The make instruction is not finding the libraries required for compilation. They are in other folder than the usual /usr/include folder.
I'm complying a simulation software called magnum.fe I already installed all the required dependencies (FEniCS = 1.5
CMake >= 2.8
SWIG >= 2.0
G++ >= 4.0) and started to run make as the instructions suggest.
$ cd /path/to/magnum.fe
$ mkdir build
$ cd build
$ cmake ..
$ make
$ sudo make install
But when running make I get the following error:
/usr/include/petscsys.h:136:12: fatal error: petsc/mpiuni/mpi.h: No such file or directory
136 | # include <petsc/mpiuni/mpi.h>
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
The files do exist, but in other folder: /home/myusername/bin/petsc/include/mpiuni/mpi.h
I compiled petsc on /home/myusername/bin/petsc/ with the following instruction:
$ ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack
$ make all check
It compiled it sucessfully but I couldn't get the magnum.fe compilation to finish.
I tried moving each header file to /usr/include but now I'm stuck on if moving the whole petsc directory into this folder. It must be a more elegant way to do it.
Thanks
I've made it!
There are two options available:
Specify the libraries to use with the make command editing the MAKEfile, use the variable LDLIBS to set it up. Detailed usage in here: https://web.archive.org/web/20070723140628/http://arco.inf-cr.uclm.es/~david.villa/doc/repo/make/make.html#AEN36
or
Create symbolic links pointing to /usr/include. In my case I used:
ln -s /home/myusername/bin/petsc/include/* /usr/include
Related
This question already has answers here:
Why does the order in which libraries are linked sometimes cause errors in GCC?
(9 answers)
Closed 2 years ago.
Essentially I am trying to use the redland rdf libraries but I cannot link to them. When I try a simple basic program which uses the redland libraries I get these errors:
/usr/local/lib/librdf.a(rdf_init.o): In function `librdf_free_memory':
/home/ciaran/Software/redland/redland-1.0.17/src/rdf_init.c:671: undefined reference to `raptor_free_memory'
/usr/local/lib/librdf.a(rdf_init.o): In function `librdf_alloc_memory':
/home/ciaran/Software/redland/redland-1.0.17/src/rdf_init.c:689: undefined reference to `raptor_alloc_memory'
/usr/local/lib/librdf.a(rdf_init.o): In function `librdf_calloc_memory':
/home/ciaran/Software/redland/redland-1.0.17/src/rdf_init.c:707: undefined reference to `raptor_calloc_memory'
At first glance, you might just think I have a missing link library, which is what I thought until I inspected further (see below), however, the libraries are all accounted for.
A proper minimal working example is difficult in this instance because it requires getting and building the libraries that I'm trying to use. However, I've created a GitHub repository
$ git clone git#github.com:CiaranWelsh/RedlandBuildTest.git
that contains the source files necessary for building the Redland libraries as well as the example code I'm using (which breaks).
In order to build the libraries, you will also need
$ sudo apt install automake autoconf libtool gtk-doc-tools
$ sudo apt install libxml2 libxml2-dev libxslt libxslt-dev libcurl4-openssl-dev libltdl-dev
Note, I'm working on Ubuntu-18.04 on windows subsystem for Linux.
To get, build and install the libraries I'm using these terminal commands:
#raptor2
wget "http://download.librdf.org/source/raptor2-2.0.15.tar.gz"
tar -xvf raptor2-2.0.15.tar.gz
cd raptor2-2.0.15
./autogen.sh
make
sudo make install
# redland (librdf)
wget "http://download.librdf.org/source/redland-1.0.17.tar.gz"
tar -xvf redland-1.0.17.tar.gz
cd redland-1.0.17
./autogen.sh
make
sudo make install
# rasqal
wget "http://download.librdf.org/source/rasqal-0.9.33.tar.gz"
tar -xvf rasqal-0.9.33.tar.gz
cd rasqal-0.9.33
./autogen.sh
make
sudo make install
Which are available in the github repository as shell scripts (get-raptor.sh, get-rasqal.sh and get-librdf.sh).
