diff --git a/old_src/utils/iterator.h b/old_src/utils/iterator.h
deleted file mode 100644
index 73068dbbf..000000000
--- a/old_src/utils/iterator.h
+++ /dev/null
@@ -1,42 +0,0 @@
-/*!
- * Copyright 2014 by Contributors
- * \file iterator.h
- * \brief itertator interface
- * \author Tianqi Chen
- */
-#ifndef XGBOOST_UTILS_ITERATOR_H_
-#define XGBOOST_UTILS_ITERATOR_H_
-#include <cstdio>
-
-namespace xgboost {
-namespace utils {
-/*!
- * \brief iterator interface
- * \tparam DType data type
- */
-template<typename DType>
-class IIterator {
- public:
-  /*!
-   * \brief set the parameter
-   * \param name name of parameter
-   * \param val value of parameter
-   */
-  virtual void SetParam(const char *name, const char *val) {}
-  /*! \brief initialize the iterator so that we can use the iterator */
-  virtual void Init(void) {}
-  /*! \brief set before first of the item */
-  virtual void BeforeFirst(void) = 0;
-  /*! \brief move to next item */
-  virtual bool Next(void) = 0;
-  /*! \brief get current data */
-  virtual const DType &Value(void) const = 0;
- public:
-  /*! \brief constructor */
-  virtual ~IIterator(void) {}
-};
-
-}  // namespace utils
-}  // namespace xgboost
-#endif  // XGBOOST_UTILS_ITERATOR_H_
-
diff --git a/old_src/utils/omp.h b/old_src/utils/omp.h
deleted file mode 100644
index c7a04dc32..000000000
--- a/old_src/utils/omp.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/*!
- * Copyright 2014 by Contributors
- * \file omp.h
- * \brief header to handle OpenMP compatibility issues
- * \author Tianqi Chen
- */
-#ifndef XGBOOST_UTILS_OMP_H_
-#define XGBOOST_UTILS_OMP_H_
-
-#if defined(_OPENMP) && !defined(DISABLE_OPENMP)
-#include <omp.h>
-#else
-#if !defined(DISABLE_OPENMP) && !defined(_MSC_VER)
-// use pragma message instead of warning
-#pragma message("Warning: OpenMP is not available,"\
-                "xgboost will be compiled into single-thread code."\
-                "Use OpenMP-enabled compiler to get benefit of multi-threading")
-#endif
-inline int omp_get_thread_num() { return 0; }
-inline int omp_get_num_threads() { return 1; }
-inline void omp_set_num_threads(int nthread) {}
-inline int omp_get_num_procs() { return 1; }
-#endif
-
-// loop variable used in openmp
-namespace xgboost {
-#ifdef _MSC_VER
-typedef int bst_omp_uint;
-#else
-typedef unsigned bst_omp_uint;
-#endif
-}  // namespace xgboost
-
-#endif  // XGBOOST_UTILS_OMP_H_
diff --git a/old_src/utils/random.h b/old_src/utils/random.h
deleted file mode 100644
index 8e3255cf3..000000000
--- a/old_src/utils/random.h
+++ /dev/null
@@ -1,108 +0,0 @@
-/*!
