Linker Issues with boost::thread under linux using Eclipse and CMake - linux

I'm in the process of attempting to port some code across from PC to Ubuntu, and am having some issues due to limited experience developing under linux.
We use CMake to generate all our build stuff. Under windows I'm making VS2010 projects, and under Linux I'm making Eclipse projects. I've managed to get my OpenCV stuff ported across successfully, but am having major headaches trying to port my threaded boost apps.
Just so we're clear, the steps I have followed so-far on a clean Ubuntu 12 installation. (I've done 2 clean re-installs to try and fix potential library cock-ups, now I'm just giving up and asking):
Install Eclipse and Eclipse CDT using my package manager
Install CMake and CMake Gui using my package manager
Install libboost-all-dev using my package manager
So-far that's all I've done. I can create the eclipse project using CMake with no errors, so CMake is successfully finding my boost install. When I try and build through eclipse is when I get issues; The app I'm attempting to build uses boost::asio for some UDP I/O and boost::thread to create worker threads for the asio I/O services. I can successfully compile each module, but when I come to link I get spammed with errors such as:
/usr/bin/c++ CMakeFiles/RE05DevelopmentDemo.dir/main.cpp.o CMakeFiles/RE05DevelopmentDemo.dir/RE05FusionListener/RE05FusionListener.cpp.o CMakeFiles/RE05DevelopmentDemo.dir/NewEye/NewEye.cpp.o -o RE05DevelopmentDemo -rdynamic -Wl,-Bstatic -lboost_system-mt -lboost_date_time-mt -lboost_regex-mt -lboost_thread-mt -Wl,-Bdynamic
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_thread-mt.a(thread.o): In function `void boost::call_once<void (*)()>(boost::once_flag&, void (*)()) [clone .constprop.98]':
make[2]: Leaving directory `/home/david/Code/Build/Support/RE05DevDemo'
(.text+0xc8): undefined reference to `pthread_key_create'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_thread-mt.a(thread.o): In function `boost::this_thread::interruption_enabled()':
(.text+0x540): undefined reference to `pthread_getspecific'
make[1]: Leaving directory `/home/david/Code/Build/Support/RE05DevDemo'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_thread-mt.a(thread.o): In function `boost::this_thread::disable_interruption::disable_interruption()':
(.text+0x570): undefined reference to `pthread_getspecific'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_thread-mt.a(thread.o): In function `boost::this_thread::disable_interruption::disable_interruption()':
(.text+0x59f): undefined reference to `pthread_getspecific'
Some Gotchas that I have collected from other StackOverflow posts and have already checked:
The boost libs are all present at /usr/lib
I am not getting any compile errors for inability to find the boost headers, so they must be getting found.
I am trying to link statically, but I believe eclipse should be passing the correct arguments to make that happen since my CMakeLists.txt includes SET(Boost_USE_STATIC_LIBS ON)
I'm officially out of ideas here, I have tried doing local builds of boost and a bunch of other stuff with no more success. I even re-installed Ubuntu to ensure I haven't completely fracked the libs directories and links with multiple weird versions or anything else. Any help would be muchly appreciated.

Correct mechanism is to use Threads package:
find_package(Threads)
#...
target_link_libraries(my_app ${CMAKE_THREAD_LIBS_INIT} ...)
See also cmake and libpthread

When you are building your targets, add -lpthread and it will compile.
See this other thread.

OK, so I found the solution.
It was to do with the absence of the -lpthread flag in the link command. In order to get CMake to link appropriately, then the TARGET_LINK_LIBRARIES line needs to be edited. My edit is:
Original:
TARGET_LINK_LIBRARIES( RE05DevelopmentDemo ${Boost_LIBRARIES} )
Modified and working:
IF(WIN32)
TARGET_LINK_LIBRARIES( RE05DevelopmentDemo ${Boost_LIBRARIES} )
ELSE(WIN32)
TARGET_LINK_LIBRARIES( RE05DevelopmentDemo ${Boost_LIBRARIES} pthread )
ENDIF(WIN32)
I'm guessing that I should probably change the ELSE(WIN32) to an elseif for or use the CMake command FindThreads to link in pthread if needed, but I'm not sure how to do that at the moment and have more imporatant things on my plate given the time I've lost. Interestingly enough, I noticed my link command now has two -lpthread flags appended at the end, one after another, but everything is still compiling quite happily.

