Segmentation fault (core dumped) when 'make runtest'

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Darcy

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Oct 20, 2019, 9:47:08 PM10/20/19

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I've tried to solve this problem for a few days, but I can't. If someone can help me, I'll appreciate.

Pre-information:
I have two ubuntu16 servers, one with four GTX1080( abbr. server A below), one with four Titan Xp( abbr. server B below). GCC version are both 5.4.0 20160609, make version are both GNU Make 4.1.
I succeed build caffe on Server A, the Makefile.config is :

## Refer to http://caffe.berkeleyvision.org/installation.html
# Contributions simplifying and improving our build system are welcome!

# cuDNN acceleration switch (uncomment to build with cuDNN).
USE_CUDNN := 1

# CPU-only switch (uncomment to build without GPU support).
# CPU_ONLY := 1

# uncomment to disable IO dependencies and corresponding data layers
# USE_OPENCV := 0
# USE_LEVELDB := 0
# USE_LMDB := 0
# This code is taken from https://github.com/sh1r0/caffe-android-lib
# USE_HDF5 := 0

# uncomment to allow MDB_NOLOCK when reading LMDB files (only if necessary)
#	You should not set this flag if you will be reading LMDBs with any
#	possibility of simultaneous read and write
# ALLOW_LMDB_NOLOCK := 1

# Uncomment if you're using OpenCV 3
# OPENCV_VERSION := 3

# To customize your choice of compiler, uncomment and set the following.
# N.B. the default for Linux is g++ and the default for OSX is clang++
# CUSTOM_CXX := g++

# CUDA directory contains bin/ and lib/ directories that we need.
CUDA_DIR := /usr/local/cuda
# On Ubuntu 14.04, if cuda tools are installed via
# "sudo apt-get install nvidia-cuda-toolkit" then use this instead:
# CUDA_DIR := /usr

# CUDA architecture setting: going with all of them.
# For CUDA < 6.0, comment the *_50 through *_61 lines for compatibility.
# For CUDA < 8.0, comment the *_60 and *_61 lines for compatibility.
# For CUDA >= 9.0, comment the *_20 and *_21 lines for compatibility.
CUDA_ARCH :=	-gencode arch=compute_30,code=sm_30 \
		-gencode arch=compute_35,code=sm_35 \
		-gencode arch=compute_50,code=sm_50 \
		-gencode arch=compute_52,code=sm_52 \
		-gencode arch=compute_60,code=sm_60 \
		-gencode arch=compute_61,code=sm_61 \
		-gencode arch=compute_61,code=compute_61

# BLAS choice:
# atlas for ATLAS (default)
# mkl for MKL
# open for OpenBlas
BLAS := atlas
# Custom (MKL/ATLAS/OpenBLAS) include and lib directories.
# Leave commented to accept the defaults for your choice of BLAS
# (which should work)!
# BLAS_INCLUDE := /path/to/your/blas
# BLAS_LIB := /path/to/your/blas

# Homebrew puts openblas in a directory that is not on the standard search path
# BLAS_INCLUDE := $(shell brew --prefix openblas)/include
# BLAS_LIB := $(shell brew --prefix openblas)/lib

# This is required only if you will compile the matlab interface.
# MATLAB directory should contain the mex binary in /bin.
# MATLAB_DIR := /usr/local
# MATLAB_DIR := /Applications/MATLAB_R2012b.app

# NOTE: this is required only if you will compile the python interface.
# We need to be able to find Python.h and numpy/arrayobject.h.
#PYTHON_INCLUDE := /usr/include/python2.7 \
#		/usr/lib/python2.7/dist-packages/numpy/core/include
# Anaconda Python distribution is quite popular. Include path:
# Verify anaconda location, sometimes it's in root.
# ANACONDA_HOME := $(HOME)/anaconda
# PYTHON_INCLUDE := $(ANACONDA_HOME)/include \
		# $(ANACONDA_HOME)/include/python2.7 \
		# $(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include

