Unify logging facilities. (#3982)

* Unify logging facilities.

* Enhance `ConsoleLogger` to handle different verbosity.
* Override macros from `dmlc`.
* Don't use specialized gamma when building with GPU.
* Remove verbosity cache in monitor.
* Test monitor.
* Deprecate `silent`.
* Fix doc and messages.
* Fix python test.
* Fix silent tests.

src/common/device_helpers.cuh

@@ -480,7 +480,7 @@ class BulkAllocator {
   }
 
   template <typename... Args>
-  void Allocate(int device_idx, bool silent, Args... args) {
+  void Allocate(int device_idx, Args... args) {
     size_t size = GetSizeBytes(args...);
 
     char *ptr = AllocateDevice(device_idx, size, MemoryT);

src/common/math.h

@@ -116,7 +116,6 @@ inline static bool CmpSecond(const std::pair<float, unsigned> &a,
 #if XGBOOST_STRICT_R_MODE
 // check nan
 bool CheckNAN(double v);
-double LogGamma(double v);
 #else
 template<typename T>
 inline bool CheckNAN(T v) {
@@ -126,9 +125,19 @@ inline bool CheckNAN(T v) {
   return std::isnan(v);
 #endif
 }
+#endif  // XGBOOST_STRICT_R_MODE_
+
+// GPU version is not uploaded in CRAN anyway.
+// Specialize only when using R with CPU.
+#if XGBOOST_STRICT_R_MODE && !defined(XGBOOST_USE_CUDA)
+double LogGamma(double v);
+
+#else  // Not R or R with GPU.
+
 template<typename T>
 XGBOOST_DEVICE inline T LogGamma(T v) {
 #ifdef _MSC_VER
+
 #if _MSC_VER >= 1800
   return lgamma(v);
 #else
@@ -136,12 +145,15 @@ XGBOOST_DEVICE inline T LogGamma(T v) {
                 ", poisson regression will be disabled")
   utils::Error("lgamma function was not available until VS2013");
   return static_cast<T>(1.0);
-#endif
+#endif  // _MSC_VER >= 1800
+
 #else
   return lgamma(v);
 #endif
 }
-#endif  // XGBOOST_STRICT_R_MODE_
+
+#endif  // XGBOOST_STRICT_R_MODE && !defined(XGBOOST_USE_CUDA)
+
 }  // namespace common
 }  // namespace xgboost
 #endif  // XGBOOST_COMMON_MATH_H_

src/common/timer.h

@@ -49,15 +49,19 @@ struct Monitor {
     Timer timer;
     size_t count{0};
   };
-  bool debug_verbose = false;
   std::string label = "";
   std::map<std::string, Statistics> statistics_map;
   Timer self_timer;
+  bool IsVerbose() {
+    // Don't cache debug verbosity in here to deal with changed parameter.
+    return (ConsoleLogger::GlobalVerbosity() == ConsoleLogger::LV::kDebug);
+  }
 
+ public:
   Monitor() { self_timer.Start(); }
 
   ~Monitor() {
-    if (!debug_verbose) return;
+    if (!IsVerbose()) return;
 
     LOG(CONSOLE) << "======== Monitor: " << label << " ========";
     for (auto &kv : statistics_map) {
@@ -70,13 +74,12 @@ struct Monitor {
     }
     self_timer.Stop();
   }
-  void Init(std::string label, bool debug_verbose) {
-    this->debug_verbose = debug_verbose;
+  void Init(std::string label) {
     this->label = label;
   }
   void Start(const std::string &name) { statistics_map[name].timer.Start(); }
   void Start(const std::string &name, GPUSet devices) {
-    if (debug_verbose) {
+    if (IsVerbose()) {
 #ifdef __CUDACC__
       for (auto device : devices) {
         cudaSetDevice(device);
@@ -91,7 +94,7 @@ struct Monitor {
     statistics_map[name].count++;
   }
   void Stop(const std::string &name, GPUSet devices) {
-    if (debug_verbose) {
+    if (IsVerbose()) {
 #ifdef __CUDACC__
       for (auto device : devices) {
         cudaSetDevice(device);