Related

How to build a .so for export to another machine? [duplicate]

I'm very new to Yesod and I'm having trouble building Yesod statically
so I can deploy to Heroku.
I have changed the default .cabal file to reflect static compilation
if flag(production)
cpp-options: -DPRODUCTION
ghc-options: -Wall -threaded -O2 -static -optl-static
else
ghc-options: -Wall -threaded -O0
And it no longer builds. I get a whole bunch of warnings and then a
slew of undefined references like this:
Linking dist/build/personal-website/personal-website ...
/usr/lib/ghc-7.0.3/libHSrts_thr.a(Linker.thr_o): In function
`internal_dlopen':
Linker.c:(.text+0x407): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/ghc-7.0.3/unix-2.4.2.0/libHSunix-2.4.2.0.a(HsUnix.o): In
function `__hsunix_getpwent':
HsUnix.c:(.text+0xa1): warning: Using 'getpwent' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/ghc-7.0.3/unix-2.4.2.0/libHSunix-2.4.2.0.a(HsUnix.o): In
function `__hsunix_getpwnam_r':
HsUnix.c:(.text+0xb1): warning: Using 'getpwnam_r' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/usr/lib/libpq.a(thread.o): In function `pqGetpwuid':
(.text+0x15): warning: Using 'getpwuid_r' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/libpq.a(ip.o): In function `pg_getaddrinfo_all':
(.text+0x31): warning: Using 'getaddrinfo' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/ghc-7.0.3/site-local/network-2.3.0.2/
libHSnetwork-2.3.0.2.a(BSD__63.o): In function `sD3z_info':
(.text+0xe4): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/ghc-7.0.3/site-local/network-2.3.0.2/
libHSnetwork-2.3.0.2.a(BSD__164.o): In function `sFKc_info':
(.text+0x12d): warning: Using 'getprotobyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/ghc-7.0.3/site-local/network-2.3.0.2/
libHSnetwork-2.3.0.2.a(BSD__155.o): In function `sFDs_info':
(.text+0x4c): warning: Using 'getservbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/libpq.a(fe-misc.o): In function `pqSocketCheck':
(.text+0xa2d): undefined reference to `SSL_pending'
/usr/lib/libpq.a(fe-secure.o): In function `SSLerrmessage':
(.text+0x31): undefined reference to `ERR_get_error'
/usr/lib/libpq.a(fe-secure.o): In function `SSLerrmessage':
(.text+0x41): undefined reference to `ERR_reason_error_string'
/usr/lib/libpq.a(fe-secure.o): In function `initialize_SSL':
(.text+0x2f8): undefined reference to `SSL_check_private_key'
/usr/lib/libpq.a(fe-secure.o): In function `initialize_SSL':
(.text+0x3c0): undefined reference to `SSL_CTX_load_verify_locations'
(... snip ...)
If I just compile with just -static and without -optl-static
everything builds fine but the application crashes when it tries to
start on Heroku.
2011-12-28T01:20:51+00:00 heroku[web.1]: Starting process with command
`./dist/build/personal-website/personal-website -p 41083`
2011-12-28T01:20:51+00:00 app[web.1]: ./dist/build/personal-website/
personal-website: error while loading shared libraries: libgmp.so.10:
cannot open shared object file: No such file or directory
2011-12-28T01:20:52+00:00 heroku[web.1]: State changed from starting
to crashed
I tried adding libgmp.so.10 to the LD_LIBRARY_PATH as suggested in here
and then got the following error:
2011-12-28T01:31:23+00:00 app[web.1]: ./dist/build/personal-website/
personal-website: /lib/libc.so.6: version `GLIBC_2.14' not found
(required by ./dist/build/personal-website/personal-website)
2011-12-28T01:31:23+00:00 app[web.1]: ./dist/build/personal-website/
personal-website: /lib/libc.so.6: version `GLIBC_2.14' not found
(required by /app/dist/build/personal-website/libgmp.so.10)
