I have this problem, I am trying to build caffe on debian machine, I will build everything but at the end at linking I get multiple undefined references to google::protobuf::...
I am attaching file with build log, containing error messages (build_caffe.txt).
Both libprotobuf-dev and protoc are installled. (output of dpkg -s is in proto.txt)
Here is how I build caffe.
export CXX=g++-4.9
export CC=gcc-4.9
cmake -D CUDA_HOST_COMPILER=/usr/bin/x86_64-linux-gnu-gcc-4.9 -D CUDA_USE_STATIC_CUDA_RUNTIME=OFF ..
make all
Does anyone know a solution for this problem please?
proto.txt
build_caffe.txt
Looks like your protobuf was compiled using a different version of gcc. Try to remove protobuf from your system and install it from sources, using the same gcc version you would like to use fro Caffe. (/usr/bin/x86_64-linux-gnu-gcc-4.9 according to your command).
EDIT:
If you can't install the updated protobuf, edit $CAFFE_ROOT/cmake/ProtoBuf.cmake and make the following changes:
#find_package( Protobuf REQUIRED ) # 1. Comment out this line
# 2. explicitly define protobuf's directories
set(PROTOBUF_INCLUDE_DIR path_to_protobuf/src/google/protobuf)
set(PROTOBUF_LIBRARIES path_to_where_protobuf_libs_are_built_to)
# 3. Explicitly set the full path to protoc executable
set(PROTOBUF_PROTOC_EXECUTABLE path_to_where_the_new_protoc_executable_is_build_to)
# ... Continue as usual
list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${PROTOBUF_INCLUDE_DIR})
list(APPEND Caffe_LINKER_LIBS PUBLIC ${PROTOBUF_LIBRARIES})
#...
Related
I am trying to use the CGAL library to display a 2D Delaunay triangulation, like in the example here
My code looks like this:
#include <iostream>
#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Delaunay_triangulation_2.h>
#include <CGAL/draw_triangulation_2.h>
typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef CGAL::Delaunay_triangulation_2<K> Triangulation;
typedef Triangulation::Point Point;
int main(void){
Point a(1,1), b(2,1), c(2,2), d(1,2);
Triangulation T;
T.insert(a);
T.insert(b);
T.insert(c);
T.insert(d);
CGAL::draw(T);
return 0;
}
When I try to compile this code with g++ -o cgalTest.exe cgalTest.cpp -lCGAL -lgmp the program compiles successfully, but on runtime I get Impossible to draw because CGAL_USE_BASIC_VIEWER is not defined
By searching on Google, I found someone that suggested using g++ -o cgalTest.exe cgalTest.cpp -lCGAL -lgmp -DCGAL_USE_BASIC_VIEWER which produces the following error on compile time: /usr/include/CGAL/Qt/Basic_viewer_qt.h:30:10: fatal error: QApplication: No such file or directory #include <QApplication>
I am using ubuntu 19.04, so I installed CGAl using sudo apt-get install libcgal-dev and sudo apt-get install libcgal-qt5-dev
I tried to install sudo apt-get install libqt5svg5-dev libqt5opengl5-dev as well to solve the error, but to no avail.
Do I need to install additional libraries? Maybe the compilation must be done differently?
Thank you
Ok, for anyone facing the same problem, here is how I solved it:
First, I used the locate QApplication command to find the location of the QApplication header file on my system. Be sure to run sudo updatedb before using locate. If locate doesn't find the location of QApplication then you are missing qt libraries. Try sudo apt-get install qt5-default and the other libraries I mentioned in my question, run sudo updatedb and try locate QApplication again.
When you find the path to QApplication just use the -I option to instruct the compiler to use it. Here is an example g++ -o delaunayTest delaunayTest.cpp -lCGAL -lgmp -lCGAL_Qt5 -DCGAL_USE_BASIC_VIEWER -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets/ (because in my case, QApplication was inside the directory /usr/include/x86_64-linux-gnu/qt5/QtWidgets/)
Trying to compile with this, you will probably get another header file error. Repeat the same process using locate until you get no more header file errors.
At that point, you will likely encounter an undefined reference to symbol error.
To solve this, use locate again to find the location of the file that caused the error (for example libQt5OpenGL.so.5) and add the path to the compilation command as is (for example g++ -o delaunayTest delaunayTest.cpp /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5) along with all the previous options.
You will probably get several undefined reference to symbol errors as well. Just keep using the same method until you don't get any.
At this point the program should compile properly and run properly.