- * Copyright 2014 by Contributors
- * \file xgboost_random.h
- * \brief PRNG to support random number generation
- * \author Tianqi Chen: tianqi.tchen@gmail.com
- *
- * Use standard PRNG from stdlib
- */
-#ifndef XGBOOST_UTILS_RANDOM_H_
-#define XGBOOST_UTILS_RANDOM_H_
-
-#include <cmath>
-#include <cstdlib>
-#include <vector>
-#include <algorithm>
-#include "./utils.h"
-
-/*! namespace of PRNG */
-namespace xgboost {
-namespace random {
-#ifndef XGBOOST_CUSTOMIZE_PRNG_
-/*! \brief seed the PRNG */
-inline void Seed(unsigned seed) {
-  srand(seed);
-}
-/*! \brief basic function, uniform */
-inline double Uniform(void) {
-  return static_cast<double>(rand()) / (static_cast<double>(RAND_MAX)+1.0); // NOLINT(*)
-}
-/*! \brief return a real number uniform in (0,1) */
-inline double NextDouble2(void) {
-  return (static_cast<double>(rand()) + 1.0) / (static_cast<double>(RAND_MAX)+2.0); // NOLINT(*)
-}
-/*! \brief return  x~N(0,1) */
-inline double Normal(void) {
-  double x, y, s;
-  do {
-    x = 2 * NextDouble2() - 1.0;
-    y = 2 * NextDouble2() - 1.0;
-    s = x*x + y*y;
-  } while (s >= 1.0 || s == 0.0);
-
-  return x * sqrt(-2.0 * log(s) / s);
-}
-#else
-// include declarations, to be implemented
-void Seed(unsigned seed);
-double Uniform(void);
-double Normal(void);
-#endif
-
-/*! \brief return a real number uniform in [0,1) */
-inline double NextDouble(void) {
-  return Uniform();
-}
-/*! \brief return a random number in n */
-inline uint32_t NextUInt32(uint32_t n) {
-  return (uint32_t)std::floor(NextDouble() * n);
-}
-/*! \brief return  x~N(mu,sigma^2) */
-inline double SampleNormal(double mu, double sigma) {
-  return Normal() * sigma + mu;
-}
-/*! \brief  return 1 with probability p, coin flip */
-inline int SampleBinary(double p) {
-  return NextDouble() < p;
-}
-
-template<typename T>
-inline void Shuffle(T *data, size_t sz) {
-  if (sz == 0) return;
-  for (uint32_t i = (uint32_t)sz - 1; i > 0; i--) {
-    std::swap(data[i], data[NextUInt32(i + 1)]);
-  }
-}
-// random shuffle the data inside, require PRNG
-template<typename T>
-inline void Shuffle(std::vector<T> &data) { // NOLINT(*)
-  Shuffle(&data[0], data.size());
-}
-
-/*! \brief random number generator with independent random number seed*/
-struct Random{
-  /*! \brief set random number seed */
-  inline void Seed(unsigned sd) {
-    this->rseed = sd;
-#if defined(_MSC_VER) || defined(_WIN32)
-    ::xgboost::random::Seed(sd);
-#endif
-  }
-  /*! \brief return a real number uniform in [0,1) */
-  inline double RandDouble(void) {
-    // use rand instead of rand_r in windows, for MSVC it is fine since rand is threadsafe
-    // For cygwin and mingw, this can slows down parallelism,
-    // but rand_r is only used in objective-inl.hpp, won't affect speed in general
-    // todo, replace with another PRNG
-#if defined(_MSC_VER) || defined(_WIN32) || defined(XGBOOST_STRICT_CXX98_)
-    return Uniform();
-#else
-    return static_cast<double>(rand_r(&rseed)) / (static_cast<double>(RAND_MAX) + 1.0);
-#endif
-  }
-  // random number seed
-  unsigned rseed;
-};
-}  // namespace random
-}  // namespace xgboost
-#endif  // XGBOOST_UTILS_RANDOM_H_
diff --git a/old_src/utils/thread.h b/old_src/utils/thread.h
deleted file mode 100644
index a6e8e7fdc..000000000
--- a/old_src/utils/thread.h
+++ /dev/null
@@ -1,260 +0,0 @@
-/*!
