xgboost-patch.diff

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 22e8c476..d58fa73a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.2)
 project(xgboost)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/modules")
-find_package(OpenMP)
+#find_package(OpenMP)
 
 set_default_configuration_release()
 msvc_use_static_runtime()
@@ -50,6 +50,8 @@ if(USE_AVX)
   add_definitions(-DXGBOOST_USE_AVX)
 endif()
 
+# We need this to be present when any file included dmlc headers is included (not just for dmlc code)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DDISABLE_OPENMP")
 
 # compiled code customizations for R package
 if(R_LIB)
@@ -190,7 +192,7 @@ else()
     OUTPUT_NAME xgboost
   )
   set_output_directory(runxgboost ${PROJECT_SOURCE_DIR})
-  target_link_libraries(runxgboost ${LINK_LIBRARIES})
+  target_link_libraries(runxgboost ${LINK_LIBRARIES} pthread)
 
   # Shared library
   add_library(xgboost SHARED $<TARGET_OBJECTS:objxgboost>)
diff --git a/dmlc-core b/dmlc-core
--- a/dmlc-core
+++ b/dmlc-core
@@ -1 +1 @@
-Subproject commit b5bec5481df86e8e6728d8bd80a61d87ef3b2cd5
+Subproject commit b5bec5481df86e8e6728d8bd80a61d87ef3b2cd5-dirty
diff --git a/include/xgboost/base.h b/include/xgboost/base.h
index 24ff4d39..77ffedb4 100644
--- a/include/xgboost/base.h
+++ b/include/xgboost/base.h
@@ -51,7 +51,7 @@
 #endif
 
 #if defined(__GNUC__) && ((__GNUC__ == 4 && __GNUC_MINOR__ >= 8) || __GNUC__ > 4) && \
-    !defined(__CUDACC__)
+    !defined(__CUDACC__) && !defined(DISABLE_OPENMP)
 #include <parallel/algorithm>
 #define XGBOOST_PARALLEL_SORT(X, Y, Z) __gnu_parallel::sort((X), (Y), (Z))
 #define XGBOOST_PARALLEL_STABLE_SORT(X, Y, Z) \
diff --git a/jvm-packages/create_jni.py b/jvm-packages/create_jni.py
index 8ce0aa1b..703a2630 100755
--- a/jvm-packages/create_jni.py
+++ b/jvm-packages/create_jni.py
@@ -14,7 +14,7 @@ if sys.platform.startswith("linux"):
 
 
 CONFIG = {
-    "USE_OPENMP": "ON",
+    "USE_OPENMP": "OFF",
     "USE_HDFS": "OFF",
     "USE_AZURE": "OFF",
     "USE_S3": "OFF",
@@ -85,7 +85,7 @@ if __name__ == "__main__":
                 maybe_generator = ""
 
             args = ["-D{0}:BOOL={1}".format(k, v) for k, v in CONFIG.items()]
-            run("cmake .. " + " ".join(args) + maybe_generator)
+            run("cmake .. -DCMAKE_VERBOSE_MAKEFILE=1 " + " ".join(args) + maybe_generator)
             run("cmake --build . --config Release")
 
         with cd("demo/regression"):
diff --git a/rabit b/rabit
--- a/rabit
+++ b/rabit
@@ -1 +1 @@
-Subproject commit a764d45cfb438cc9f15cf47ce586c02ff2c65d0f
+Subproject commit a764d45cfb438cc9f15cf47ce586c02ff2c65d0f-dirty