From 12d52b65375e5dba5b63611e93082ec3a151f280 Mon Sep 17 00:00:00 2001
From: Stefan Eilemann <Stefan.Eilemann@epfl.ch>
Date: Fri, 3 Jun 2016 14:09:09 +0200
Subject: [PATCH 1/2] Cleanup

---
 brion/plugin/compartmentReportHDF5.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/brion/plugin/compartmentReportHDF5.cpp b/brion/plugin/compartmentReportHDF5.cpp
index 54166d9..a5cfac1 100644
--- a/brion/plugin/compartmentReportHDF5.cpp
+++ b/brion/plugin/compartmentReportHDF5.cpp
@@ -456,10 +456,9 @@ bool CompartmentReportHDF5::writeCompartments( const uint32_t gid,
         boost::scoped_array< float > mapping( new float[compCount] );
         size_t i = 0;
         for( size_t j = 0; j < counts.size(); ++j )
-        {
             for( size_t k = 0; k < counts[j]; ++k )
                 mapping[i++] = j;
-        }
+
         dataset.write( mapping.get(), H5::PredType::NATIVE_FLOAT );
         return true;
     }

From d98d3c2cdc252d5813e9a396ad2085ce4f6caac5 Mon Sep 17 00:00:00 2001
From: Stefan Eilemann <Stefan.Eilemann@epfl.ch>
Date: Mon, 13 Jun 2016 16:03:35 +0200
Subject: [PATCH 2/2] Implement (mem)cache for synapse files

---
 .gitsubprojects   |  8 ++++----
 brion/synapse.cpp | 45 +++++++++++++++++++++++++++++++++++++++++++--
 tests/synapse.cpp |  2 +-
 3 files changed, 48 insertions(+), 7 deletions(-)

diff --git a/.gitsubprojects b/.gitsubprojects
index 86088f6..d50f3ea 100644
--- a/.gitsubprojects
+++ b/.gitsubprojects
@@ -1,5 +1,5 @@
 # -*- mode: cmake -*-
-git_subproject(Servus https://github.com/HBPVIS/Servus.git 62873a5)
-git_subproject(Lunchbox https://github.com/Eyescale/Lunchbox.git b990d7f)
-git_subproject(vmmlib https://github.com/Eyescale/vmmlib.git f6fda2d)
-git_subproject(MVDTool https://github.com/BlueBrain/MVDTool.git f6af9a4)
+git_subproject(Servus https://github.com/HBPVIS/Servus.git 134b674)
+git_subproject(Lunchbox https://github.com/Eyescale/Lunchbox.git 440fded)
+git_subproject(vmmlib https://github.com/Eyescale/vmmlib.git 10d93e6)
+git_subproject(MVDTool https://github.com/BlueBrain/MVDTool.git 03d8138)
diff --git a/brion/synapse.cpp b/brion/synapse.cpp
index d563cd8..cd09a10 100644
--- a/brion/synapse.cpp
+++ b/brion/synapse.cpp
@@ -1,4 +1,6 @@
-/* Copyright (c) 2013-2015, EPFL/Blue Brain Project
+
+/* Copyright (c) 2013-2016, EPFL/Blue Brain Project
+ *                          bbp-open-source@googlegroups.com
  *                          Daniel Nachbaur <daniel.nachbaur@epfl.ch>
  *
  * This file is part of Brion <https://github.com/BlueBrain/Brion>
@@ -27,13 +29,21 @@
 #include <boost/lexical_cast.hpp>
 #include <boost/regex.hpp>
 #include <H5Cpp.h>
+#include <lunchbox/atomic.h>
 #include <lunchbox/log.h>
+#include <lunchbox/persistentMap.h>
 #include <lunchbox/scopedMutex.h>
 
+
 namespace brion
 {
 namespace detail
 {
+namespace
+{
+static lunchbox::a_ssize_t _cacheHits;
+static lunchbox::a_ssize_t _cacheMiss;
+}
 
 struct Dataset
 {
@@ -49,6 +59,8 @@ class SynapseFile : public boost::noncopyable
 {
 public:
     explicit SynapseFile( const std::string& source )
+        : _cache( lunchbox::PersistentMap::createCache( ))
+        , _cacheKey( fs::canonical( fs::path( source )).generic_string( ))
     {
         lunchbox::ScopedWrite mutex( detail::_hdf5Lock );
 
@@ -92,8 +104,32 @@ class SynapseFile : public boost::noncopyable
         if( !bits.any( ))
             return SynapseMatrix();
 
-        lunchbox::ScopedWrite mutex( detail::_hdf5Lock );
+        std::string cacheKey;
+        if( _cache )
+        {
+            cacheKey = _cacheKey + "/" + lexical_cast< std::string >( gid ) +
+                       "/" + lexical_cast< std::string >( attributes );
+            const std::string& cached = (*_cache)[ cacheKey ];
+            if( !cached.empty( ))
+            {
+                if( (++_cacheHits % 5000) == 0 )
+                    LBDEBUG << int( float( _cacheHits ) /
+                                    float( _cacheHits+_cacheMiss )*100.f + .5f )
+                            << "% cache hit rate" << std::endl;
+
+                const size_t dim0 = cached.size() / bits.count() /
+                                    sizeof( float );
+                SynapseMatrix values( boost::extents[ dim0 ][ bits.count( )]);
+                ::memcpy( values.data(), cached.data(), cached.size( ));
+                return values;
+            }
+            if( (++_cacheMiss % 5000) == 0 )
+                LBDEBUG << int( float( _cacheHits ) /
+                                float( _cacheHits + _cacheMiss ) * 100.f + .5f )
+                        << "% cache hit rate" << std::endl;
+        }
 
+        lunchbox::ScopedWrite mutex( detail::_hdf5Lock );
         Dataset dataset;
         if( !_openDataset( gid, dataset ))
             return SynapseMatrix();
@@ -116,6 +152,9 @@ class SynapseFile : public boost::noncopyable
 
         dataset.dataset.read( values.data(), H5::PredType::NATIVE_FLOAT,
                               targetspace, dataset.dataspace );
+        if( _cache )
+            _cache->insert( cacheKey, values.data(),
+                            dataset.dims[0] * bits.count() * sizeof( float ));
         return values;
     }
 
@@ -192,6 +231,8 @@ class SynapseFile : public boost::noncopyable
     }
 
 private:
+    lunchbox::PersistentMapPtr _cache;
+    std::string _cacheKey;
     H5::H5File _file;
     size_t _numAttributes;
 };
diff --git a/tests/synapse.cpp b/tests/synapse.cpp
index f2c8c8f..ed030ef 100644
--- a/tests/synapse.cpp
+++ b/tests/synapse.cpp
@@ -206,7 +206,7 @@ BOOST_AUTO_TEST_CASE( perf )
     const brion::Synapse synapseFile( path.string( ));
 
     brion::GIDSet gids;
-    for( uint32_t i = 1; i <= 1000; ++ i)
+    for( uint32_t i = 1; i <= 1000; ++i )
         gids.insert( i );
 
     namespace bp = boost::posix_time;