- * Copyright by Contributors
- * \file thread.h
- * \brief this header include the minimum necessary resource
- * for multi-threading that can be compiled in windows, linux, mac
- * \author Tianqi Chen
- */
-#ifndef XGBOOST_UTILS_THREAD_H_ // NOLINT(*)
-#define XGBOOST_UTILS_THREAD_H_ // NOLINT(*)
-
-#ifdef _MSC_VER
-#include <windows.h>
-#include <process.h>
-#include "./utils.h"
-namespace xgboost {
-namespace utils {
-/*! \brief simple semaphore used for synchronization */
-class Semaphore {
- public :
-  inline void Init(int init_val) {
-    sem = CreateSemaphore(NULL, init_val, 10, NULL);
-    utils::Check(sem != NULL, "create Semaphore error");
-  }
-  inline void Destroy(void) {
-    CloseHandle(sem);
-  }
-  inline void Wait(void) {
-    utils::Check(WaitForSingleObject(sem, INFINITE) == WAIT_OBJECT_0, "WaitForSingleObject error");
-  }
-  inline void Post(void) {
-    utils::Check(ReleaseSemaphore(sem, 1, NULL) != 0, "ReleaseSemaphore error");
-  }
-
- private:
-  HANDLE sem;
-};
-
-/*! \brief mutex under windows */
-class Mutex {
- public:
-  inline void Init(void) {
-    utils::Check(InitializeCriticalSectionAndSpinCount(&mutex, 0x00000400) != 0,
-                   "Mutex::Init fail");
-  }
-  inline void Lock(void) {
-    EnterCriticalSection(&mutex);
-  }
-  inline void Unlock(void) {
-    LeaveCriticalSection(&mutex);
-  }
-  inline void Destroy(void) {
-    DeleteCriticalSection(&mutex);
-  }
-
- private:
-  friend class ConditionVariable;
-  CRITICAL_SECTION mutex;
-};
-
-// conditional variable that uses pthread
-class ConditionVariable {
- public:
-  // initialize conditional variable
-  inline void Init(void) {
-    InitializeConditionVariable(&cond);
-  }
-  // destroy the thread
-  inline void Destroy(void) {
-    // DeleteConditionVariable(&cond);
-  }
-  // wait on the conditional variable
-  inline void Wait(Mutex *mutex) {
-    utils::Check(SleepConditionVariableCS(&cond, &(mutex->mutex), INFINITE) != 0,
-                 "ConditionVariable:Wait fail");
-  }
-  inline void Broadcast(void) {
-    WakeAllConditionVariable(&cond);
-  }
-  inline void Signal(void) {
-    WakeConditionVariable(&cond);
-  }
-
- private:
-  CONDITION_VARIABLE cond;
-};
-
-/*! \brief simple thread that wraps windows thread */
-class Thread {
- private:
-  HANDLE    thread_handle;
-  unsigned  thread_id;
- public:
-  inline void Start(unsigned int __stdcall entry(void*p), void *param) {
-    thread_handle = (HANDLE)_beginthreadex(NULL, 0, entry, param, 0, &thread_id);
-  }
-  inline int Join(void) {
-    WaitForSingleObject(thread_handle, INFINITE);
-    return 0;
-  }
-};
-/*! \brief exit function called from thread */
-inline void ThreadExit(void *status) {
-  _endthreadex(0);
-}
-#define XGBOOST_THREAD_PREFIX unsigned int __stdcall
-}  // namespace utils
-}  // namespace xgboost
-#else
-// thread interface using g++
-#include <semaphore.h>
-#include <pthread.h>
-#include <errno.h>
-namespace xgboost {
-namespace utils {
-/*!\brief semaphore class */
-class Semaphore {
-  #ifdef __APPLE__
-
- private:
-  sem_t* semPtr;
-  char sema_name[20];
-
- private:
-  inline void GenRandomString(char *s, const int len) {
-    static const char alphanum[] = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ";
-    for (int i = 0; i < len; ++i) {
-      s[i] = alphanum[rand() % (sizeof(alphanum) - 1)];
-    }
-    s[len] = 0;
-  }
-
- public:
-  inline void Init(int init_val) {
-    sema_name[0] = '/';
-    sema_name[1] = 's';
-    sema_name[2] = 'e';
-    sema_name[3] = '/';
-    GenRandomString(&sema_name[4], 16);
