So I got several shared libraries that I am trying to permanently install on my Ubuntu system but I am having some difficulty with it.
I want to install the libraries and the headers in a separate folder under /usr/local/lib and /usr/local/include (for example a folder named agony) so it would be clean and removing them would just require that I delete those folders. so it looks something like this:
/usr/local/lib/agony/libbtiGPIO.so
/usr/local/lib/agony/libbtiDSP.so
...
/usr/local/include/agony/GPIO.h
/usr/local/include/agony/DSP.h
...
And I added a file here /etc/ld.so.conf.d/agony.conf which include a line describing the path to the library folder:
$ cat /etc/ld.so.conf.d/agony.conf
/usr/local/lib/agony
and I perform sudo ldconfig to update the library database.
So to double check if the library is found I do ldconfig -p | grep bti* and
I see the following result:
$ ldconfig -p | grep bti
...
libbtiGPIO.so (libc6,x86-64) => /usr/local/lib/agony/libbtiGPIO.so
libbtiDSP.so (libc6,x86-64) => /usr/local/lib/agony/libbtiDSP.so
...
At this point I should be able to use the libraries without specifying the library path. But When I attempt to compile an application without providing the library path (-L) it fails. However, when I supply gcc with the library path ex:
gcc source.c -L /usr/local/lib/agony output -lbtiGPIO -lbtiDSP
it works!!
I don't want to use LD_LIBRARY_PATH environment variable because this library is going to be used everywhere on the system and I don't want other compilers to worry about providing LD_LIBRARY_PATH.
What am I doing wrong here?
At this point I should be able to use the libraries without specifying the library path
Here lies the confusion.
You have built your shared library libbtiGPIO.so (just sticking with that one),
placed it in /usr/local/lib/agony, and updated the ldconfig database accordingly.
The effect of that is when you run a program that has been linked with libbtiGPIO
then the dynamic linker (/lib/x86_64-linux-gnu/ld-2.21.so, or similar) will know where to look
to load that library into the process and you will not need to tell it by setting an LD_LIBRARY_PATH in the environment.
However, you haven't done anything that affects the list of default library
search directories that are hardwired into your build of gcc, that it passes to
the linker (/usr/bin/ld) when you link a program with libbtiGPIO in the first place.
That list of default search directories is what you will find if your do a verbose
build of your program - gcc -v ... - and then pick out the value of LIBRARY_PATH
from the output, e.g.
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/5/:\
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/:\
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/:\
/lib/x86_64-linux-gnu/:\
/lib/../lib/:\
/usr/lib/x86_64-linux-gnu/:\
/usr/lib/../lib/:\
/usr/lib/gcc/x86_64-linux-gnu/5/../../../:\
/lib/:\
/usr/lib
/usr/local/lib/agony is not one of those and to make it one of those you
would have to build gcc from source yourself. Hence, in order to link your
program with libbtiGPIO you still need to tell ld where to find it with
-L/usr/local/lib/agony -lbtiGPIO.
man, you misunderstand the procedure of complier and link.
First, libbtiGPIO.so is a shared link library not a static link library. it is important to know those difference .
Then you need to know something else. changing ld.so.conf.d/*.conf and run sudo ldconfig, it affects the procedure of link. in other words, if you don't add agony.conf and sudo ldconfig, you will receive a error when you run ./a.out rather than gcc source.c -L ...., the gcc command can run successfully even thougth you don't ldconfig.
Finally,if you don't pollute the LD_LIBRARY_PATH environment variable, you have to add -L ... options in your gcc command. What'more, if you don't want to input too many words in your shell frequently, you can learn to use Makefile.
Related
I'm attempting to install a library that will be used generally on this node. Currently the library is installed in a location that includes it's version name /opt/sample-x.y.z/lib/libsample.so. Ideally I'd like to be able to update the library, change the sys configs and not bother other devs with needing to change paths on trivial changes. I've added the library directory to the /etc/ld.so.conf.d/sample.conf and run ldconfig, but this only seems to affect loading not linking.
When I run ldconfig -v | grep sample, I correctly see libsample.so.
However, whenever I run ld -lsample --verbose, it fails to find the library. In the verbose output, it details the directories that it searches and the one I added with ldconfig isn't there. As a workaround, I tested adding a symlink to the library in /usr/lib and ld was able to find it.