# Uncomment to use Python 3 (default is Python 2)
PYTHON_LIBRARIES := boost_python3 python3.5m
PYTHON_INCLUDE := /usr/include/python3.5m \
                 /usr/lib/python3.5/dist-packages/numpy/core/include

# We need to be able to find libpythonX.X.so or .dylib.
PYTHON_LIB := /usr/lib
# PYTHON_LIB := $(ANACONDA_HOME)/lib

# Homebrew installs numpy in a non standard path (keg only)
# PYTHON_INCLUDE += $(dir $(shell python -c 'import numpy.core; print(numpy.core.__file__)'))/include
# PYTHON_LIB += $(shell brew --prefix numpy)/lib

# Uncomment to support layers written in Python (will link against Python libs)
WITH_PYTHON_LAYER := 1

# Whatever else you find you need goes here.
INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/hdf5/serial

# If Homebrew is installed at a non standard location (for example your home directory) and you use it for general dependencies
# INCLUDE_DIRS += $(shell brew --prefix)/include
# LIBRARY_DIRS += $(shell brew --prefix)/lib

# NCCL acceleration switch (uncomment to build with NCCL)
# https://github.com/NVIDIA/nccl (last tested version: v1.2.3-1+cuda8.0)
# USE_NCCL := 1

# Uncomment to use `pkg-config` to specify OpenCV library paths.
# (Usually not necessary -- OpenCV libraries are normally installed in one of the above $LIBRARY_DIRS.)
# USE_PKG_CONFIG := 1

# N.B. both build and distribute dirs are cleared on `make clean`
BUILD_DIR := build
DISTRIBUTE_DIR := distribute

# Uncomment for debugging. Does not work on OSX due to https://github.com/BVLC/caffe/issues/171
# DEBUG := 1

# The ID of the GPU that 'make runtest' will use to run unit tests.
TEST_GPUID := 0

# enable pretty build (comment to see full commands)
Q ?= @

I edited two line of Makefile :

change:
NVCCFLAGS +=-ccbin=$(CXX) -Xcompiler-fPIC $(COMMON_FLAGS)
to：
NVCCFLAGS += -D_FORCE_INLINES -ccbin=$(CXX) -Xcompiler -fPIC $(COMMON_FLAGS)
change:
LIBRARIES += glog gflags protobuf boost_system boost_filesystem m
to：
LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_serial_hl hdf5_serial

But I use the same configuration on server B, it doesn't work.
no error when ' make all -j8 ' and ' make test -j8 ', but errors occurred when ' make runtest ':

........................................  

[----------] 2 tests from InternalThreadTest
[ RUN      ] InternalThreadTest.TestRandomSeed
*** Aborted at 1571325377 (unix time) try "date -d @1571325377" if you are using GNU date ***
PC: @     0x7f0e1ef36d44 __GI___pthread_mutex_lock
*** SIGSEGV (@0x190) received by PID 27872 (TID 0x7f0e21c71b00) from PID 400; stack trace: ***
    @     0x7f0e1eb984b0 (unknown)
    @     0x7f0e1ef36d44 __GI___pthread_mutex_lock
    @     0x7f0e1ffb626a boost::thread::interrupt()
    @     0x7f0e1f9260b9 caffe::InternalThread::StopInternalThread()
    @           0x67b22f caffe::InternalThreadTest_TestRandomSeed_Test::TestBody()
    @           0x74b843 testing::internal::HandleExceptionsInMethodIfSupported<>()
    @           0x744e5a testing::Test::Run()
    @           0x744fa8 testing::TestInfo::Run()
    @           0x745085 testing::TestCase::Run()
    @           0x74635f testing::internal::UnitTestImpl::RunAllTests()
    @           0x746683 testing::UnitTest::Run()
    @           0x45c7b2 main
    @     0x7f0e1eb83830 __libc_start_main
    @           0x463c19 _start
    @                0x0 (unknown)
Segmentation fault (core dumped)
Makefile:542: recipe for target 'runtest' failed
make: *** [runtest] Error 139

Then I uncomment# USE_OPENCV := 0to disable opencv, it still doesn't work, then uncomment #CPU_ONLY := 1 to disable GPU, it still doesn't work.