[rabit harden] include osx in tests, address time_wait on port assignment, enable all tests

.gitignore

@@ -37,8 +37,12 @@ recommonmark
 recom
 _*
 
+#mpi lib
+mpich/
+mpich-3.2/
+
 # Jetbrain
 .idea
 cmake-build-debug/
-
+.vscode/
 

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "dmlc-core"]
 	path = dmlc-core
-	url = https://github.com/dmlc/dmlc-core
+	url = https://github.com/chenqin/dmlc-core
+	branch = py3

.travis.yml

@@ -1,5 +1,12 @@
-# disable sudo to use container based build
-sudo: false
+sudo: true
+
+os:
+  - linux
+  - osx
+
+osx_image: xcode9.3
+
+dist: xenial
 
 # Use Build Matrix to do lint and build seperately
 env:
@@ -10,51 +17,65 @@ env:
     - TASK=build
     - TASK=mpi-build
     - TASK=cmake-build
-    - TASK=test CXX=g++-4.8
+    - TASK=test CXX=g++
 
 # dependent apt packages
-dist: xenial
 addons:
   apt:
+    sources:
+      - llvm-toolchain-trusty-5.0
+      - ubuntu-toolchain-r-test
+      - george-edison55-precise-backports
     packages:
       - doxygen
-      - libopenmpi-dev
       - wget
       - git
       - libcurl4-openssl-dev
       - unzip
       - python-numpy
       - gcc-4.8
       - g++-4.8
-      - openmpi-bin
-      - openmpi-common
       - openssh-client
       - openssh-server
-      - libopenmpi-dev
+      - python3
+      - python3-setuptools
+  homebrew:
+    packages:
+      - gcc49
+      - openssl
+      - libgit2
+      - python3
+    update: true
 
 before_install:
   - export TRAVIS=dmlc-core/scripts/travis/
   - source ${TRAVIS}/travis_setup_env.sh
+  - ${TRAVIS}/travis_osx_install.sh
 
 install:
-  - pip install --user cpplint pylint kubernetes urllib3
+  - if [[ ${TRAVIS_OS_NAME} == "linux" ]]; then sudo apt-get install python3-pip; fi
+  - if [[ ${TRAVIS_OS_NAME} == "osx" ]]; then brew install python3; fi
+  - pip3 install cpplint pylint urllib3
+  - pip3 install websocket-client kubernetes
 
 script: scripts/travis_script.sh
 
-
-before_cache:
-  - ${TRAVIS}/travis_before_cache.sh
-
-
 cache:
   directories:
     - ${HOME}/.cache/usr
+    - ${HOME}/.cache/pip
+    - mpich
 
+before_cache:
+  - ${TRAVIS}/travis_before_cache.sh
+
+after_success:
+  - tree build
+  - bash <(curl -s https://codecov.io/bash) -a '-o src/ src/*.c'
 
 notifications:
 # Emails are sent to the committer's git-configured email address by default,
   email:
     on_success: change
     on_failure: always
 
-

Makefile

@@ -1,23 +1,26 @@
 OS := $(shell uname)
 
-export MPICXX = mpicxx
-export LDFLAGS=  -Llib
+export WARNFLAGS= -Wall -Wextra -Wno-unused-parameter -Wno-unknown-pragmas -std=c++11
+export CFLAGS = -O3 $(WARNFLAGS) -I $(DMLC)/include -I include/
+export LDFLAGS =-Llib
 