Note that if you have multiple versions of qt installed, then the above might not work properly (If for example you have software that uses qt like MATLAB or anaconda installed in your system. You will know because locate will produce many paths for each file on the steps above). In such a case, I suggest building a Virtual Machine, downloading the CGAL libraries and qt5-default and following the above steps there, since it is very likely this won't work in a system with multiple qt installations.
Another option (maybe the easiest), using CMake, is to generate the file using the builtin script:
From the source file directory, run cgal_create_CMakeLists -c Qt5
Edit the generated CMakeLists.txt adding the line add_definitions(-DCGAL_USE_BASIC_VIEWER)
My generated and edited CMakeLists.txt:
# Created by the script cgal_create_CMakeLists
# This is the CMake script for compiling a set of CGAL applications.
cmake_minimum_required(VERSION 3.1...3.15)
project( tmp_cgal )
# CGAL and its components
find_package( CGAL QUIET COMPONENTS Qt5 )
if ( NOT CGAL_FOUND )
message(STATUS "This project requires the CGAL library, and will not be compiled.")
return()
endif()
add_definitions(-DCGAL_USE_BASIC_VIEWER) # <==== I've added this
# Boost and its components
find_package( Boost REQUIRED )
if ( NOT Boost_FOUND )
message(STATUS "This project requires the Boost library, and will not be compiled.")
return()
endif()
# include for local directory
# include for local package
# Creating entries for all C++ files with "main" routine
# ##########################################################
create_single_source_cgal_program( "b.cpp" )
Create a build directory: mkdir build
Change directory: cd build
Generate the build files: cmake ..
Build: make
Run the binary file. For me it's ./b because my source file was b.cpp
Environment:
These instructions should work for an Ubuntu 20.04.1 (or similar) with the packages libcgal-dev, libcgal-qt5-dev and qtbase5-dev installed (and, of course, cmake, make and g++).
Main references:
doc1 and doc2
[Ubuntu]
I have compiled CGAL locally:
/path/to/cgal/
/lib/
libCGAL_Core.so libCGAL_Core.so.13.0.2
libCGAL_ImageIO.so.13 libCGAL.so libCGAL.so.13.0.2
libCGAL_Core.so.13 libCGAL_ImageIO.so
libCGAL_ImageIO.so.13.0.2 libCGAL.so.13
/include/
/CGAL/
version.h compiler_config.h
And I have managed to satisfy all of the graph-tool requirements except cgal (at least all of the requirements checked up to cgal):
./configure --with-boost=/path/to/boost --with-cgal=/path/to/cgal
And I get all successes up and until I get the following error message:
checking for __gmpz_init in -lgmp... yes
checking for __gmpz_init in -lgmp... (cached) yes
checking whether CGAL is available in /path/to/cgal... no
configure: error: CGAL library not found.
// the harshest part is that it seems to be searching in the correct
// directory.
I have tried specifying different points in the cgal build directory. The cgal compilation command I used was (from build directory):
cmake path/to/cgal_src_dir -DCMAKE_BUILD_TYPE=Release;
Next, I tried adding includes:
./configure --with-boost=$boost --with-cgal=path/to/cgal CPPFLAGS="-I path/to/cgal/include -I $HOME/.local/include" LDFLAGS="-L path/to/cgal/lib -L $HOME/.local/lib -Wl,-rpath=$HOME/.local/lib"
I will admit that I don't understand the -Wl,-rpath= part, I copied that from the graph-tool installation guide. The .local/lib folder contains the files for the other components, such as gmp, expat, sparsehash, etc.
This is not exact answer but as asked by OP will help in finishing installation, so please don't vote blindly.
To create debian package of libcgal open your CMakeList.txt and at the end of file add:
#--------------------------------------------------------------------
# Create debian files
#--------------------------------------------------------------------
if (UNIX AND NOT APPLE)
SET(CPACK_GENERATOR "DEB")
SET(CPACK_PACKAGE_NAME "libcgal-all")
SET(CPACK_PACKAGE_VERSION "${CGAL_VERSION}")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "C++ library for computational geometry (development files)\n CGAL (Computational Geometry Algorithms Library) makes the most important of the solutions and methods developed in computational geometry available to users in industry and academia in a C++ library. The goal is to provide easy access to useful, reliable geometric algorithms.\n .\n This package contains the header files and static libraries for libCGAL.so, libCGAL_Core.so, and libCGAL_ImageIO.so. The header files and static libraries for libCGAL_Qt4.so can be found in the package libcgal-qt4-dev.")