-    if ((semPtr = sem_open(sema_name, O_CREAT, 0644, init_val)) == SEM_FAILED) {
-      perror("sem_open");
-      exit(1);
-    }
-    utils::Check(semPtr != NULL, "create Semaphore error");
-  }
-  inline void Destroy(void) {
-    if (sem_close(semPtr) == -1) {
-      perror("sem_close");
-      exit(EXIT_FAILURE);
-    }
-    if (sem_unlink(sema_name) == -1) {
-      perror("sem_unlink");
-      exit(EXIT_FAILURE);
-    }
-  }
-  inline void Wait(void) {
-    sem_wait(semPtr);
-  }
-  inline void Post(void) {
-    sem_post(semPtr);
-  }
-  #else
-
- private:
-  sem_t sem;
-
- public:
-  inline void Init(int init_val) {
-    if (sem_init(&sem, 0, init_val) != 0) {
-      utils::Error("Semaphore.Init:%s", strerror(errno));
-    }
-  }
-  inline void Destroy(void) {
-    if (sem_destroy(&sem) != 0) {
-      utils::Error("Semaphore.Destroy:%s", strerror(errno));
-    }
-  }
-  inline void Wait(void) {
-    if (sem_wait(&sem) != 0) {
-      utils::Error("Semaphore.Wait:%s", strerror(errno));
-    }
-  }
-  inline void Post(void) {
-    if (sem_post(&sem) != 0) {
-      utils::Error("Semaphore.Post:%s", strerror(errno));
-    }
-  }
-  #endif
-};
-
-// mutex that works with pthread
-class Mutex {
- public:
-  inline void Init(void) {
-    pthread_mutex_init(&mutex, NULL);
-  }
-  inline void Lock(void) {
-    pthread_mutex_lock(&mutex);
-  }
-  inline void Unlock(void) {
-    pthread_mutex_unlock(&mutex);
-  }
-  inline void Destroy(void) {
-    pthread_mutex_destroy(&mutex);
-  }
-
- private:
-  friend class ConditionVariable;
-  pthread_mutex_t mutex;
-};
-
-// conditional variable that uses pthread
-class ConditionVariable {
- public:
-  // initialize conditional variable
-  inline void Init(void) {
-    pthread_cond_init(&cond, NULL);
-  }
-  // destroy the thread
-  inline void Destroy(void) {
-    pthread_cond_destroy(&cond);
-  }
-  // wait on the conditional variable
-  inline void Wait(Mutex *mutex) {
-    pthread_cond_wait(&cond, &(mutex->mutex));
-  }
-  inline void Broadcast(void) {
-    pthread_cond_broadcast(&cond);
-  }
-  inline void Signal(void) {
-    pthread_cond_signal(&cond);
-  }
-
- private:
-  pthread_cond_t cond;
-};
-
-/*!\brief simple thread class */
-class Thread {
- private:
-  pthread_t thread;
- public :
-  inline void Start(void * entry(void*), void *param) { // NOLINT(*)
-    pthread_attr_t attr;
-    pthread_attr_init(&attr);
-    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
-    pthread_create(&thread, &attr, entry, param);
-  }
-  inline int Join(void) {
-    void *status;
-    return pthread_join(thread, &status);
-  }
-};
-inline void ThreadExit(void *status) {
-  pthread_exit(status);
-}
-}  // namespace utils
-}  // namespace xgboost
-#define XGBOOST_THREAD_PREFIX void *
-#endif  // Linux
-#endif  // XGBOOST_UTILS_THREAD_H_  NOLINT(*)
diff --git a/old_src/utils/thread_buffer.h b/old_src/utils/thread_buffer.h
deleted file mode 100644
index 8acb8ffd0..000000000
--- a/old_src/utils/thread_buffer.h
+++ /dev/null
@@ -1,257 +0,0 @@
-/*!
- * Copyright 2014 by Contributors
- * \file thread_buffer.h
- * \brief  multi-thread buffer, iterator, can be used to create parallel pipeline
- * \author Tianqi Chen
- */
-#ifndef XGBOOST_UTILS_THREAD_BUFFER_H_
-#define XGBOOST_UTILS_THREAD_BUFFER_H_
-
-#include <vector>
-#include <cstring>
-#include <cstdlib>
-#include "./utils.h"
-// threading util could not run on solaris
-#ifndef XGBOOST_STRICT_CXX98_
-#include "./thread.h"
-#endif
-
-namespace xgboost {
-namespace utils {
-#if !defined(XGBOOST_STRICT_CXX98_)
-/*!