-OS := $(shell uname)
+#download mpi
+#echo $(shell scripts/mpi.sh)
+
+MPICXX=./mpich/bin/mpicxx
 
 ifeq ($(OS), Darwin)
     ifndef CC
-        export CC = $(if $(shell which clang), clang, gcc)
+        export CC = gcc-4.9
     endif
     ifndef CXX
-        export CXX = $(if $(shell which clang++), clang++, g++)
+        export CXX = g++-4.9
     endif
 else
     ifeq ($(OS), FreeBSD)
          ifndef CXX
              export CXX = g++6
          endif
-         export MPICXX = /usr/local/mpi/bin/mpicxx
          export LDFLAGS= -Llib -Wl,-rpath=/usr/local/lib/gcc6
     else
         # linux defaults
@@ -27,13 +30,10 @@ else
         ifndef CXX
             export CXX = g++
         endif
-        LDFLAGS += -lrt
+        LDFLAGS +=-lrt
     endif
 endif
 
-export WARNFLAGS= -Wall -Wextra -Wno-unused-parameter -Wno-unknown-pragmas -std=c++11
-export CFLAGS = -O3 $(WARNFLAGS)
-
 #----------------------------
 # Settings for power and arm arch
 #----------------------------
@@ -69,8 +69,10 @@ BPATH=.
 MPIOBJ= $(BPATH)/engine_mpi.o
 OBJ= $(BPATH)/allreduce_base.o $(BPATH)/allreduce_robust.o $(BPATH)/engine.o $(BPATH)/engine_empty.o $(BPATH)/engine_mock.o\
 	$(BPATH)/c_api.o $(BPATH)/engine_base.o
-SLIB= lib/librabit.so lib/librabit_mpi.so lib/librabit_mock.so lib/librabit_base.so
-ALIB= lib/librabit.a lib/librabit_mpi.a lib/librabit_empty.a lib/librabit_mock.a lib/librabit_base.a
+SLIB= lib/librabit.so lib/librabit_mock.so lib/librabit_base.so
+ALIB= lib/librabit.a lib/librabit_empty.a lib/librabit_mock.a lib/librabit_base.a
+MPISLIB= lib/librabit_mpi.so
+MPIALIB= lib/librabit_mpi.a
 HEADERS=src/*.h include/rabit/*.h include/rabit/internal/*.h
 DMLC=dmlc-core
 
@@ -95,22 +97,29 @@ lib/librabit_empty.a: $(BPATH)/engine_empty.o $(BPATH)/c_api.o
 lib/librabit_mpi.a lib/librabit_mpi.so: $(MPIOBJ)
 
 $(OBJ) :
-	$(CXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) ) -I include/ -I $(DMLC)/include
-
-$(MPIOBJ) :
-	$(MPICXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) ) -I $(DMLC)/include
+	$(CXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) )
 
 $(ALIB):
 	ar cr $@ $+
 
 $(SLIB) :
 	$(CXX) $(CFLAGS) -shared -o $@ $(filter %.cpp %.o %.c %.cc %.a, $^) $(LDFLAGS)
 
+$(MPIOBJ) :
+	$(MPICXX) -c $(CFLAGS) -I./mpich/include -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) )
+
+$(MPIALIB):
+	ar cr $@ $+
+
+$(MPISLIB) :
+	$(MPICXX) $(CFLAGS) -I./mpich/include -shared -o $@ $(filter %.cpp %.o %.c %.cc %.a, $^) \
+	$(LDFLAGS) -L./mpich/lib -Wl,-rpath,./mpich/lib -lmpi
+
 lint:
 	$(DMLC)/scripts/lint.py rabit $(LINT_LANG) src include
 
 doc doxygen:
 	cd include; doxygen ../doc/Doxyfile; cd -
 
 clean:
-	$(RM) $(OBJ) $(MPIOBJ) $(ALIB) $(MPIALIB) $(SLIB) *~ src/*~ include/*~ include/*/*~
+	$(RM)  $(OBJ) $(MPIOBJ) $(ALIB) $(MPIALIB) $(SLIB) *~ src/*~ include/*~ include/*/*~

