finish mushroom example

.gitignore

@@ -46,3 +46,6 @@ Debug
 *csv
 *.cpage.col
 *.cpage
+xgboost
+xgboost-mpi
+train*

Makefile

@@ -30,9 +30,9 @@ io.o: src/io/io.cpp src/io/*.hpp src/utils/*.h src/learner/dmatrix.h src/*.h
 sync_mpi.o: src/sync/sync_mpi.cpp 
 sync_empty.o: src/sync/sync_empty.cpp 
 main.o: src/xgboost_main.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h 
-xgboost:  updater.o gbm.o io.o main.o sync_empty.o
 xgboost-mpi:  updater.o gbm.o io.o main.o sync_mpi.o 
-wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h $(OBJ)
+xgboost:  updater.o gbm.o io.o main.o sync_empty.o
+wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp src/utils/*.h src/*.h src/learner/*.hpp src/learner/*.h  updater.o gbm.o io.o sync_empty.o
 
 $(BIN) : 
 	$(CXX) $(CFLAGS) $(LDFLAGS) -o $@ $(filter %.cpp %.o %.c, $^)

demo/mpi/README.md

@@ -0,0 +1,3 @@
+This folder contains toy example script to run xgboost-mpi. 
+
+This is an experimental distributed version of xgboost

demo/mpi/mpi.conf

@@ -0,0 +1,36 @@
+# General Parameters, see comment for each definition
+# choose the booster, can be gbtree or gblinear
+booster = gbtree
+# choose logistic regression loss function for binary classification
+objective = binary:logistic
+
+# Tree Booster Parameters
+# step size shrinkage
+eta = 1.0 
+# minimum loss reduction required to make a further partition
+gamma = 1.0 
+# minimum sum of instance weight(hessian) needed in a child
+min_child_weight = 1 
+# maximum depth of a tree
+max_depth = 3 
+
+# Task Parameters
+# the number of round to do boosting
+num_round = 2
+# 0 means do not save any model except the final round model
+save_period = 0 
+use_buffer = 0
+
+
+# The path of training data %d is the wildcard for the rank of the data
+# The idea is each process take a feature matrix with subset of columns
+#
+data = "train.col%d" 
+
+# The path of validation data, used to monitor training process, here [test] sets name of the validation set
+eval[test] = "../data/agaricus.txt.test" 
+# evaluate on training data as well each round
+eval_train = 1
+
+# The path of test data, need to use full data of test, try not use it, or keep an subsampled version
+test:data = "agaricus.txt.test"      

demo/mpi/runexp-mpi.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+if [[ $# -ne 1 ]]
+then
+    echo "Usage: nprocess"
+    exit -1
+fi
+
+rm -rf train.col*
+k=$1
+
+# split the lib svm file into k subfiles
+python splitsvm.py ../data/agaricus.txt.train train $k
+
+# run xgboost mpi
+mpirun -n $k ../../xgboost-mpi  mpi.conf 
+
+# the model can be directly loaded by single machine xgboost solver, as usuall
+../../xgboost mpi.conf task=dump model_in=0002.model fmap=../data/featmap.txt name_dump=dump.nice.$k.txt
+cat dump.nice.$k.txt

demo/mpi/splitsvm.py

@@ -0,0 +1,32 @@
+#!/usr/bin/python
+import sys
+import random
+
+# split libsvm file into different subcolumns
+if len(sys.argv) < 4:
+    print ('Usage:<fin> <fo> k')
+    exit(0)
+
+random.seed(10)
+fmap = {}
+
+k = int(sys.argv[3])
+fi = open( sys.argv[1], 'r' )
+fos = []
+
+for i in range(k):
+    fos.append(open( sys.argv[2]+'.col%d' % i, 'w' ))
+    
+for l in open(sys.argv[1]):
+    arr = l.split()
+    for f in fos:
+        f.write(arr[0])
+    for it in arr[1:]:
+        fid = int(it.split(':')[0])
+        if fid not in fmap:
+            fmap[fid] = random.randint(0, k-1)
+        fos[fmap[fid]].write(' '+it)
+    for f in fos:
+        f.write('\n')
+for f in fos:    
+    f.close()