- * \brief buffered loading iterator that uses multithread
- * this template method will assume the following parameters
- * \tparam Elem element type to be buffered
- * \tparam ElemFactory factory type to implement in order to use thread buffer
- */
-template<typename Elem, typename ElemFactory>
-class ThreadBuffer {
- public:
-  /*!\brief constructor */
-  ThreadBuffer(void) {
-    this->init_end = false;
-    this->buf_size = 30;
-  }
-  ~ThreadBuffer(void) {
-    if (init_end) this->Destroy();
-  }
-  /*!\brief set parameter, will also pass the parameter to factory */
-  inline void SetParam(const char *name, const char *val) {
-    using namespace std;
-    if (!strcmp( name, "buffer_size")) buf_size = atoi(val);
-    factory.SetParam(name, val);
-  }
-  /*!
-   * \brief initalize the buffered iterator
-   * \param param a initialize parameter that will pass to factory, ignore it if not necessary
-   * \return false if the initialization can't be done, e.g. buffer file hasn't been created
-   */
-  inline bool Init(void) {
-    if (!factory.Init()) return false;
-    for (int i = 0; i < buf_size; ++i) {
-      bufA.push_back(factory.Create());
-      bufB.push_back(factory.Create());
-    }
-    this->init_end = true;
-    this->StartLoader();
-    return true;
-  }
-  /*!\brief place the iterator before first value */
-  inline void BeforeFirst(void) {
-    // wait till last loader end
-    loading_end.Wait();
-    // critical zone
-    current_buf = 1;
-    factory.BeforeFirst();
-    // reset terminate limit
-    endA = endB = buf_size;
-    // wake up loader for first part
-    loading_need.Post();
-    // wait til first part is loaded
-    loading_end.Wait();
-    // set current buf to right value
-    current_buf = 0;
-    // wake loader for next part
-    data_loaded = false;
-    loading_need.Post();
-    // set buffer value
-    buf_index = 0;
-  }
-  /*! \brief destroy the buffer iterator, will deallocate the buffer */
-  inline void Destroy(void) {
-    // wait until the signal is consumed
-    this->destroy_signal = true;
-    loading_need.Post();
-    loader_thread.Join();
-    loading_need.Destroy();
-    loading_end.Destroy();
-    for (size_t i = 0; i < bufA.size(); ++i) {
-      factory.FreeSpace(bufA[i]);
-    }
-    for (size_t i = 0; i < bufB.size(); ++i) {
-      factory.FreeSpace(bufB[i]);
-    }
-    bufA.clear(); bufB.clear();
-    factory.Destroy();
-    this->init_end = false;
-  }
-  /*!
-   * \brief get the next element needed in buffer
-   * \param elem element to store into
-   * \return whether reaches end of data
-   */
-  inline bool Next(Elem &elem) { // NOLINT(*)
-    // end of buffer try to switch
-    if (buf_index == buf_size) {
-      this->SwitchBuffer();
-      buf_index = 0;
-    }
-    if (buf_index >= (current_buf ? endA : endB)) {
-      return false;
-    }
-    std::vector<Elem> &buf = current_buf ? bufA : bufB;
-    elem = buf[buf_index];
-    ++buf_index;
-    return true;
-  }
-  /*!