SET(CPACK_PACKAGE_CONTACT "bordeo")
SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libboost-dev, libboost-thread-dev, libboost-system-dev, libboost-program-options-dev, libgmp10-dev, libmpfr-dev, zlib1g-dev")
SET(CPACK_DEBIAN_PACKAGE_REPLACES "libcgal10, libcgal-dev")
INCLUDE(CPack)
endif()
In case you don't have any dependency remove whole line of SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libcln6, libcln-dev, libreadline6, libreadline6-dev, flex, bison"), and change others as it seems fit.
Now go to the terminal and issue following commands in cgal directory
mkdir build
cd build
cmake-gui ..
# set CMAKE_INSTALL_PREFIX to `~/.local
cmake ..
make -j4
cpack ..
you will find your debian built. Extract or install the debian to ~/.local.
Once this is done go to graph tool directory and start the build like
./configure --prefix="/wherever" --with-boost=/path/to/boost --with-cgal=~/.local
make -j4
make install
Hope this will solve your problem.
I am on ubuntu 16.04.
Here what I did:
installed gperftools :
sudo apt-get install google-perftools libgoogle-perftools-dev
downloaded FindGperftools.cmake from: https://github.com/vast-io/vast/blob/master/cmake/FindGperftools.cmake
renamed FindGperftools.cmake to GperftoolsConfig.cmake and placed it in a cmake folder in my package
added to CMakelists.txt:
set (Gperftools_DIR "${CMAKE_CURRENT_LIST_DIR}/cmake/")
find_package(Gperftools REQUIRED)
in same CMakelists.txt, link my executable:
target_link_libraries(my_executable ${GPERFTOOLS_PROFILER})
in a terminal, export the CPUPROFILE environment variable:
export CPUPROFILE=/my_path/prof.out
in the same terminal, run the executable:
./my_executable
There is no error message, but the log file /my_path/prof.out is not created.
If I run "ldd" on "my_executable", it does not show any linkage against profiler (ldd ./my_executable | grep profil does not result in anything).
Yet, when looking at files in the build folder, the compiler seems to do the linkage (-lprofile is there).
Anything I may have forgotten?
Note: not sure it is relevant, but I use catkin.
This looks like ubuntu's (and non-standard) linker feature to not link libraries which symbols are directly not used. Try adding -Wl,-no-as-needed to your LDFLAGS (and make sure it is passed before -lprofiler).
Hi everyone,
I have some trouble trying to use the SFML library.I've tried different thing to make it work but always failing.
I downloaded the official package but nothing worked when I tried to compile a basic program.
I downloaded the version 2.4.1and put includes folder in /src/local/include/ and libs files in /src/local/lib/. It was better than with the official package : I successfully got my .o. But the linking phase told me to install the jpeg library. So I did it but it was already installed on my system (Fedora 25) and doesn't changed anything. I saw on some forums that fedora use an other library to create jpeg picture : libjpeg-turbo which is a fork of the libjpeg. I have tried many thing to force my linux to use the libjpeg 8 instead of the one installed but without success.
To make it work I tried the last solution : compile the SFML myself. So I downloaded sources, launch cmake and saw that it was missing lot something like 8 libraries to my laptop. After installed all those libraries I compile and install the SFML with the make target. Once it was done the compiling phase still working but the linking phase return me a obscure message for me (I translated it) :
/usr/bin/ld: test: hidden symbol « __cpu_model » in
/usr/lib/gcc/x86_64-redhat-linux/6.2.1/libgcc.a(cpuinfo.o) is
referenced by DSO
/usr/bin/ld : Failure during final link editing : Wrong value
collect2: error : ld has returned 1 execution status code
Do anyone know what's wrong ?
