diff --git a/.gitignore b/.gitignore
index 62f3b823f..3d427e30d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -69,4 +69,4 @@ nb-configuration*
 .pydevproject
 .settings/
 build
-
+config.mk
diff --git a/Makefile b/Makefile
index 2406102b3..5fdf20021 100644
--- a/Makefile
+++ b/Makefile
@@ -1,38 +1,10 @@
-ifndef CC
-export CC  = $(if $(shell which gcc-5),gcc-5,gcc)
-endif
-ifndef CXX
-export CXX = $(if $(shell which g++-5),g++-5,g++)
-endif
-
-export LDFLAGS= -pthread -lm
-export CFLAGS= -Wall -O3 -msse2  -Wno-unknown-pragmas -funroll-loops -fPIC -Iinclude
-
-ifndef LINT_LANG
-	LINT_LANG= "all"
-endif
-
-ifeq ($(OS), Windows_NT)
-	export CXX = g++ -m64
-	export CC = gcc -m64
-endif
-
-UNAME= $(shell uname)
-
-ifeq ($(UNAME), Linux)
-	LDFLAGS += -lrt
-endif
-
-ifeq ($(no_omp),1)
-	CFLAGS += -DDISABLE_OPENMP
+ifndef config
+ifneq ("$(wildcard ./config.mk)","")
+	config = config.mk
 else
-	ifeq ($(omp_mac_static),1)
-		CFLAGS += -static-libgcc -static-libstdc++ -L. -fopenmp
-	else
-		CFLAGS += -fopenmp
-	endif
+	config = make/config.mk
+endif
 endif
-
 
 ifndef DMLC_CORE
 	DMLC_CORE = dmlc-core
@@ -42,21 +14,60 @@ ifndef RABIT
 	RABIT = rabit
 endif
 
+ROOTDIR = $(CURDIR)
+UNAME= $(shell uname)
+
+include $(config)
+ifeq ($(USE_OPENMP), 0)
+	export NO_OPENMP = 1
+endif
+include $(DMLC_CORE)/make/dmlc.mk
+
+# use customized config file
+ifndef CC
+export CC  = $(if $(shell which gcc-5),gcc-5,gcc)
+endif
+ifndef CXX
+export CXX = $(if $(shell which g++-5),g++-5,g++)
+endif
+
+ifeq ($(OS), Windows_NT)
+	export CXX = g++ -m64
+	export CC = gcc -m64
+endif
+
+export LDFLAGS= -pthread -lm $(ADD_LDFLAGS) $(DMLC_LDFLAGS)
+export CFLAGS= -Wall -O3 -msse2  -Wno-unknown-pragmas -funroll-loops -fPIC -Iinclude $(ADD_CFLAGS)
+CFLAGS += -I$(DMLC_CORE)/include -I$(RABIT)/include
+
+ifndef LINT_LANG
+	LINT_LANG= "all"
+endif
+
+ifeq ($(UNAME), Linux)
+	LDFLAGS += -lrt
+endif
+
+ifeq ($(USE_OPENMP), 1)
+	CFLAGS += -fopenmp
+else
+	CFLAGS += -DDISABLE_OPENMP
+endif
+
 # specify tensor path
-.PHONY: clean all lint
+.PHONY: clean all lint clean_all
 
 all: lib/libxgboost.a lib/libxgboost.so
 
 $(DMLC_CORE)/libdmlc.a:
-	+ cd $(DMLC_CORE); make libdmlc.a; cd $(ROOTDIR)
+	+ cd $(DMLC_CORE); make libdmlc.a config=$(ROOTDIR)/$(config); cd $(ROOTDIR)
 
-$(RABIT)/lib/librabit.a:
-	+ cd $(RABIT); make lib/librabit.a; cd $(ROOTDIR)
+$(RABIT)/lib/$(LIB_RABIT):
+	+ cd $(RABIT); make lib/$(LIB_RABIT); cd $(ROOTDIR)
 