And my minimal CMake script (also in the repository):
cmake_minimum_required(VERSION 3.15)
project(RedlandBuildTest)
set(CMAKE_CXX_STANDARD 14)
find_library(RAPTOR2_STATIC_LIBRARY
NAMES libraptor2.a
PATHS /usr/local/lib
)
find_path(RAPTOR2_INCLUDE_DIR
NAMES raptor2.h
PATHS /usr/local/include/raptor2
)
find_library(RASQAL_STATIC_LIBRARY
NAMES librasqal.a
PATHS /usr/local/lib
)
find_path(RASQAL_INCLUDE_DIR
NAMES rasqal.h
PATHS /usr/local/include/rasqal
)
find_library(LIBRDF_STATIC_LIBRARY
NAMES librdf.a
PATHS /usr/local/lib
)
find_path(LIBRDF_INCLUDE_DIR
NAMES librdf.h
PATHS /usr/local/include
)
add_executable(RedlandBuildTest main.c)
target_include_directories(RedlandBuildTest PRIVATE
${RAPTOR2_INCLUDE_DIR}
${RASQAL_INCLUDE_DIR}
${LIBRDF_INCLUDE_DIR}
)
target_link_libraries(RedlandBuildTest PRIVATE
${RAPTOR2_STATIC_LIBRARY}
${RASQAL_STATIC_LIBRARY}
${LIBRDF_STATIC_LIBRARY}
curl
xml2
xslt
ltdl
)
get_target_property(LINK_LIBRARIES RedlandBuildTest LINK_LIBRARIES)
get_target_property(INCLUDE_DIRECTORIES RedlandBuildTest INCLUDE_DIRECTORIES)
message(STATUS "
LINK_LIBRARIES ${LINK_LIBRARIES}
INCLUDE_DIRECTORIES ${INCLUDE_DIRECTORIES}
")
message(STATUS "
RAPTOR2_STATIC_LIBRARY ${RAPTOR2_STATIC_LIBRARY}
RAPTOR2_INCLUDE_DIR ${RAPTOR2_INCLUDE_DIR}
RASQAL_STATIC_LIBRARY ${RASQAL_STATIC_LIBRARY}
RASQAL_INCLUDE_DIR ${RASQAL_INCLUDE_DIR}
LIBRDF_STATIC_LIBRARY ${LIBRDF_STATIC_LIBRARY}
LIBRDF_INCLUDE_DIR ${LIBRDF_INCLUDE_DIR}
")
And the output of the CMake command:
#(looks good)
LINK_LIBRARIES /usr/local/lib/libraptor2.a;/usr/local/lib/librasqal.a;/usr/local/lib/librdf.a;curl;xml2;xslt;ltdl
INCLUDE_DIRECTORIES /usr/local/include/raptor2;/usr/local/include/rasqal;/usr/local/include
RAPTOR2_STATIC_LIBRARY /usr/local/lib/libraptor2.a
RAPTOR2_INCLUDE_DIR /usr/local/include/raptor2
RASQAL_STATIC_LIBRARY /usr/local/lib/librasqal.a
RASQAL_INCLUDE_DIR /usr/local/include/rasqal
LIBRDF_STATIC_LIBRARY /usr/local/lib/librdf.a
LIBRDF_INCLUDE_DIR /usr/local/include
To build, I'm using CLion which just does this in the background:
mkdir build && cd build
CMake ..
make
Thus giving me linker errors. I have dug a little deeper by using nm to inspect the contents of the Redland libraries.
$nm -A librdf.a > librdf.a.nmoutput.txt
$nm -A libraptor2.a > libraptor2.a.nmoutput.txt
$nm -A librasqal.a > librasqal.a.nmoutput.txt
The first offending undfined reference error
/usr/local/lib/librdf.a(rdf_init.o): In function `librdf_free_memory':
/home/ciaran/Software/redland/redland-1.0.17/src/rdf_init.c:671: undefined reference to `raptor_free_memory'
is in function librdf_free_memory, which is a defined reference inside librdf.a
# librdf.a.nmoutput.txt
...
librdf.a:rdf_init.o:0000000000000740 T librdf_free_memory
...