-   * \brief get the factory object
-   */
-  inline ElemFactory &get_factory(void) {
-    return factory;
-  }
-  inline const ElemFactory &get_factory(void) const {
-    return factory;
-  }
-  // size of buffer
-  int  buf_size;
-
- private:
-  // factory object used to load configures
-  ElemFactory factory;
-  // index in current buffer
-  int buf_index;
-  // indicate which one is current buffer
-  int current_buf;
-  // max limit of visit, also marks termination
-  int endA, endB;
-  // double buffer, one is accessed by loader
-  // the other is accessed by consumer
-  // buffer of the data
-  std::vector<Elem> bufA, bufB;
-  // initialization end
-  bool init_end;
-  // singal whether the data is loaded
-  bool data_loaded;
-  // signal to kill the thread
-  bool destroy_signal;
-  // thread object
-  Thread loader_thread;
-  // signal of the buffer
-  Semaphore loading_end, loading_need;
-  /*!
-   * \brief slave thread
-   * this implementation is like producer-consumer style
-   */
-  inline void RunLoader(void) {
-    while (!destroy_signal) {
-      // sleep until loading is needed
-      loading_need.Wait();
-      std::vector<Elem> &buf = current_buf ? bufB : bufA;
-      int i;
-      for (i = 0; i < buf_size ; ++i) {
-        if (!factory.LoadNext(buf[i])) {
-          int &end = current_buf ? endB : endA;
-          end = i;  // marks the termination
-          break;
-        }
-      }
-      // signal that loading is done
-      data_loaded = true;
-      loading_end.Post();
-    }
-  }
-  /*!\brief entry point of loader thread */
-  inline static XGBOOST_THREAD_PREFIX LoaderEntry(void *pthread) {
-    static_cast< ThreadBuffer<Elem, ElemFactory>* >(pthread)->RunLoader();
-    return NULL;
-  }
-  /*!\brief start loader thread */
-  inline void StartLoader(void) {
-    destroy_signal = false;
-    // set param
-    current_buf = 1;
-    loading_need.Init(1);
-    loading_end .Init(0);
-    // reset terminate limit
-    endA = endB = buf_size;
-    loader_thread.Start(LoaderEntry, this);
-    // wait until first part of data is loaded
-    loading_end.Wait();
-    // set current buf to right value
-    current_buf = 0;
-    // wake loader for next part
-    data_loaded = false;
-    loading_need.Post();
-    buf_index = 0;
-  }
-  /*!\brief switch double buffer */
-  inline void SwitchBuffer(void) {
-    loading_end.Wait();
-    // loader shall be sleep now, critcal zone!
-    current_buf = !current_buf;
-    // wake up loader
-    data_loaded = false;
-    loading_need.Post();
-  }
-};
-#else
-// a dummy single threaded ThreadBuffer
-// use this to resolve R's solaris compatibility for now
-template<typename Elem, typename ElemFactory>
-class ThreadBuffer {
- public:
-  ThreadBuffer() : init_end_(false) {}
-  ~ThreadBuffer() {
-    if (init_end_) {
-      factory_.FreeSpace(data_);
-      factory_.Destroy();
-    }
-  }
-  inline void SetParam(const char *name, const char *val) {
-  }
-  inline bool Init(void) {
-    if (!factory_.Init()) return false;
-    data_ = factory_.Create();
-    return (init_end_ = true);
-  }
-  inline void BeforeFirst(void) {
-    factory_.BeforeFirst();
-  }
-  inline bool Next(Elem &elem) { // NOLINT(*)
-    if (factory_.LoadNext(data_)) {
-      elem = data_; return true;
-    } else {
-      return false;
-    }
-  }
-  inline ElemFactory &get_factory() {
-    return factory_;
-  }
-  inline const ElemFactory &get_factory() const {
-    return factory_;
-  }
-
- private:
-  // initialized
-  bool init_end_;
-  // current data
-  Elem data_;
-  // factory object used to load configures
-  ElemFactory factory_;
-};
-#endif  // !defined(XGBOOST_STRICT_CXX98_)
-}  // namespace utils
-}  // namespace xgboost
-#endif  // XGBOOST_UTILS_THREAD_BUFFER_H_
diff --git a/old_src/utils/utils.h b/old_src/utils/utils.h
deleted file mode 100644
index 4d06d3c61..000000000
--- a/old_src/utils/utils.h
+++ /dev/null
@@ -1,188 +0,0 @@
-/*!