SFML has issues with gcc 5.3 and newer. Currently GCC is version 6.3.1 in Fedora 25 repositories. You should apply this patch:
diff --git a/src/SFML/Graphics/CMakeLists.txt b/src/SFML/Graphics/CMakeLists.txt
index 6f02fb6..bdc84e7 100644
--- a/src/SFML/Graphics/CMakeLists.txt
+++ b/src/SFML/Graphics/CMakeLists.txt
## -148,6 +148,13 ## add_definitions(-DSTBI_FAILURE_USERMSG)
# when gcc is used; otherwise saving PNGs may crash in stb_image_write
if(SFML_COMPILER_GCC)
set_source_files_properties(${SRCROOT}/ImageLoader.cpp PROPERTIES COMPILE_FLAGS -fno-strict-aliasing)
+
+endif()
+
+# see https://bugs.launchpad.net/ubuntu/+source/gcc-5/+bug/1568899
+if(SFML_COMPILER_GCC AND BUILD_SHARED_LIBS)
+ message(WARNING "Applying workaround for https://bugs.launchpad.net/ubuntu/+source/gcc-5/+bug/1568899")
+ list(APPEND GRAPHICS_EXT_LIBS "-lgcc_s -lgcc")
endif()
# define the sfml-graphics target
If you do not want to download the SFML git repository, just open src/SFML/Graphics/CMakeLists.txt, locate the if conditional statement with the ImageLoader.cpp comment (line 150) and append the lines added by the patch. The end result should look like this:
# ImageLoader.cpp must be compiled with the -fno-strict-aliasing
# when gcc is used; otherwise saving PNGs may crash in stb_image_write
if(SFML_COMPILER_GCC)
set_source_files_properties(${SRCROOT}/ImageLoader.cpp PROPERTIES COMPILE_FLAGS -fno-strict-aliasing)
endif()
# see https://bugs.launchpad.net/ubuntu/+source/gcc-5/+bug/1568899
if(SFML_COMPILER_GCC AND BUILD_SHARED_LIBS)
message(WARNING "Applying workaround for https://bugs.launchpad.net/ubuntu/+source/gcc-5/+bug/1568899")
list(APPEND GRAPHICS_EXT_LIBS "-lgcc_s -lgcc")
endif()
I would like to do the following: If CCache is present in PATH, use "ccache g++" for compilation, else use g++. I tried writing a small my-cmake script containing
CC="ccache gcc" CXX="ccache g++" cmake $*
but it does not seem to work (running make still does not use ccache; I checked this using CMAKE_VERBOSE_MAKEFILE on).
Update:
As per this link I tried changing my script to
cmake -D CMAKE_CXX_COMPILER="ccache" -D CMAKE_CXX_COMPILER_ARG1="g++" -D CMAKE_C_COMPILER="ccache" -D CMAKE_C_COMPILER_ARG1="gcc" $*
but cmake bails out complaining that a test failed on using the compiler ccache (which can be expected).
As of CMAKE 3.4 you can do:
-DCMAKE_CXX_COMPILER_LAUNCHER=ccache
It is now possible to specify ccache as a launcher for compile commands and link commands (since cmake 2.8.0). That works for Makefile and Ninja generator. To do this, just set the following properties :
find_program(CCACHE_FOUND ccache)
if(CCACHE_FOUND)
set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK ccache) # Less useful to do it for linking, see edit2
endif(CCACHE_FOUND)
It is also possible to set these properties only for specific directories or targets.
For Ninja, this is possible since version 3.4.
For XCode, Craig Scott gives a workaround in his answer.
Edit : Thanks to uprego and Lekensteyn's comment, I edited the answer to check if ccache is available before using it as launcher and for which generators is it possible to use a compile launcher.
Edit2: #Emilio Cobos recommended to avoid doing that for the linking part as ccache doesn't improve linking speed and can mess with other types of cache like sccache
I personally have /usr/lib/ccache in my $PATH. This directory contains loads of symlinks for every possible name the compiler could be called from (like gcc and gcc-4.3), all pointing to ccache.
And I didn't even create the symlinks. That directory comes pre-filled when I install ccache on Debian.
From CMake 3.1, it is possible to use ccache with the Xcode generator and Ninja is supported from CMake 3.4 onwards. Ninja will honour RULE_LAUNCH_COMPILE just like the Unix Makefiles generator (so #Babcool's answer gets you there for Ninja too), but getting ccache working for the Xcode generator takes a little more work. The following article explains the method in detail, focussing on a general implementation which works for all three CMake generators and making no assumptions about setting up ccache symlinks or the underlying compiler used (it still lets CMake decide the compiler):
https://crascit.com/2016/04/09/using-ccache-with-cmake/
The general gist of the article is as follows. The start of your CMakeLists.txt file should be set up something like this:
cmake_minimum_required(VERSION 2.8)
find_program(CCACHE_PROGRAM ccache)
if(CCACHE_PROGRAM)