src/learner/learner-inl.hpp

@@ -10,6 +10,7 @@
 #include <utility>
 #include <string>
 #include <limits>
+#include "../sync/sync.h"
 #include "./objective.h"
 #include "./evaluation.h"
 #include "../gbm/gbm.h"
@@ -61,6 +62,7 @@ class BoostLearner {
       buffer_size += mats[i]->info.num_row();
       num_feature = std::max(num_feature, static_cast<unsigned>(mats[i]->info.num_col()));
     }
+    sync::AllReduce(&num_feature, 1, sync::kMax);
     char str_temp[25];
     if (num_feature > mparam.num_feature) {
       utils::SPrintf(str_temp, sizeof(str_temp), "%u", num_feature);

src/sync/sync.h

@@ -15,11 +15,16 @@ namespace sync {
 /*! \brief reduce operator supported */
 enum ReduceOp {
   kSum,
+  kMax,
   kBitwiseOR
 };
 
 /*! \brief get rank of current process */
 int GetRank(void);
+/*! 
+ * \brief this is used to check if sync module is a true distributed implementation, or simply a dummpy
+ */
+bool IsDistributed(void);
 /*! \brief intiialize the synchronization module */
 void Init(int argc, char *argv[]);
 /*! \brief finalize syncrhonization module */

src/sync/sync_empty.cpp

@@ -6,18 +6,28 @@ namespace sync {
 int GetRank(void) {
   return 0;
 }
+
 void Init(int argc, char *argv[]) {
 }
+
 void Finalize(void) {
 }
+
+bool IsDistributed(void) {
+  return false;
+}
+
 template<>
 void AllReduce<uint32_t>(uint32_t *sendrecvbuf, int count, ReduceOp op) {
 }
+
 template<>
 void AllReduce<float>(float *sendrecvbuf, int count, ReduceOp op) {
 }
+
 void Bcast(std::string *sendrecv_data, int root) {
 }
+
 ReduceHandle::ReduceHandle(void) : handle(NULL) {}
 ReduceHandle::~ReduceHandle(void) {}
 void ReduceHandle::Init(ReduceFunction redfunc, bool commute) {}

src/sync/sync_mpi.cpp

@@ -12,6 +12,10 @@ void Init(int argc, char *argv[]) {
   MPI::Init(argc, argv);
 }
 
+bool IsDistributed(void) {
+  return true;
+}
+
 void Finalize(void) {
   MPI::Finalize();
 }
@@ -20,6 +24,7 @@ void AllReduce_(void *sendrecvbuf, int count, const MPI::Datatype &dtype, Reduce
   switch(op) {
     case kBitwiseOR: MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE, sendrecvbuf, count, dtype, MPI::BOR); return;
     case kSum: MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE, sendrecvbuf, count, dtype, MPI::SUM); return;
+    case kMax: MPI::COMM_WORLD.Allreduce(MPI_IN_PLACE, sendrecvbuf, count, dtype, MPI::MAX); return;
   }
 }
 

src/tree/updater_distcol-inl.hpp

@@ -93,9 +93,15 @@ class DistColMaker : public ColMaker<TStats> {
       while (fsplits.size() != 0 && fsplits.back() >= p_fmat->NumCol()) {
         fsplits.pop_back();
       }
-      // setup BitMap
+      // bitmap is only word concurrent, set to bool first
-      bitmap.Resize(this->position.size());
+      {
-      bitmap.Clear();
+        bst_omp_uint ndata = static_cast<bst_omp_uint>(this->position.size());
+        boolmap.resize(ndata);
+        #pragma omp parallel for schedule(static)
+        for (bst_omp_uint j = 0; j < ndata; ++j) {
+            boolmap[j] = 0;
+        }        
+      }
       utils::IIterator<ColBatch> *iter = p_fmat->ColIterator(fsplits);
       while (iter->Next()) {
         const ColBatch &batch = iter->Value();
@@ -110,15 +116,16 @@ class DistColMaker : public ColMaker<TStats> {
             const int nid = this->DecodePosition(ridx);
             if (!tree[nid].is_leaf() && tree[nid].split_index() == fid) {
               if (fvalue < tree[nid].split_cond()) {
-                if (!tree[nid].default_left()) bitmap.SetTrue(ridx);
+                if (!tree[nid].default_left()) boolmap[ridx] = 1;
               } else {
-                if (tree[nid].default_left()) bitmap.SetTrue(ridx);
+                if (tree[nid].default_left()) boolmap[ridx] = 1;
               }
             }
           }
         }
       }
       