scripts/mpi.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+if [ -f mpich/lib/libmpich.so ]; then
+  echo "libmpich.so found -- nothing to build."
+else
+  echo "Downloading mpich source."
+  wget http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
+  tar xfz mpich-3.2.tar.gz
+  rm mpich-3.2.tar.gz*
+  echo "configuring and building mpich."
+  cd mpich-3.2
+  #CC=gcc CXX=g++ CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64
+  ./configure \
+          --prefix=`pwd`/../mpich \
+          --enable-static=false \
+          --enable-alloca=true \
+          --disable-long-double \
+          --enable-threads=single \
+          --enable-fortran=no \
+          --enable-fast=all \
+          --enable-g=none \
+          --enable-timing=none \
+          --enable-cxx
+  make -j4
+  make install
+  cd -
+fi

scripts/travis_script.sh

@@ -15,6 +15,7 @@ if [ ${TASK} == "build" ]; then
 fi
 
 if [ ${TASK} == "mpi-build" ]; then
+    ./scripts/mpi.sh
     cd test
     make mpi && make speed_test.mpi || exit -1
 fi

src/allreduce_base.cc

@@ -131,6 +131,8 @@ void AllreduceBase::Shutdown(void) {
   utils::TCPSocket tracker = this->ConnectTracker();
   tracker.SendStr(std::string("shutdown"));
   tracker.Close();
+  // close listening sockets
+  sock_listen.Close();
   utils::TCPSocket::Finalize();
 }
 void AllreduceBase::TrackerPrint(const std::string &msg) {
@@ -271,12 +273,26 @@ void AllreduceBase::ReConnectLinks(const char *cmd) {
          "ReConnectLink failure 4");
   Assert(tracker.RecvAll(&next_rank, sizeof(next_rank)) == sizeof(next_rank),
          "ReConnectLink failure 4");
-  // create listening socket
-  utils::TCPSocket sock_listen;
-  sock_listen.Create();
-  int port = sock_listen.TryBindHost(slave_port, slave_port + nport_trial);
-  utils::Check(port != -1, "ReConnectLink fail to bind the ports specified");
-  sock_listen.Listen();
+
+  if (sock_listen == INVALID_SOCKET || sock_listen.AtMark()) {
+    if (!sock_listen.IsClosed()) {
+      sock_listen.Close();
+    }
+    // create listening socket
+    sock_listen.Create();
+    sock_listen.SetKeepAlive(true);
+    // http://deepix.github.io/2016/10/21/tcprst.html
+    sock_listen.SetLinger(0);
+    // [slave_port, slave_port+1 .... slave_port + newrank ...slave_port + nport_trial)
+    // work around processes bind to same port without set reuse option,
+    // start explore from slave_port + newrank towards end
+    port = sock_listen.TryBindHost(slave_port+ newrank%nport_trial, slave_port + nport_trial);
+    // if no port bindable, explore first half of range
+    if (port == -1) sock_listen.TryBindHost(slave_port, newrank% nport_trial + slave_port);
+
+    utils::Check(port != -1, "ReConnectLink fail to bind the ports specified");
+    sock_listen.Listen();
+  }
 
   // get number of to connect and number of to accept nodes from tracker
   int num_conn, num_accept, num_error = 1;
@@ -311,6 +327,7 @@ void AllreduceBase::ReConnectLinks(const char *cmd) {
              "ReConnectLink failure 9");
       Assert(tracker.RecvAll(&hrank, sizeof(hrank)) == sizeof(hrank),
              "ReConnectLink failure 10");
+
       r.sock.Create();
       if (!r.sock.Connect(utils::SockAddr(hname.c_str(), hport))) {
         num_error += 1; r.sock.Close(); continue;
@@ -357,8 +374,7 @@ void AllreduceBase::ReConnectLinks(const char *cmd) {
     }
     if (!match) all_links.push_back(r);
   }
-  // close listening sockets
-  sock_listen.Close();
+
   this->parent_index = -1;
   // setup tree links and ring structure
   tree_links.plinks.clear();

src/allreduce_base.h

@@ -521,6 +521,10 @@ class AllreduceBase : public IEngine {
   int world_size;
   // connect retry time
   int connect_retry;
+  // backdoor listening peer connection
+  utils::TCPSocket sock_listen;
+  // backdoor port
+  int port = 0;
 };
 }  // namespace engine
 }  // namespace rabit

src/allreduce_robust.cc

@@ -51,12 +51,10 @@ void AllreduceRobust::Shutdown(void) {
   utils::Assert(RecoverExec(NULL, 0, ActionSummary::kCheckAck, ActionSummary::kSpecialOp),
                 "Shutdown: check ack must return true");
 
