Author: nanxiao

Porting CUDA program from ArchLinux to Ubuntu 16.04

Today I ported a CUDA project from Arch Linux to Ubuntu 16.04, and this post records the pitfalls.

(0) Update cmake to newest version (follow this);

(1) Specify nvcc path in CMakeLists.txt:

SET(CMAKE_CUDA_COMPILER /usr/local/cuda-9.0/bin/nvcc)

otherwise, following error may generate:

......
No CMAKE_CUDA_COMPILER could be found.
......

(2) Since Ubuntu 16.04‘s default compiler is still gcc-5, install gcc-6 first, then pass gcc-6 as default compiler for nvcc:

......
SET(CMAKE_CXX_STANDARD 11)
SET(CMAKE_CUDA_FLAGS "-std=c++11 -ccbin gcc-6")
......

(3) Execute cmake command:

cmake -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 -DCMAKE_BUILD_TYPE=Release ..

References:
Not Locating CUDA Compiler;
CMake: How to pass mode dependent compile flags to nvcc in visual studio environment;
Tensorflow crashes on build on Ubuntu 16.04 when building for skylake (avx512).

 

OpenBSD saves me again! — Debug a memory corruption issue

Yesterday, I came across a third-part library issue, which crashes at allocating memory:

......
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f594a5a9b6b in _int_malloc () from /usr/lib/libc.so.6
(gdb) bt
#0  0x00007f594a5a9b6b in _int_malloc () from /usr/lib/libc.so.6
#1  0x00007f594a5ab503 in malloc () from /usr/lib/libc.so.6
#2  0x00007f594b13f159 in operator new (sz=5767168) at /build/gcc/src/gcc/libstdc++-v3/libsupc++/new_op.cc:50
......

It is obvious that the memory tags are corrupted, but who is the murder? Since the library involves a lot of maths computation, it is not an easy task to grasp the code quickly. So I need to find another way:

(1) Open all warnings during compilation: -Wall. Nothing found.

(2) Use valgrind, but unfortunately, valgrind crashes itself:

......
valgrind: the 'impossible' happened:
   Killed by fatal signal

host stacktrace:
==43326==    at 0x58053139: get_bszB_as_is (m_mallocfree.c:303)
==43326==    by 0x58053139: get_bszB (m_mallocfree.c:315)
==43326==    by 0x58053139: vgPlain_arena_malloc (m_mallocfree.c:1799)
==43326==    by 0x5800BA84: vgMemCheck_new_block (mc_malloc_wrappers.c:372)
==43326==    by 0x5800BD39: vgMemCheck___builtin_vec_new (mc_malloc_wrappers.c:427)
==43326==    by 0x5809F785: do_client_request (scheduler.c:1866)
==43326==    by 0x5809F785: vgPlain_scheduler (scheduler.c:1433)
==43326==    by 0x580AED50: thread_wrapper (syswrap-linux.c:103)
==43326==    by 0x580AED50: run_a_thread_NORETURN (syswrap-linux.c:156)

sched status:
  running_tid=1
......

(3) Change compiler, use clang instead of gcc, and hope it can give me some clues. Still no effect.

(4) Switch Operating System from Linux to OpenBSD, the program crashes again. But this time, it tells me where the memory corruption occurs:

......
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x000014b07f01e52d in addMod (r=<error reading variable>, a=4693443247995522, b=28622907746665631,
......

I figure out the issue quickly, and not bother to understand the whole code. OpenBSD saves me again, thanks!

 

Reflection on one-year usage of OpenBSD

I have used OpenBSD for more than one year, and it is time to give a summary of the experience:

(1) What do I get from OpenBSD?

a) A good UNIX tutorial. When I am curious about some UNIXcommands’ implementation, I will refer to OpenBSD source code, and I actually gain something every time. E.g., refresh socket programming skills from nc; know how to process file efficiently from cat.

b) A better test bed. Although my work focus on developing programs on Linux, I will try to compile and run applications on OpenBSD if it is possible. One reason is OpenBSD usually gives more helpful warnings. E.g., hint like this:

......
warning: sprintf() is often misused, please use snprintf()
......

Or you can refer this post which I wrote before. The other is sometimes program run well on Linux may crash on OpenBSD, and OpenBSD can help you find hidden bugs.

c) Some handy tools. E.g. I find tcpbench is useful, so I ported it into Linuxfor my own usage (project is here).

(2) What I give back to OpenBSD?

a) Patches. Although most of them are trivial modifications, they are still my contributions.

b) Write blog posts to share experience about using OpenBSD.

c) Develop programs for OpenBSD/*BSD: lscpu and free.

d) Porting programs into OpenBSD: E.g., I find google/benchmark is a nifty tool, but lacks OpenBSD support, I submitted PR and it is accepted. So you can use google/benchmark on OpenBSD now.

Generally speaking, the time invested on OpenBSD is rewarding. If you are still hesitating, why not give a shot?

Be wary of “Boost”, not “boost” in CMakeLists.txt

In Cygwin, the following statements in CMakeLists.txt:

......
find_package(boost 1.66 REQUIRED COMPONENTS system)
if(Boost_FOUND)
    include_directories(${Boost_INCLUDE_DIRS})
    add_executable(play main.cpp)
    target_link_libraries(play ${Boost_LIBRARIES})
endif()
......

causes following errors:

......
CMakeFiles/play.dir/main.cpp.o: In function `boost::system::error_code::error_code()':
/usr/include/boost/system/error_code.hpp:449: undefined reference to `boost::system::system_category()'
/usr/include/boost/system/error_code.hpp:449:(.text$_ZN5boost6system10error_codeC1Ev[_ZN5boost6system10error_codeC1Ev]+0x17): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::system_category()'
CMakeFiles/play.dir/main.cpp.o: In function `boost::system::error_category::std_category::equivalent(int, std::error_condition const&) const':
/usr/include/boost/system/error_code.hpp:676: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:676:(.text$_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0xa9): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:679: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:679:(.text$_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0xe4): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::generic_category()'
CMakeFiles/play.dir/main.cpp.o: In function `boost::system::error_category::std_category::equivalent(std::error_code const&, int) const':
/usr/include/boost/system/error_code.hpp:706: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:706:(.text$_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xab): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:709: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:709:(.text$_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xe6): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:721: undefined reference to `boost::system::generic_category()'
/usr/include/boost/system/error_code.hpp:721:(.text$_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0x1be): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::generic_category()'
CMakeFiles/play.dir/main.cpp.o: In function `boost::asio::error::get_system_category()':
/usr/include/boost/asio/error.hpp:229: undefined reference to `boost::system::system_category()'
/usr/include/boost/asio/error.hpp:229:(.text$_ZN5boost4asio5error19get_system_categoryEv[_ZN5boost4asio5error19get_system_categoryEv]+0x9): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `boost::system::system_category()'
collect2: error: ld returned 1 exit status

Change boost to Boost:

find_package(Boost 1.66 REQUIRED COMPONENTS system)
......

All is OK now!