# Support Unix Makefiles and Ninja
set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${CCACHE_PROGRAM}")
endif()
project(SomeProject)
get_property(RULE_LAUNCH_COMPILE GLOBAL PROPERTY RULE_LAUNCH_COMPILE)
if(RULE_LAUNCH_COMPILE AND CMAKE_GENERATOR STREQUAL "Xcode")
# Set up wrapper scripts
configure_file(launch-c.in launch-c)
configure_file(launch-cxx.in launch-cxx)
execute_process(COMMAND chmod a+rx
"${CMAKE_BINARY_DIR}/launch-c"
"${CMAKE_BINARY_DIR}/launch-cxx")
# Set Xcode project attributes to route compilation through our scripts
set(CMAKE_XCODE_ATTRIBUTE_CC "${CMAKE_BINARY_DIR}/launch-c")
set(CMAKE_XCODE_ATTRIBUTE_CXX "${CMAKE_BINARY_DIR}/launch-cxx")
set(CMAKE_XCODE_ATTRIBUTE_LD "${CMAKE_BINARY_DIR}/launch-c")
set(CMAKE_XCODE_ATTRIBUTE_LDPLUSPLUS "${CMAKE_BINARY_DIR}/launch-cxx")
endif()
The two script template files launch-c.in and launch-cxx.in look like this (they should be in the same directory as the CMakeLists.txt file):
launch-c.in:
#!/bin/sh
export CCACHE_CPP2=true
exec "${RULE_LAUNCH_COMPILE}" "${CMAKE_C_COMPILER}" "$#"
launch-cxx.in:
#!/bin/sh
export CCACHE_CPP2=true
exec "${RULE_LAUNCH_COMPILE}" "${CMAKE_CXX_COMPILER}" "$#"
The above uses RULE_LAUNCH_COMPILE alone for Unix Makefiles and Ninja, but for the Xcode generator it relies on help from CMake's CMAKE_XCODE_ATTRIBUTE_... variables support. The setting of the CC and CXX user-defined Xcode attributes to control the compiler command and LD and LDPLUSPLUS for the linker command is not, as far as I can tell, a documented feature of Xcode projects, but it does seem to work. If anyone can confirm it is officially supported by Apple, I'll update the linked article and this answer accordingly.
I didn't like to set a symlink from g++ to ccache. And CXX="ccache g++" didn't work for me as some cmake test case wanted to have just the compiler program without attributes.
So I used a small bash script instead:
#!/bin/bash
ccache g++ "$#"
and saved it as an executable in /usr/bin/ccache-g++.
Then C configured cmake to use /usr/bin/ccache-g++ as C++ compiler.
This way it passes the cmake test cases and I feel more comfortable than having symlinks that I might forget about in 2 or 3 weeks and then maybe wonder if something doesn't work...
I verified the following works (source: this link):
CC="gcc" CXX="g++" cmake -D CMAKE_CXX_COMPILER="ccache" -D CMAKE_CXX_COMPILER_ARG1="g++" -D CMAKE_C_COMPILER="ccache" -D CMAKE_C_COMPILER_ARG1="gcc" $*
Update: I later realized that even this does not work. Strangely it works every alternate time (the other times cmake complains).
Let me add one important item that was not mentioned here before.
While bootstrapping a minimalistic build system from the ubuntu:18.04 docker image, I've found that order of installation makes a difference.
In my case ccache worked fine when calling gcc, but failed to catch invocations of the same compiler by the other names: cc and c++.
To fully install ccache, you need to make sure all compilers are installed first, or add a call to update-ccache symlinks to be safe.
sudo /usr/sbin/update-ccache-symlinks
export PATH="/usr/lib/ccache/:$PATH"```
... and then (due to updated symlinks) also calls to cc and c++ get caught!
In my opinion the best way is to symlink gcc,g++ to ccache, but if you would like to use within cmake, try this:
export CC="ccache gcc" CXX="ccache g++" cmake ...
Here are 2 methods I think are clean/robust, and also don't pollute your CMake code.
1.) Set environment variables
This method is nice since you don't have to individually set it up for each CMake project. The con is you may not want ccache for each CMake project.
# Requires CMake 3.17 (https://cmake.org/cmake/help/latest/envvar/CMAKE_LANG_COMPILER_LAUNCHER.html)
export CMAKE_CXX_COMPILER_LAUNCHER=/usr/bin/ccache
export CMAKE_C_COMPILER_LAUNCHER=/usr/bin/ccache
2.) Pass in cache variables during project configuration
Con a bit annoying to do for each project. This can be negated by your IDE though.
# Requires CMake 3.4
$ cmake ... -D CMAKE_CXX_COMPILER_LAUNCHER=/usr/bin/ccache \
-D CMAKE_C_COMPILER_LAUNCHER=/usr/bin/ccache
NOTE: It isn't really necessary to specify the full path.
If ccache is in your path you can just specify ccache instead.
export CMAKE_CXX_COMPILER_LAUNCHER=ccache
export CMAKE_C_COMPILER_LAUNCHER=ccache
It is extending #Nicolas answer.
Add following line to your cmake file:
list(PREPEND CMAKE_PROGRAM_PATH /usr/lib/ccache)
Or add it as argument to cmake configuration step:
cmake -DCMAKE_PROGRAM_PATH=/usr/lib/ccache