-  // one worker shutdowns and closes sockets while rest still run kCheckAck,
-  // seems has something to do with time-wait state in tcp connection,
-  // this cause rest workers checkandrecover and hang inf,
-  // https://github.com/dmlc/xgboost/pull/3818
-  // TODO(Chen Qin): a fundamental fix for this
-  sleep(1);
+#if defined (__APPLE__)
+        sleep(1);
+#endif
+
   AllreduceBase::Shutdown();
 }
 /*!

src/socket.h

@@ -276,13 +276,21 @@ class TCPSocket : public Socket{
    * \brief enable/disable TCP keepalive
    * \param keepalive whether to set the keep alive option on
    */
-  inline void SetKeepAlive(bool keepalive) {
+  void SetKeepAlive(bool keepalive) {
     int opt = static_cast<int>(keepalive);
     if (setsockopt(sockfd, SOL_SOCKET, SO_KEEPALIVE,
                    reinterpret_cast<char*>(&opt), sizeof(opt)) < 0) {
       Socket::Error("SetKeepAlive");
     }
   }
+  inline void SetLinger(int timeout = 0) {
+    struct linger sl;
+    sl.l_onoff = 1;    /* non-zero value enables linger option in kernel */
+    sl.l_linger = timeout;    /* timeout interval in seconds */
+    if (setsockopt(sockfd, SOL_SOCKET, SO_LINGER, &sl, sizeof(sl)) == -1) {
+      Socket::Error("SO_LINGER");
+    }
+  }
   /*!
    * \brief create the socket, call this before using socket
    * \param af domain

test/Makefile

@@ -1,4 +1,4 @@
-export MPICXX = mpicxx
+MPICXX=../mpich/bin/mpicxx
 export LDFLAGS=  -L../lib -pthread -lm
 export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -fPIC -I../include -I ../dmlc-core/include -std=c++11
 
@@ -27,11 +27,17 @@ OBJ = $(RABIT_OBJ) speed_test.o model_recover.o local_recover.o lazy_recover.o
 MPIBIN = speed_test.mpi
 .PHONY: clean all lib mpi
 
+.PHONY: lib all
+
 all: $(BIN)
+
 lib:
-	cd ..;make;cd -
+	cd ..;make clean;make;cd -
+
+.PHONY: mpi
 mpi:
 	cd ..;make mpi;cd -
+
 # programs
 speed_test.o: speed_test.cc ../include/rabit/*.h lib mpi
 model_recover.o: model_recover.cc ../include/rabit/*.h lib
@@ -52,7 +58,8 @@ $(OBJ) :
 	$(CXX) -c $(CFLAGS) -o $@ $(firstword $(filter %.cpp %.c %.cc, $^) )
 
 $(MPIBIN) :
-	$(MPICXX) $(CFLAGS) -o $@ $(filter %.cpp %.o %.c %.cc, $^) ../lib/librabit_mpi.so $(LDFLAGS)
+	$(MPICXX) $(CFLAGS) -I../mpich/include -shared -o $@ $(filter %.cpp %.o %.c %.cc, $^) \
+    ../lib/librabit_mpi.so $(LDFLAGS) -L../mpich/lib -Wl,-rpath,../mpich/lib -lmpi
 
 clean:
 	$(RM) $(OBJ) $(BIN) $(MPIBIN) $(MPIOBJ) *~ ../src/*~