prefetch_impl.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: prefetch_impl.cpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 19:23:32 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: prefetch_impl.cpp,v 1000.2 2004/06/01 19:23:32 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Author: Aleksey Grichenko, Eugene Vasilchenko
- *
- * File Description:
- * Prefetch implementation
- *
- */
- #include <ncbi_pch.hpp>
- #include <objmgr/impl/prefetch_impl.hpp>
- #include <corelib/ncbimtx.hpp>
- #include <objmgr/bioseq_handle.hpp>
- #include <objmgr/scope.hpp>
- #include <objmgr/impl/tse_info.hpp>
- #include <objmgr/impl/scope_impl.hpp>
- #include <objmgr/impl/data_source.hpp>
- #include <objmgr/seqmatch_info.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- // NOTE: Max. value for semaphore must be prefetch depth + 1, because
- // one extra-Post will be called when the token impl. is released.
- CPrefetchToken_Impl::CPrefetchToken_Impl(const TIds& ids, unsigned int depth)
- : m_TokenCount(0),
- m_TSESemaphore(depth, max(depth+1, depth)),
- m_Non_locking(false)
- {
- m_Ids = ids;
- }
- CPrefetchToken_Impl::~CPrefetchToken_Impl(void)
- {
- return;
- }
- void CPrefetchToken_Impl::x_InitPrefetch(CScope& scope)
- {
- m_TSEs.resize(m_Ids.size());
- m_CurrentId = 0;
- CRef<CDataSource> source(scope.GetImpl().GetFirstLoaderSource());
- if (!source) {
- return;
- }
- source->Prefetch(*this);
- }
- void CPrefetchToken_Impl::x_SetNon_locking(void)
- {
- m_Non_locking = true;
- }
- void CPrefetchToken_Impl::AddResolvedId(size_t id_idx, TTSE_Lock tse)
- {
- CFastMutexGuard guard(m_Lock);
- if ( m_Non_locking ) {
- m_TSESemaphore.Post();
- return;
- }
- if (m_Ids.empty() || id_idx < m_CurrentId) {
- // Token has been cleaned or id already passed, do not lock the TSE
- return;
- }
- m_TSEs[id_idx] = tse;
- int count = ++m_TSEMap[tse];
- if (count > 1) {
- // One more ID found in a prefetched TSE
- m_TSESemaphore.Post();
- }
- }
- bool CPrefetchToken_Impl::IsEmpty(void) const
- {
- CFastMutexGuard guard(m_Lock);
- return m_Ids.empty();
- }
- CPrefetchToken_Impl::operator bool(void) const
- {
- CFastMutexGuard guard(m_Lock);
- return m_CurrentId < m_Ids.size();
- }
- CBioseq_Handle CPrefetchToken_Impl::NextBioseqHandle(CScope& scope)
- {
- TTSE_Lock tse;
- CSeq_id_Handle id;
- {{
- CFastMutexGuard guard(m_Lock);
- // Can not call bool(*this) - creates deadlock
- _ASSERT(m_CurrentId < m_Ids.size());
- id = m_Ids[m_CurrentId];
- // Keep temporary TSE lock
- tse = m_TSEs[m_CurrentId];
- m_TSEs[m_CurrentId].Reset();
- ++m_CurrentId;
- if ( tse ) {
- TTSE_Map::iterator it = m_TSEMap.find(tse);
- if ( --(it->second) < 1 ) {
- m_TSEMap.erase(it);
- // Signal that next TSE or next token may be prefetched
- m_TSESemaphore.Post();
- }
- }
- }}
- return scope.GetBioseqHandle(id);
- }
- void CPrefetchToken_Impl::AddTokenReference(void)
- {
- ++m_TokenCount;
- }
- void CPrefetchToken_Impl::RemoveTokenReference(void)
- {
- if ( !(--m_TokenCount) ) {
- // No more tokens, reset the queue
- CFastMutexGuard guard(m_Lock);
- m_Ids.clear();
- m_TSEs.clear();
- m_CurrentId = 0;
- // Allow the thread to process next token
- m_TSESemaphore.Post();
- }
- }
- CPrefetchThread::CPrefetchThread(CDataSource& data_source)
- : m_DataSource(data_source),
- m_Stop(false)
- {
- return;
- }
- CPrefetchThread::~CPrefetchThread(void)
- {
- return;
- }
- void CPrefetchThread::AddRequest(CPrefetchToken_Impl& token)
- {
- {{
- CFastMutexGuard guard(m_Lock);
- m_Queue.Put(Ref(&token));
- }}
- }
- void CPrefetchThread::Terminate(void)
- {
- {{
- CFastMutexGuard guard(m_Lock);
- m_Stop = true;
- }}
- // Unlock the thread
- m_Queue.Put(CRef<CPrefetchToken_Impl>(0));
- }
- void* CPrefetchThread::Main(void)
- {
- do {
- CRef<CPrefetchToken_Impl> token = m_Queue.Get();
- {{
- CFastMutexGuard guard(m_Lock);
- if (m_Stop) {
- return 0;
- }
- _ASSERT( token );
- if ( token->IsEmpty() ) {
- // Token may have been canceled
- continue;
- }
- }}
- bool release_token = false;
- for (size_t i = 0; ; ++i) {
- {{
- CFastMutexGuard guard(m_Lock);
- if (m_Stop) {
- return 0;
- }
- }}
- CSeq_id_Handle id;
- token->m_TSESemaphore.Wait();
- {{
- // m_Ids may be cleaned up by the token, check size
- // on every iteration.
- CFastMutexGuard guard(token->m_Lock);
- i = max(i, token->m_CurrentId);
- if (i >= token->m_Ids.size()) {
- // Can not release token now - mutex is still locked
- release_token = true;
- break;
- }
- id = token->m_Ids[i];
- }}
- try {
- CSeqMatch_Info info = m_DataSource.BestResolve(id);
- if ( info ) {
- TTSE_Lock tse(&info.GetTSE_Info());
- if (tse) {
- token->AddResolvedId(i, tse);
- }
- }
- } catch (...) {
- // BestResolve() failed, go to the next id.
- }
- }
- if (release_token) {
- token.Reset();
- }
- } while (true);
- return 0;
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: prefetch_impl.cpp,v $
- * Revision 1000.2 2004/06/01 19:23:32 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- *
- * Revision 1.5 2004/05/21 21:42:12 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.4 2004/05/07 13:47:35 grichenk
- * Removed single-id constructors.
- * Added non-locking prefetch mode.
- *
- * Revision 1.3 2004/04/26 14:15:33 grichenk
- * Catch exceptions in the prefetching thread
- *
- * Revision 1.2 2004/04/19 14:52:29 grichenk
- * Added prefetch depth limit, redesigned prefetch queue.
- *
- * Revision 1.1 2004/04/16 13:30:34 grichenk
- * Initial revision
- *
- *
- * ===========================================================================
- */