-CFLAGS += -I$(DMLC_CORE)/include -I$(RABIT)/include
 SRC = $(wildcard src/*.cc src/*/*.cc)
 OBJ = $(patsubst src/%.cc, build/%.o, $(SRC))
-LIB_DEP = $(DMLC_CORE)/libdmlc.a $(RABIT)/lib/librabit.a
+LIB_DEP = $(DMLC_CORE)/libdmlc.a $(RABIT)/lib/$(LIB_RABIT)
 ALL_DEP = $(OBJ) $(LIB_DEP)
 
 build/%.o: src/%.cc
@@ -78,7 +89,7 @@ lint:
 clean:
 	$(RM) -r build lib bin *~ */*~ */*/*~ */*/*/*~
 
-clean_all: clean
+clean: clean_all
 	cd $(DMLC_CORE); make clean; cd -
 	cd $(RABIT); make clean; cd -
 
diff --git a/build.sh b/build.sh
index 2a285597a..8480cd4f9 100755
--- a/build.sh
+++ b/build.sh
@@ -6,27 +6,14 @@
 
 # See additional instruction in doc/build.md
 
-#for building static OpenMP lib in MAC for easier installation in MAC
-#doesn't work with XCode clang/LLVM since Apple doesn't support, 
-#needs brew install gcc 4.9+ with OpenMP. By default the static link is OFF
-static_omp=0
-if ((${static_omp}==1)); then
-    rm libgomp.a
-    ln -s `g++ -print-file-name=libgomp.a`
-    make clean
-    make omp_mac_static=1
-    echo "Successfully build multi-thread static link xgboost"
-    exit 0
-fi
-
 if make; then
     echo "Successfully build multi-thread xgboost"
 else
     echo "-----------------------------"
     echo "Building multi-thread xgboost failed"
     echo "Start to build single-thread xgboost"
-    make clean
-    make no_omp=1
+    make clean_all
+    make config=config/mininum.mk
     echo "Successfully build single-thread xgboost"
     echo "If you want multi-threaded version"
     echo "See additional instructions in doc/build.md"
diff --git a/make/config.mk b/make/config.mk
new file mode 100644
index 000000000..1bf0d7738
--- /dev/null
+++ b/make/config.mk
@@ -0,0 +1,48 @@
+#-----------------------------------------------------
+#  xgboost: the configuration compile script
+#
+#  If you want to change the configuration, please use the following
+#  steps. Assume you are on the root directory of xgboost.
+#  First copy the this file so that any local changes will be ignored by git
+#
+#  $ cp make/config.mk .
+#
+#  Next modify the according entries, and then compile by
+#
+#  $ make
+#
+#  or build in parallel with 8 threads
+#
+#  $ make -j8
+#----------------------------------------------------
+
+# choice of compiler, by default use system preference.
+# export CC = gcc
+# export CXX = g++
+# export MPICXX = mpicxx
+
+# the additional link flags you want to add
+ADD_LDFLAGS =
+
+# the additional compile flags you want to add
+ADD_CFLAGS =
+
+# Whether enable openmp support, needed for multi-threading.
+USE_OPENMP = 1
+
+# whether use HDFS support during compile
+USE_HDFS = 0
+
+# whether use AWS S3 support during compile
+USE_S3 = 0
+
+# whether use Azure blob support during compile
+USE_AZURE = 0
+
+# Rabit library version,
+# - librabit.a Normal distributed version.
+# - librabit_empty.a Non distributed mock version,
+LIB_RABIT = librabit.a
+
+# path to libjvm.so
+LIBJVM=$(JAVA_HOME)/jre/lib/amd64/server
diff --git a/make/minimum.mk b/make/minimum.mk
new file mode 100644
index 000000000..f9bef57bd
--- /dev/null
+++ b/make/minimum.mk
@@ -0,0 +1,22 @@
+#-----------------------------------------------------
+# xgboost: minumum dependency configuration,
+# see config.mk for template.
+#----------------------------------------------------
+
+# Whether enable openmp support, needed for multi-threading.
+USE_OPENMP = 0
+
+# whether use HDFS support during compile
+USE_HDFS = 0
+
+# whether use AWS S3 support during compile
+USE_S3 = 0
+
+# whether use Azure blob support during compile
+USE_AZURE = 0
+
+# Rabit library version,
+# - librabit.a Normal distributed version.
+# - librabit_empty.a Non distributed mock version,
+LIB_RABIT = librabit_empty.a
+