+      bitmap.InitFromBool(boolmap);
       // communicate bitmap
       sync::AllReduce(BeginPtr(bitmap.data), bitmap.data.size(), sync::kBitwiseOR);
       const std::vector<bst_uint> &rowset = p_fmat->buffered_rowset();
@@ -159,6 +166,7 @@ class DistColMaker : public ColMaker<TStats> {
     
    private:
     utils::BitMap bitmap;
+    std::vector<int> boolmap;
     sync::Reducer<SplitEntry> reducer;
   };
   // we directly introduce pruner here

src/utils/bitmap.h

@@ -7,6 +7,7 @@
  */
 #include <vector>
 #include "./utils.h"
+#include "./omp.h"
 
 namespace xgboost {
 namespace utils {
@@ -35,6 +36,25 @@ struct BitMap {
   inline void SetTrue(size_t i) {
     data[i >> 5] |= (1 << (i & 31U));
   }
+  /*! \brief initialize the value of bit map from vector of bool*/
+  inline void InitFromBool(const std::vector<int> &vec) {
+    this->Resize(vec.size());
+    // parallel over the full cases
+    bst_omp_uint nsize = static_cast<bst_omp_uint>(vec.size() / 32);
+    #pragma omp parallel for schedule(static)
+    for (bst_omp_uint i = 0; i < nsize; ++i) {
+      uint32_t res = 0;
+      for (int k = 0; k < 32; ++k) {
+        int bit = vec[(i << 5) | k];
+        res |= (bit << k);
+      }
+      data[i] = res;
+    }
+    if (nsize != vec.size()) data.back() = 0;
+    for (size_t i = nsize; i < vec.size(); ++i) {
+      if (vec[i]) this->SetTrue(i);
+    }
+  }
   /*! \brief clear the bitmap, set all places to false */
   inline void Clear(void) {
     std::fill(data.begin(), data.end(), 0U);

src/xgboost_main.cpp

@@ -14,7 +14,7 @@ namespace xgboost {
 /*!
  * \brief wrapping the training process 
  */
-class BoostLearnTask{
+class BoostLearnTask {
  public:
   inline int Run(int argc, char *argv[]) {
     if (argc < 2) {
@@ -31,6 +31,9 @@ class BoostLearnTask{
         this->SetParam(name, val);
       }
     }
+    if (sync::IsDistributed()) {
+      this->SetParam("updater", "distcol");
+    }
     if (sync::GetRank() != 0) {
       this->SetParam("silent", "2");
     }
@@ -93,6 +96,7 @@ class BoostLearnTask{
     name_pred = "pred.txt";
     name_dump = "dump.txt";
     model_dir_path = "./";
+    load_part = 0;
     data = NULL;
   }
   ~BoostLearnTask(void){
@@ -103,13 +107,20 @@ class BoostLearnTask{
   }
  private:
   inline void InitData(void) {
+    if (strchr(train_path.c_str(), '%') != NULL) {
+      char s_tmp[256];
+      utils::SPrintf(s_tmp, sizeof(s_tmp), train_path.c_str(), sync::GetRank());
+      train_path = s_tmp;
+      load_part = 1;
+    }
+
     if (name_fmap != "NULL") fmap.LoadText(name_fmap.c_str());
     if (task == "dump") return;
     if (task == "pred") {
       data = io::LoadDataMatrix(test_path.c_str(), silent != 0, use_buffer != 0);
     } else {
       // training
-      data = io::LoadDataMatrix(train_path.c_str(), silent != 0, use_buffer != 0);
+      data = io::LoadDataMatrix(train_path.c_str(), silent != 0 && load_part == 0, use_buffer != 0);
       utils::Assert(eval_data_names.size() == eval_data_paths.size(), "BUG");
       for (size_t i = 0; i < eval_data_names.size(); ++i) {
         deval.push_back(io::LoadDataMatrix(eval_data_paths[i].c_str(), silent != 0, use_buffer != 0));
@@ -182,6 +193,7 @@ class BoostLearnTask{
     fclose(fo);
   }
   inline void SaveModel(const char *fname) const {
+    if (sync::GetRank() != 0) return;
     utils::FileStream fo(utils::FopenCheck(fname, "wb"));
     learner.SaveModel(fo);
     fo.Close();
@@ -205,6 +217,8 @@ class BoostLearnTask{
  private:
   /*! \brief whether silent */
   int silent;
+  /*! \brief special load */
+  int load_part;
   /*! \brief whether use auto binary buffer */
   int use_buffer;
   /*! \brief whether evaluate training statistics */