- * Copyright 2014 by Contributors
- * \file utils.h
- * \brief simple utils to support the code
- * \author Tianqi Chen
- */
-#ifndef XGBOOST_UTILS_UTILS_H_
-#define XGBOOST_UTILS_UTILS_H_
-
-#define _CRT_SECURE_NO_WARNINGS
-#include <cstdio>
-#include <string>
-#include <cstdlib>
-#include <vector>
-#include <stdexcept>
-
-#ifndef XGBOOST_STRICT_CXX98_
-#include <cstdarg>
-#endif
-
-#if !defined(__GNUC__)
-#define fopen64 std::fopen
-#endif
-#ifdef _MSC_VER
-// NOTE: sprintf_s is not equivalent to snprintf,
-// they are equivalent when success, which is sufficient for our case
-#define snprintf sprintf_s
-#define vsnprintf vsprintf_s
-#else
-#ifdef _FILE_OFFSET_BITS
-#if _FILE_OFFSET_BITS == 32
-#pragma message("Warning: FILE OFFSET BITS defined to be 32 bit")
-#endif
-#endif
-
-#ifdef __APPLE__
-#define off64_t off_t
-#define fopen64 std::fopen
-#endif
-
-extern "C" {
-#include <sys/types.h>
-}
-#endif
-
-#ifdef _MSC_VER
-typedef unsigned char uint8_t;
-typedef unsigned __int16 uint16_t;
-typedef unsigned __int32 uint32_t;
-typedef unsigned __int64 uint64_t;
-typedef __int64 int64_t;
-#else
-#include <inttypes.h>
-#endif
-
-namespace xgboost {
-/*! \brief namespace for helper utils of the project */
-namespace utils {
-
-/*! \brief error message buffer length */
-const int kPrintBuffer = 1 << 12;
-
-#ifndef XGBOOST_CUSTOMIZE_MSG_
-/*!
- * \brief handling of Assert error, caused by inappropriate input
- * \param msg error message
- */
-inline void HandleAssertError(const char *msg) {
-  fprintf(stderr, "AssertError:%s\n", msg);
-  exit(-1);
-}
-/*!
- * \brief handling of Check error, caused by inappropriate input
- * \param msg error message
- */
-inline void HandleCheckError(const char *msg) {
-  throw std::runtime_error(msg);
-}
-inline void HandlePrint(const char *msg) {
-  printf("%s", msg);
-}
-#else
-#ifndef XGBOOST_STRICT_CXX98_
-// include declarations, some one must implement this
-void HandleAssertError(const char *msg);
-void HandleCheckError(const char *msg);
-void HandlePrint(const char *msg);
-#endif
-#endif
-#ifdef XGBOOST_STRICT_CXX98_
-// these function pointers are to be assigned
-extern "C" void (*Printf)(const char *fmt, ...);
-extern "C" int (*SPrintf)(char *buf, size_t size, const char *fmt, ...);
-extern "C" void (*Assert)(int exp, const char *fmt, ...);
-extern "C" void (*Check)(int exp, const char *fmt, ...);
-extern "C" void (*Error)(const char *fmt, ...);
-#else
-/*! \brief printf, print message to the console */
-inline void Printf(const char *fmt, ...) {
-  std::string msg(kPrintBuffer, '\0');
-  va_list args;
-  va_start(args, fmt);
-  vsnprintf(&msg[0], kPrintBuffer, fmt, args);
-  va_end(args);
-  HandlePrint(msg.c_str());
-}
-/*! \brief portable version of snprintf */
-inline int SPrintf(char *buf, size_t size, const char *fmt, ...) {
-  va_list args;
-  va_start(args, fmt);
-  int ret = vsnprintf(buf, size, fmt, args);
-  va_end(args);
-  return ret;
-}
-
-/*! \brief assert an condition is true, use this to handle debug information */
-inline void Assert(bool exp, const char *fmt, ...) {
-  if (!exp) {
-    std::string msg(kPrintBuffer, '\0');
-    va_list args;
-    va_start(args, fmt);
-    vsnprintf(&msg[0], kPrintBuffer, fmt, args);