2011-12-28T01:31:25+00:00 heroku[web.1]: State changed from starting
to crashed
2011-12-28T01:31:25+00:00 heroku[web.1]: Process exited
It seems that the version of libc that I'm compiling against is
different. I tried also adding libc to the batch of libraries the
same way I did for libgmp but this results in a segmentation fault
when the application starts on the Heroku side.
Everything works fine on my PC. I'm running 64bit archlinux with ghc
7.0.3. The blog post on the official Yesod blog looked pretty easy
but I'm stumped at this point. Anyone have any ideas? If there's a way to get this thing working without building statically I'm open to that too.
EDIT
Per Employed Russians answer I did the following to fix this.
First created a new directory lib under the project directory and copied the missing shared libraries into it. You can get this information by running ldd path/to/executable and heroku run ldd path/to/executable and comparing the output.
I then did heroku config:add LD_LIBRARY_PATH=./lib so when the application is started the dynamic linker will look for libraries in the new lib directory.
Finally I created an ubuntu 11.10 virtual machine and built and deployed to Heroku from there, this has an old enough glibc that it works on the Heroku host.
Edit:
I've since written a tutorial on the Yesod wiki
I have no idea what Yesod is, but I know exactly what each of your other errors means.
First, you should not try to link statically. The warning you get is exactly right: if you link statically, and use one of the routines for which you are getting the warning, then you must arrange to run on a system with exactly the same version of libc.so.6 as the one you used at build time.
Contrary to popular belief, static linking produces less, not more, portable executables on Linux.
Your other (static) link errors are caused by missing libopenssl.a at link time.
But let's assume that you are going to go the "sane" route, and use dynamic linking.
For dynamic linking, Linux (and most other UNIXes) support backward compatibility: an old binary continues to work on newer systems. But they don't support forward compatibility (a binary built on a newer system will generally not run on an older one).
But that's what you are trying to do: you built on a system with glibc-2.14 (or newer), and you are running on a system with glibc-2.13 (or older).
The other thing you need to know is that glibc is composed of some 200+ binaries that must all match exactly. Two key binaries are /lib/ld-linux.so and /lib/libc.so.6 (but there are many more: libpthread.so.0, libnsl.so.1, etc. etc). If some of these binaries came from different versions of glibc, you usually get a crash. And that is exactly what you got, when you tried to place your glibc-2.14 libc.so.6 on the LD_LIBRARY_PATH -- it no longer matches the system /lib/ld-linux.
So what are the solutions? There are several possibilities (in increasing difficulty):
You could copy ld-2.14.so (the target of /lib/ld-linux symlink) to the target system, and invoke it explicitly:
/path/to/ld-2.14.so --library-path <whatever> /path/to/your/executable
This generally works, but can confuse an application that looks at argv[0], and breaks for applications that re-exec themselves.
You could build on an older system.
You could use appgcc (this option has disappeared, see this for description of what it used to be).
You could set up a chroot environment matching the target system, and build inside that chroot.
You could build yourself a Linux-to-olderLinux crosscompiler
You have several issues.
