Author: nanxiao

Downgrade boost on Ubuntu 16.04

In the past 2 days, I was tortured by boost. The default boostversion on Ubuntu 16.04 is 1.58, but I met following compile errors:

......
/usr/include/boost/multi_index/detail/bucket_array.hpp: In static member function ‘static std::size_t boost::multi_index::detail::bucket_array_base<_>::size_index(std::size_t)’:
/usr/include/boost/multi_index/detail/bucket_array.hpp:84:62: error: invalid use of non-lvalue array
     const std::size_t *bound=std::lower_bound(sizes,sizes+sizes_length,n);
                                                              ^~~~~~~~~~~~
/usr/include/boost/multi_index/detail/bucket_array.hpp:85:25: error: invalid use of non-lvalue array
     if(bound==sizes+sizes_length)--bound;
                         ^~~~~~~~~~~~
/usr/include/boost/multi_index/detail/bucket_array.hpp:86:22: error: invalid use of non-lvalue array
     return bound-sizes;
......

I downgraded boost to 1.55; and downloaded and built it:

$ ./bootstrap.sh --prefix=/usr/local  
$ sudo ./b2 -a -q install

This time I found the default gcc-5 could not compile successfully. So I followed this post to install gcc-6, and modified/home/nan/boost_1_55_0/tools/build/v2/user-config.jam file to use gcc-6 to compile boost:

......
# Configure specific gcc version, giving alternative name to use.
using gcc : 6 : g++-6 ;
......

Then my project can be compiled successfully. Check gcc search header file path and library path:

$ echo | gcc-6 -E -Wp,-v -
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/6/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/lib/gcc/x86_64-linux-gnu/6/include
 /usr/local/include
 /usr/lib/gcc/x86_64-linux-gnu/6/include-fixed
 /usr/include/x86_64-linux-gnu
 /usr/include
......

$ ldconfig -v 2>/dev/null | grep -v ^$'\t'
/usr/local/cuda-9.0/targets/x86_64-linux/lib:
/usr/lib/x86_64-linux-gnu/libfakeroot:
/usr/local/lib:
/lib/x86_64-linux-gnu:
/usr/lib/x86_64-linux-gnu:
/usr/lib/nvidia-384:
/usr/lib32/nvidia-384:
/lib32:
/usr/lib32:
/lib:
/usr/lib:
/usr/lib/nvidia-384/tls: (hwcap: 0x8000000000000000)
/usr/lib32/nvidia-384/tls: (hwcap: 0x8000000000000000)

You will find the fresh installed boost 1.55 (in /usr/local directory) always be found before default boost 1.58 (header files are in /usr/include/boostand libraries in /usr/lib/x86_64-linux-gnu).

Update keyring first if your Arch Linux is old enough

My Arch Linux is not updated for nearly 3 months. When running pacman -Syu, it prompts following errors:

$ sudo pacman -Syu
......
error: python-dnspython: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python-dnspython-1.16.0-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: python-distlib: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python-distlib-0.2.8-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: python-pytoml: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python-pytoml-0.1.20-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: python2-distlib: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python2-distlib-0.2.8-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: python2-dnspython: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python2-dnspython-1.16.0-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: python2-pytoml: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/python2-pytoml-0.1.20-1-any.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: qbittorrent: signature from "Eli Schwartz <eschwartz@archlinux.org>" is unknown trust
:: File /var/cache/pacman/pkg/qbittorrent-4.1.5-1-x86_64.pkg.tar.xz is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n]
error: failed to commit transaction (invalid or corrupted package)
Errors occurred, no packages were upgraded.
......

The solution is updating archlinux-keyring first:

$ sudo pacman -S archlinux-keyring

Then all goes well!

Modifying memory pool helps me find a hidden bug

My project has a CUDA memory pool which uses C++‘s std::queue. Allocating from the head of queue:

ptr = q.front();
q.pop();

While freeing memory insert it into the tail of queue:

q.push(ptr);

I changed the implementation from std::queue to std::deque. Both allocating and freeing all occur in the front of queue:

ptr = q.front();
q.pop_front();
......
q.push_front(ptr);

This modification helps me find a hidden bug which is releasing memory early. In origin code, the memory is inserted at the end of queue. So there is a interval between it is reused by other threads and current thread, and the work can still be done correctly as long as it is not reused by others. But after using std::deque, the memory is immediately used by other threads, which disclose the bug.

 

Beware of synchronizing steam when using “default-stream per-thread” in CUDA

Yesterday, I refactored a project through adding”--default-stream per-thread” option to improve its performance. Unfortunately, program will crash in cudaMemcpy:

Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f570d3eb7f0 in ?? () from /usr/lib/libcuda.so.1
[Current thread is 1 (Thread 0x7f5620fa1700 (LWP 31206))]
(gdb) bt
#0  0x00007f570d3eb7f0 in ?? () from /usr/lib/libcuda.so.1
#1  0x00007f570d45ffef in ?? () from /usr/lib/libcuda.so.1
#2  0x00007f570d3bff90 in ?? () from /usr/lib/libcuda.so.1
#3  0x00007f570d3198d5 in ?? () from /usr/lib/libcuda.so.1
#4  0x00007f570d319da7 in ?? () from /usr/lib/libcuda.so.1
#5  0x00007f570d21d665 in ?? () from /usr/lib/libcuda.so.1
#6  0x00007f570d21de08 in ?? () from /usr/lib/libcuda.so.1
#7  0x00007f570d352455 in cuMemcpy_ptds () from /usr/lib/libcuda.so.1
#8  0x00007f570ee1b0f9 in cudart::driverHelper::memcpyDispatch(void*, void const*, unsigned long, cudaMemcpyKind, bool) ()
   from /home/xiaonan/DSI_cuRlib_v2.0/build/src/libtest.so
#9  0x00007f570ede70f9 in cudart::cudaApiMemcpy_ptds(void*, void const*, unsigned long, cudaMemcpyKind) () from /home/xiaonan/DSI_cuRlib_v2.0/build/src/libtest.so
#10 0x00007f570ee2772b in cudaMemcpy_ptds ()
   from /home/xiaonan/DSI_cuRlib_v2.0/build/src/libtest.so  
......

After reading GPU Pro Tip: CUDA 7 Streams Simplify Concurrency and How to Overlap Data Transfers in CUDA C/C++ carefully, I found the root cause. Because in my program, the CUDA memory is allocated through cudaMalloc (not unified memory), I also need synchronizing stream, like this:

cudaMemcpy(d_x, x, N*sizeof(float), cudaMemcpyDefault);  
cudaStreamSynchronize(0);