When we look for the undefined reference to raptor_free_memory, we se that it is indeed undefined inside librdf.a..
#librdf.a.nmoutput.txt
...
librdf.a:rdf_init.o: U raptor_free_memory
...
But this should be in libraptor2.a anyway, and if we look we see that it is indeed there and defined as it should be:
# libraptor2.a.nmoutput.txt
...
libraptor2.a:raptor_general.o:0000000000000863 T raptor_free_memory
...
My understanding is that the process of linking should essentially fill the undefined reference inside librdf.a with the definition inside libraptor.a, but this clearly is not happening.
Why is this happening?
When your static libraries have dependencies on each other, the link order matters (see this response).
If librdf depends on the libraptor library (as indicated by the link error), the libraptor library should be listed after librdf when specified to the linker. Try re-arranging the list of libraries in your target_link_libraries() command to adhere to this ordering, based on your library dependencies.
I am trying to compile the master branch of Vc on my system but make is not working and not giving any erorrs.
cmake ran fine with the only missing things being Intel SDE not found and MIC SDK was not found!.
if I run:
$ ls
cmake CMakeCache.txt CMakeFiles cmake_install.cmake CTestCustom.cmake Makefile
$ make
$
I can see the makefile in the directory but the prompt just returns empty and no action is performed by make. Is the Makefile broken?
I installed gcc version 5.1 locally on a cluster having OS as CentOS where I dont have root access (so i cant use any commands like 'sudo'). (The global gcc version installed is 4.4). I also modified the path variable to include the path to my local version at the beginning of the path variable. Before, when I was trying to install boost using the global version, it worked fine. But now, when I try to install boost, it shows the following error:
/users/home/head/cmp/soft/sft/gcc/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.1.0/cc1: error while loading shared libraries: libisl.so.10: cannot open shared object file: No such file or directory
Any ideas on how to fix this will be highly appreciated.
Follow the instructions at https://gcc.gnu.org/wiki/InstallingGCC
Specifically, don't install ISL manually in some non-standard path, because GCC needs to find its shared libraries at run-time.
The simplest solution is to use the download_prerequisites script to add the GMP, MPFR, MPC and ISL source code to the GCC source tree, which will cause GCC to build them for you automatically, and link to them statically.
I have the same issue. I solved it as follows:
Download the source code of isl available here
Unzip and install: ./configure && make && make install
cp /usr/local/lib/libisl* /usr/lib
Note: a symlink also works:
$ cd /usr/lib
$ ln -s /usr/local/lib/libisl.so.10 libisl.so.10
You can do the same in Debian distros:
apt-get install libisl-dev
Adjust the references of shared libs:
$ cp /usr/local/lib/libisl* /usr/lib
Note: a symlink also works:
$ cd /usr/lib
$ ln -s /usr/local/lib/libisl.so.10 libisl.so.10
I have an OSX 10.7 computer with a non-administrator account, and was attempting to install the pre-compiled versions of gcc and g++ found here. I've attempted to use the answers presented in these questions (three different links) to compile some code with g++, to confusing avail. I have a folder structure like this:
~/code/:
usr/:
local/:
bin/ (3.6MB)
include/ (8.6MB)
lib/ (51MB)
libexec/ (49MB)
share/ (16MB)
c++/:
source/ (contains .cpp files)
g++ -v returns this:
code USER$ usr/local/bin/g++ -v
Using built-in specs.
COLLECT_GCC=usr/local/bin/g++
COLLECT_LTO_WRAPPER=/Users/USERNAME/code/usr/local/bin/../libexec/gcc/ x86_64-apple-darwin11.4.0/4.7.1/lto-wrapper
Target: x86_64-apple-darwin11.4.0
Configured with: ../gcc-4.7.1/configure --enable-languages=fortran
Thread model: posix
gcc version 4.7.1 (GCC)
An attempt at compiling a file that "#include"s only iostream:
$ usr/local/bin/g++ c++/source/test.cpp -o ex6
In file included from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/bits/postypes.h:42:0,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/iosfwd:42,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/ios:39,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/ostream:40,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/iostream:40,
from c++/source/ex6.cpp:1:
/Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/cwchar:46:19: fatal error: wchar.h: No such file or directory
compilation terminated.