You should not build production binaries on bleeding edge distributions. The libraries on the production system will not be forward compatible.
You should not link glibc statically - it will always at runtime try to load additional libraries. For example cpu-based assembly. That is what your first warnings are about.
The last linker errors look like they are related to a missing openssl library on the command line.
But all in all - downgrade your distribution.
I had similar problems launching to Heroku (which uses glibc-2.11) where I had an application that required glibc-2.14, but I did not have access to the source and could not re-build it. I tried many things and nothing worked.
My workaround was to launch the service on Amazon Elastic Beanstalk and just provide an API interface.
I found the information provided useful as well, I think the various descriptions miss a critical issue I also ran into while forcing an updated version of Vagrant to start working again.
It's the dependency references internal to something like complicated installs, like Yesod to Heroku. Those interanl refences need to be preserved.
This is the script I wrote to make problems go away (at least, hopefully, for a little while):
#!/bin/bash
cd $HOME/
GLIBC_VERSION="2.17"
GLIBC_PREFIX="/usr/glibc/"
VAGRANT_VERSION="2.2.19"
# Install the basic build system utilities.
yum groupinstall -y "Development tools"
yum install -y curl patchelf
# Grab the tarball with the GNU libc source code.
curl -Lfo glibc-${GLIBC_VERSION}.tar.gz "https://ftp.gnu.org/gnu/glibc/glibc-${GLIBC_VERSION}.tar.gz"
echo "a3b2086d5414e602b4b3d5a8792213feb3be664ffc1efe783a829818d3fca37a glibc-${GLIBC_VERSION}.tar.gz" | sha256sum -c || exit 1
# Extract the secrets and get ready to rumble.
tar xzvf glibc-${GLIBC_VERSION}.tar.gz
# The configure script requrires an independent build directory.
mkdir -p glibc-build && cd glibc-build
# Configure glibc with a GLIBC_PREFIX so it doesn't conflict with distro libc files..
../glibc-${GLIBC_VERSION}/configure --prefix="${GLIBC_PREFIX}" --libdir="${GLIBC_PREFIX}/lib" \
--libexecdir="${GLIBC_PREFIX}/lib" --enable-multi-arch
# Compile and then install GNU libc.
make -j8 && make install
# Download and install Vagrant.
curl -Lfo vagrant_${VAGRANT_VERSION}_x86_64.rpm "https://releases.hashicorp.com/vagrant/${VAGRANT_VERSION}/vagrant_${VAGRANT_VERSION}_x86_64.rpm"
echo "990e8d2159032915f21c0f1ccdcbca1a394f7937e06e43dc1dabe605d208dc20 vagrant_${VAGRANT_VERSION}_x86_64.rpm" | sha256sum -c || exit 1
yum install -y vagrant_${VAGRANT_VERSION}_x86_64.rpm
# Patch the binaries and shared libraries inside the Vagrant directory, so they use the new version of GNU libc.
(find /opt/vagrant/ -type f -exec file {} \; )| grep "dynamically linked" | awk -F':' '{print $1}' | while read FILE ; do
patchelf --set-rpath /opt/vagrant/embedded/lib:/opt/vagrant/embedded/lib64:/usr/glibc/lib:/usr/lib64:/lib64:/lib --set-interpreter /usr/glibc/lib/ld-linux-x86-64.so.2 "${FILE}"
done
The script should be pretty easy to understand, and adapt easily to whatever MacGuffin you want to make work, provied you understand it.
The only tricky part is the rpath you pass to patchelf. Upi need to make sure you preserve the search paths, and precedence your software requires. Or you end up fixing one problem only to create another equally frustrating roadblock.
P.S. Don't forget the update the hashes for any file you down. In particular, you need to compile/install a different version of GNU libc, you will need to update that hash to match the version you want to use.

