> elements, e.g. an
* @link AllocString @endlink of integers.
* @param[in] size The number of objects to split.
* @param[in] count The number of chunks.
*
* @section Remarks
*
* The first <tt>count - 1</tt> chunks will have the size <tt>ceil(size / count)</tt>, the last chunk will contain the
* rest.
*
* @section Examples
*
* Most simple case for splitting.
*
* @code{.cpp}
* String<unsigned> splitters;
* computeSplitters(splitters, 10, 5);
* // splitters == {0, 5, 10}
* @endcode
*
* In this case, the last chunks will stay empty.
*
* @code{.cpp}
* computeSplitters(splitters, 3, 5);
* // splitters == {0, 1, 2, 3, 3, 3}
* @endcode
*/
template <typename TPosString, typename TSize, typename TCount>
void computeSplitters(TPosString & splitters, TSize size, TCount count)
{
typedef typename Value<TPosString>::Type TPos;
SEQAN_ASSERT_GEQ(count, (TCount)0);
resize(splitters, count + 1);
TSize blockLength = (size / count) + 1;
TCount rest = size % count;
TPos pos = 0;
TCount i = 0;
// the first (size % count) many blocks have length (size / count) + 1
for (; i < rest; ++i, pos += blockLength)
splitters[i] = pos;
// the remaining blocks have length (size / count)
--blockLength;
for (; i <= count; ++i, pos += blockLength)
splitters[i] = pos;
SEQAN_ASSERT_EQ(back(splitters), static_cast<TPos>(size));
}
} // namespace seqan
#endif // SEQAN_PARALLEL_PARALLEL_SPLITTING_H_
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