-    va_end(args);
-    HandleAssertError(msg.c_str());
-  }
-}
-
-/*!\brief same as assert, but this is intended to be used as message for user*/
-inline void Check(bool exp, const char *fmt, ...) {
-  if (!exp) {
-    std::string msg(kPrintBuffer, '\0');
-    va_list args;
-    va_start(args, fmt);
-    vsnprintf(&msg[0], kPrintBuffer, fmt, args);
-    va_end(args);
-    HandleCheckError(msg.c_str());
-  }
-}
-
-/*! \brief report error message, same as check */
-inline void Error(const char *fmt, ...) {
-  {
-    std::string msg(kPrintBuffer, '\0');
-    va_list args;
-    va_start(args, fmt);
-    vsnprintf(&msg[0], kPrintBuffer, fmt, args);
-    va_end(args);
-    HandleCheckError(msg.c_str());
-  }
-}
-#endif
-
-/*! \brief replace fopen, report error when the file open fails */
-inline std::FILE *FopenCheck(const char *fname, const char *flag) {
-  std::FILE *fp = fopen64(fname, flag);
-  Check(fp != NULL, "can not open file \"%s\"\n", fname);
-  return fp;
-}
-}  // namespace utils
-// easy utils that can be directly accessed in xgboost
-/*! \brief get the beginning address of a vector */
-template<typename T>
-inline T *BeginPtr(std::vector<T> &vec) { // NOLINT(*)
-  if (vec.size() == 0) {
-    return NULL;
-  } else {
-    return &vec[0];
-  }
-}
-/*! \brief get the beginning address of a vector */
-template<typename T>
-inline const T *BeginPtr(const std::vector<T> &vec) {
-  if (vec.size() == 0) {
-    return NULL;
-  } else {
-    return &vec[0];
-  }
-}
-inline char* BeginPtr(std::string &str) { // NOLINT(*)
-  if (str.length() == 0) return NULL;
-  return &str[0];
-}
-inline const char* BeginPtr(const std::string &str) {
-  if (str.length() == 0) return NULL;
-  return &str[0];
-}
-}  // namespace xgboost
-#endif  // XGBOOST_UTILS_UTILS_H_
diff --git a/old_src/utils/base64-inl.h b/src/common/base64.h
similarity index 100%
rename from old_src/utils/base64-inl.h
rename to src/common/base64.h
diff --git a/old_src/utils/config.h b/src/common/config.h
similarity index 100%
rename from old_src/utils/config.h
rename to src/common/config.h
diff --git a/old_src/utils/quantile.h b/src/common/quantile.h
similarity index 100%
rename from old_src/utils/quantile.h
rename to src/common/quantile.h
diff --git a/old_src/tree/updater_basemaker-inl.hpp b/src/tree/updater_basemaker-inl.h
similarity index 100%
rename from old_src/tree/updater_basemaker-inl.hpp
rename to src/tree/updater_basemaker-inl.h
diff --git a/old_src/tree/updater_histmaker-inl.hpp b/src/tree/updater_histmaker.cc
similarity index 100%
rename from old_src/tree/updater_histmaker-inl.hpp
rename to src/tree/updater_histmaker.cc
diff --git a/old_src/tree/updater_prune-inl.hpp b/src/tree/updater_prune.cc
similarity index 100%
rename from old_src/tree/updater_prune-inl.hpp
rename to src/tree/updater_prune.cc
diff --git a/old_src/tree/updater_refresh-inl.hpp b/src/tree/updater_refresh.cc
similarity index 100%
rename from old_src/tree/updater_refresh-inl.hpp
rename to src/tree/updater_refresh.cc
diff --git a/old_src/tree/updater_skmaker-inl.hpp b/src/tree/updater_skmaker.cc
similarity index 100%
rename from old_src/tree/updater_skmaker-inl.hpp
rename to src/tree/updater_skmaker.cc