I tried compiling with some flags recommended in one of the links mentioned, like this: (with all combinations of "usr/" to "usr/local/include/" and "usr/" to "/usr/local/lib" giving the same result (which is also the same as using no flags).
$ /Users/USERNAME/code/usr/local/bin/g++ source/ex6.cpp -I/Users/USERNAME/code/usr/local/include/ -L/Users/USERNAME/code/usr/local/lib/In file included from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/bits/postypes.h:42:0,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/iosfwd:42,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/ios:39,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/ostream:40,
from /Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/iostream:40,
from source/ex6.cpp:1:
/Users/USERNAME/code/usr/local/bin/../lib/gcc/x86_64-apple-darwin11.4.0/4.7.1/../../../../include/c++/4.7.1/cwchar:46:19: fatal error: wchar.h: No such file or directory
compilation terminated.
In short, I'm having trouble understanding what the answers in the links provided are saying to do. I saw reference to a specs file, which I could find no specific information for, and "-Wl,-rpath,$(DEFAULT_LIB_INSTALL_PATH)", for which I couldn't figure out what I was supposed to substitute for "DEFAULT_LIB_INSTALL_PATH".
What should I do to point the downloaded g++ compiler to its own files without placing them in their default location, as I do not have administrative capabilities on this account?
I will provide any information as necessary.
It looks like you don't have required header files. You need to install Command Line Tools from Apple Developers site (free registration needed). The problem is that you don't have administrator account. I suggest that you ask the administrator to install the tools for you. If it is not possible you could try to extract the contents of downloaded package (DevSDK.pkg) to your local directory (Pacifist can do that) and pass the path with the missing headers to your compiler. I haven't tried that though.
While building ARM toolchain , I got the following error
checking for suffix of object files... configure: error: cannot compute suffix of object files: cannot compile
See `config.log' for more details.
make[1]: *** [configure-target-libgcc] Error 1
make[1]: Leaving directory `<path>/gcc-4.3.2-arm-elf'
make: *** [all] Error 2
what might be the problem?
Did you read http://gcc.gnu.org/wiki/FAQ#configure_suffix ?
Have you installed GMP, MPFR and MPC? Are they in your library search path?
See http://gcc.gnu.org/wiki/InstallingGCC and make sure you've followed the basic instructions. By far the simplest way to build GCC (including as a cross compiler) is to follow these instructions:
Alternatively, after extracting the GCC source archive, simply run the ./contrib/download_prerequisites script in the GCC source directory. That will download the support libraries and create symlinks, causing them to be built automatically as part of the GCC build process.
"*Building GCC is not trivial, but is not difficult if you follow the instructions carefully.
Many people rush into trying to build it without reading the installation docs properly and make one or more of these common mistakes:
1) do not run ./configure from gcc src dir (this is not supported) => you need to run configure from outside the gcc source directory
2) Note: if GCC links dynamically to the prerequisite libs (GMP/MPFR/MPC) then the shared libraries must be in the dynamic linker's path (LD_LIBRARY_PATH), both when building gcc and when using the installed compiler.*"
Simple example (without dynamic link to GMP/MPFR/MPC):
tar xzf gcc-4.8.0.tar.gz
cd gcc-4.8.0
./contrib/download_prerequisites
cd ..
mkdir objdir
cd objdir
$PWD/../gcc-4.8.0/configure --prefix=/opt/gcc-4.8.0
make
make install
Sources:
Advogato Doc -
GNU Doc
export LD_LIBRARY_PATH=/path/for/libraries:$LD_LIBRARY_PATH
path/for/libraries is where the GMP MPFR and MPC libraries are present.
I was compiling GCC on ubuntu 12.04 and these linraries present in the path /usr/local/lib