arm-none-eabi-objdump: error while loading shared libraries: libdebuginfod.so.1: cannot open shared object file

If you have an answer for this, or further information, I'd welcome it. I'm following advice from here, to offer some unsolicited help by posting this question then an answer I've already found for it.
I have a bare-metal ARM board for which I'm building a cross-toolchain, from sources for GNU binutils, gcc and gdb, and for SourceWare's Newlib. I got those four working and cross-built a DoNothing.c into an ELF file - but I couldn't disassemble it with this:
$ arm-none-eabi-objdump -S DoNothing.elf
The error was:
$ arm-none-eabi-objdump: error while loading shared libraries: libdebuginfod.so.1: cannot open shared object file: No such file or directory
I'll follow up with a solution.
The error was correct - my system didn't have libdebuginfod.so.1 installed - but I have another cross-binutils, installed from binary for a different target, and its objdump -S works fine on the same host. Why would one build of objdump complain about missing that shared library, when clearly not all builds of objdump need it?
First I tried rebuilding cross binutils, specifying --without-debuginfod as a configure option. No change, which seems odd: surely that should build tools that not only don't use debuginfod but which don't depend on it in any way. (If someone can answer that, or point out what I've misunderstood, it may help people.)
Next I figured debuginfod was inescapable (for my cross-tools built from source at least), so I'd install it to get rid of the error. It's a component of the elfutils package, but installing the latest elfutils available for my Ubuntu 20.04 system didn't bring libdebuginfod.so.1 with it.
I found a later one, for Arch Linux, whose package contents suggested it would - but its package format doesn't match Ubuntu's and installing it was going to involve a lot of work. Instead I opted to build it from the Arch Linux source package. However, running ./configure on that gave a couple of infuriatingly similar errors:
configure: checking libdebuginfod dependencies, --disable-libdebuginfod or --enable-libdebuginfo=dummy to skip
...
configure: error: dependencies not found, use --disable-libdebuginfod to disable or --enable-libdebuginfod=dummy to build a (bootstrap) dummy library.
No combination of those suggestions would allow configure for elfutils-0.182 to run to completion.
The problem of course was my own lack of understanding. The solution came from the Linux From Scratch project: what worked was to issue configure with both of the suggested options, like this:
$ ./configure --prefix=/usr \
--disable-debuginfod \
--enable-libdebuginfod=dummy \
--libdir=/lib
That gave a clean configure; make worked first time, as did make check and then sudo make install which of course installed libdebuginfod.so.1 as required. I then had an arm-none-eabi-objdump which disassembles cross-compiled ELF files without complaining.

Unable to make a portable Fortran executable in Cygwin

I'm attempting to compile a relatively simple Fortran executable so that it can be passed around to other Windows users that don't have Cygwin (or something of the sort) installed, however, I'm unable to get the executable to operate as a standalone. I've tried gfortran -static file.f and gfortran -static-libgfortran file.f, however other users always encounter this error:
The program can’t start because cygwin1.dll is missing from your computer. Try reinstalling the program to fix this problem.
From what I've read online (e.g. here), the -static option should be sufficient. I have verified that running the executable from my machine (DOS prompt) does work.
I have gcc (gfortran) version 4.7.3. I should also point out this is my first attempt at compiling portable Fortran.
Update
After realizing that this isn't a gfortran-specific issue (thanks to replies here), searches led me to related posts here and here
This is partially explained in the Cygwin FAQ. The solution is to install the mingw64-i686-gcc-fortran package with its dependencies, and cross-compile your code with i686-w64-mingw32-gfortran -static.
Just package the cygwin1.dll along with your binary file (both in the same folder) then it will run just fine.

mxe cross compiling linux to windows vtk example

I would like to know if there is an example out there, or could somebody post one, for compiling a vtk .exe app using MXE. The headers and libraries are built but I can't seem to get it to work. I have managed to get Qt working. I usually use my own makefiles and am not as familiar with cmake, qmake, etc. I need an example to show me how to make this stuff work. A working example showing the includes and links required to build a basic functioning vtk.exe application from mxe built libs and headers.
I have tried:
export PATH=/home/.../mxe/usr/bin:$PATH
i686-pc-mingw32-g++ -Wall -g -Wno-deprecated -I/home/.../include/vtk-5.8 -c app.cpp
i686-pc-mingw32-g++ -o appWindows app.o -L/home/.../lib/vtk/5.8 -lvtkRendering -lvtkGraphics -lvtkCommon -lvtkFiltering -l.. -l... etc.
I have also tried:
cmake -DCMAKE_TOOLCHAIN_FILE=/home/.../mxe/usr/i686-pc-mingw32/share/cmake/mxe-conf.cm‌​ake.
Getting libvtkRendering errors. This same procedure works with my Linux headers and binaries.
I have also tried the binaries from Point Cloud Library. Also didn't work.
I am testing this from a git clone on master for MXE. Read the mailing list for the checksum error fixes. I am currently getting an opengl error during compilation of vtk6. I am not seeing the above error mentioned.
I will post the new error messages later tonight. Please let me know if you are still getting the error.
Two years later, CMake is more and more THE reference!
Check this latest post C/C++ Development for Windows Sans Windows

