@@ -172,7 +172,6 @@ void AtomicDomain::cacheErase(uint64_t pos) const

     mEraseCache[ndx] = pos;

 }

-// TODO prevent re-allocations

 void AtomicDomain::resetCache(unsigned n)

 {

     mInsertCacheIndex = 0;

@@ -64,7 +64,6 @@ private:

     std::vector<Atom> mAtoms;

     std::map<uint64_t, uint64_t> mAtomPositions;

-    // TODO google_dense_set - first profile and benchmark

     boost::unordered_set<uint64_t> mUsedPositions;

     mutable std::vector<RawAtom> mInsertCache;

@@ -50,7 +50,8 @@ mStatistics(D.nrow(), D.ncol(), nFactor)

 Rcpp::List GapsRunner::run()

 {

     // reset the checkpoint timer

-    mLastCheckpoint = bpt_now();

+    mStartTime = bpt_now();

+    mLastCheckpoint = mStartTime;

     // cascade down the various phases of the algorithm

     // this allows for starting in the middle of the algorithm

@@ -162,6 +163,27 @@ void GapsRunner::displayStatus(const std::string &type, unsigned nIterTotal)

         Rprintf("%s %d of %d, Atoms:%lu(%lu) Chi2 = %.2f\n", type.c_str(),

             mCurrentIter + 1, nIterTotal, mASampler.nAtoms(),

             mPSampler.nAtoms(), mASampler.chi2());

+        bpt::time_duration diff = bpt_now() - mStartTime;

+        double elapsed = diff.total_milliseconds() / 1000.0;

+        Rprintf("Elapsed Time: %.3f seconds\n", elapsed);

+

+        double prop = 0.0;

+        switch (mPhase)

+        {

+            case GAPS_BURN:

+                prop = mCurrentIter;

+                break;

+            case GAPS_COOL:

+                prop = mEquilIter + mCurrentIter;

+                break;

+            case GAPS_SAMP:

+                prop = mEquilIter + mCoolIter + mCurrentIter;

+                break;

+        }   

+        prop = (double)(mEquilIter + mCoolIter + mSampleIter) / prop;

+        double est = diff.total_milliseconds() * prop / 1000.0;

+        Rprintf("Estimated Total Time: %.3f seconds\n", est);

+        Rprintf("Estimated Remaining Time: %.3f seconds\n", est - elapsed);        

     }

 }

@@ -2,7 +2,7 @@

 #define __COGAPS_GAPS_RUNNER_H__

 #include "Archive.h"

-#include "math/Matrix.h"

+#include "data_structures/Matrix.h"

 #include "GibbsSampler.h"

 #include "GapsStatistics.h"

@@ -65,6 +65,8 @@ public:

     unsigned mNumCores;

+    bpt::ptime mStartTime;

+

     void createCheckpoint();

     void makeCheckpointIfNeeded();

     void displayStatus(const std::string &type, unsigned nIterTotal);

@@ -2,7 +2,7 @@

 #define __COGAPS_GAPS_STATISTICS_H__

 #include "GibbsSampler.h"

-#include "math/Matrix.h"

+#include "data_structures/Matrix.h"

 class GapsStatistics

 {

@@ -3,7 +3,7 @@

 #include "GapsAssert.h"

 #include "Archive.h"

-#include "math/Matrix.h"

+#include "data_structures/Matrix.h"

 #include "math/Random.h"

 #include "math/Algorithms.h"

 #include "ProposalQueue.h"

@@ -8,7 +8,7 @@ OBJECTS =   AtomicDomain.o \

             RcppExports.o \

             test-runner.o \

             math/Algorithms.o \

-            math/Matrix.o \

+            data_structures/Matrix.o \

             math/Random.o \

             cpp_tests/testAlgorithms.o \

             cpp_tests/testAtomicDomain.o \

@@ -2,8 +2,6 @@

 #include "ProposalQueue.h"

 #include "math/Random.h"

-// TODO invalidate 

-

 void ProposalQueue::setNumBins(unsigned nBins)

 {

     mNumBins = nBins;

@@ -3,7 +3,7 @@

 #include "Archive.h"

 #include "AtomicDomain.h"

-#include "data_structures/FixedHashSet.h"

+#include "data_structures/EfficientSets.h"

 #include <boost/unordered_set.hpp>

 #include <stdint.h>

@@ -1,5 +1,5 @@

 #include "catch.h"

-#include "../math/Matrix.h"

+#include "../data_structures/Matrix.h"

 #include "../math/Algorithms.h"

 #define MAT_SUM(nR, nC) ((nR + nC - 2) * nR * nC / 2.f)

@@ -1,5 +1,5 @@

 #include "catch.h"

-#include "../math/Matrix.h"

+#include "../data_structures/Matrix.h"

 TEST_CASE("Test Matrix.h")

 {

similarity index 83%

rename from src/data_structures/FixedHashSet.h

rename to src/data_structures/EfficientSets.h

@@ -1,5 +1,5 @@

-#ifndef __COGAPS_FIXED_HASH_SET__

-#define __COGAPS_FIXED_HASH_SET__

+#ifndef __COGAPS_EFFICIENT_SETS_H__

+#define __COGAPS_EFFICIENT_SETS_H__

 #include <stdint.h>

@@ -20,7 +20,7 @@ public:

     void insert(uint64_t n) {mSet[n] = mCurrentKey;}

 };

-// have vector with at least some % of holes

+// have sorted vector with at least some % of holes

 // even distribute entries along it

 // when shift happens, should be minimal

similarity index 100%

rename from src/math/Matrix.cpp

rename to src/data_structures/Matrix.cpp

similarity index 100%

rename from src/math/Matrix.h

rename to src/data_structures/Matrix.h

@@ -1,5 +1,5 @@

 #include "Algorithms.h"

-#include "Matrix.h"

+#include "../data_structures/Matrix.h"

 #include "SIMD.h"

 #include <algorithm>

@@ -1,7 +1,7 @@

 #ifndef __COGAPS_ALGORITHMS_H__

 #define __COGAPS_ALGORITHMS_H__

-#include "Matrix.h"

+#include "../data_structures/Matrix.h"

 #define GAPS_SQ(x) ((x) * (x))