Building SDL2 with NDK toolchain

I wonder if anyone did managed to build the fresh SDL2 with the toolchain of the Android NDK(r8d).
SDL2 seems to be very close to the release (since yesterday it isn't "UNDER CONSTROCTION anymore: http://hg.libsdl.org/SDL/rev/0a3d2ec7af6d). It comes with an Android.mk and just compiles fine following the instructions in the bundled README.android file. My question is whether there's really no working automake based build is available or will be available to compile it on Android, or something's wrong with my toolchain setup?
I have installed the NDK toolchain following the instructions of the documentation located at $NDK/doc/STANDALONE-TOOLCHAIN.html. I'm using gcc 4.6. Here's one environment i use:
#!/bin/sh
export TOOLCHAIN=$HOME/Android/android-14-arm
export PATH=$TOOLCHAIN/bin:$PATH
export SYSROOT=$TOOLCHAIN/sysroot
export CROSS_COMPILE="arm-linux-androideabi"
export CC=$CROSS_COMPILE-gcc
export CXX=$CROSS_COMPILE-g++
export CPP=$CROSS_COMPILE-cpp
export CFLAGS="-march=armv7-a -mfloat-abi=softfp -mfpu=neon"
export LDFLAGS="-march=armv7-a -Wl,--fix-cortex-a8"
echo "Compiler set up for ARM 14"
The configure params:
./configure --host=arm-linux-androideabi --prefix=$SYSROOT/usr/local
With the same configuration i successfully built libjpeg-turbo v8 and SDL_image.
The configure script recognizes the cross-compiler, and builds the makefile, however, it finds X11 support, can't see the OpenGL ES... The make fails:
In file included from /usr/include/features.h:378:0,
from /usr/include/sys/types.h:27,
from ./include/SDL_stdinc.h:35,
...
I checked the configure log, i have no idea where the "/usr/include" comes from.
But in fact, the generated makefile adds that line in the EXTRA_CFLAGS to the compiler.
The NDK doc refers the --with-sysroot=$SYSROOT as optional, i've included it to see if it solves the problem, but that didn't help.
As a last effort i manually edited the Makefile, fixing that reference, and now the compiler complained about X11.h.
AFAIK Android has nothing to do with X11, so i guess the whole build-tree completely inappropriate to use with NDK.
I have also tried a different configuration, found in an older thread here.
Neither defining -DANDROID -mandroid -fomit-frame-pointer nor changing back to -march=armv7-a -mfloat-abi=softfp -mfpu=vfp -mthumb" solved the problem.
On previous projects, i had to refresh config.guess, and config.sub in order to get my compiler recognized. SDL doesn't seem to use those. Furthermore no Makefile.ac or Makefile.am comes with SDL to work with, and no templates for other platform could be used for a good starting point to create my own makefile. Additionally, i've never had to deal with makefiles, i really have no chance to sort out these problems. Even if it succeeds, i will probably need a configure tool as well, since i have no idea how ndk-build manages to install SDL2 without configure scripts.
Compiling the SDL sources with the project together is the only working - but ugly solution. I would like to deploy the necessary lib and header files by make install.
I hope the solution is something really easy and obvious thing that i just didn't think about...
This issue has been fixed at http://hg.libsdl.org/SDL/rev/4e57cfd9fca8 and expected for the 2.0.4 release. Note there are newer revisions with some related fixes about defines.

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