Are there other ways to add the library to the default linker path? Ideally I'm looking for a config file that I can modify similar to the one for loading.
If it matters, the node is a Centos7 node.
No, it is not possible. The paths that ld uses during the linking phase are configured via scripts which are pulled into ld during its build process. There isn't a way to update these after ld is built. There are other questions and answers related to accomplishing this for GCC specifically which seem to involve the LIBRARY_PATH environment variable. That solution, however, is gcc specific.
I am new to Linux. I see in my CMakeLists.txt the following;
target_link_libraries(app wiringPi
serializer
iothub_client
iothub_client_mqtt_transport
umqtt
aziotsharedutil
ssl
crypto
curl
pthread
m
ssl
crypto)
My question/understanding is; by doing this
Are we telling CMake tool to build wiringPi, serializer etc. and link with app(which is an executable created in my code)?
Where are all these libraries located?
When I do ldconfig -p | grep <libraryname>, for the above libraries
sometimes I find outputs like the following and sometimes nothing, why is that?
Is target_link_libraries smart enough to look for libraries under
the sub-directories too? I mean I see that some are just there under
user/lib and some are one more level under such as
/usr/lib/arm-linux-gnueabihf
pi#raspberrypi:~ $ ldconfig -p | grep curl
libcurl.so.4 (libc6,hard-float) => /usr/lib/arm-linux-gnueabihf/libcurl.so.4
libcurl-gnutls.so.4 (libc6,hard-float) => /usr/lib/arm-linux-gnueabihf/libcurl-gnutls.so.4
pi#raspberrypi:~ $ ldconfig -p | grep wiringPi
libwiringPiDev.so (libc6,hard-float) => /usr/local/lib/libwiringPiDev.so
libwiringPiDev.so (libc6,hard-float) => /usr/lib/libwiringPiDev.so
libwiringPi.so (libc6,hard-float) => /usr/local/lib/libwiringPi.so
libwiringPi.so (libc6,hard-float) => /usr/lib/libwiringPi.so
Are we telling CMake tool to build wiringPi, serializer etc. and link with app(which is an executable created in my code)?
Not exactly. That command tells CMake that the libraries wiringPi, serializer, etc. must be linked to target 'app' during the link stage for that target. It says nothing about building the libraries themselves, and usually they are expected to already be available rather than built.
Where are all these libraries located?
It can vary. The compiler has a default list of directories in which it looks for libraries. Other CMake commands can add link options that add directories to that list.
When I do ldconfig -p | grep <libraryname>, for the above libraries sometimes I find outputs like the following and sometimes
nothing, why is that?
ldconfig reports on libraries known to the dynamic linker. This is distinct from the linker that runs at compile time, and the directories and libraries the two know about are not necessarily the same. Reasons why ldconfig might not list a given library include:
The library is not installed.
Only a static version of the library is installed.
The library is not in any of the locations that the dynamic linker checks by default (additional directories can be specified when a program is launched, in at least two different ways).
Is target_link_libraries smart enough to look for libraries under the sub-directories too? I mean I see that some are just there under user/lib and some are one more level under such as /usr/lib/arm-linux-gnueabihf
This is not a function of CMake, but rather of the chosen toolchain and its configuration (on Linux, that's often the GNU toolchain, featuring GCC). It is usually safe to assume that the toolchain uses all the right standard library directories by default. CMake sometimes can successfully be instructed to search for specific libraries in other likely places, too, but target_link_libraries is not part of that.
When you pass to target_link_libraries a plain name (not a path) which is not a target, CMake just transforms this name into the linker flag. E.g. on Linux this is flag
-l<library-name>
So questions about searching the library you may address directly to the linker - CMake is out of the game here.
Edit: I resolved this issue, the solution is below.
I am building a code in a shared computing cluster dedicated for scientific computing, thus I can only control files in my home folder. Although I am using fftw as an example, I would like to understand the specific reason, why my attempt to setup LD_LIBRARY_PATH does not work.
I build the fftw and fftw_mpi libraries in my home folder like this
./configure --prefix=$HOME/install/fftw --enable-mpi --enable-shared
make install
It builds fine, but in install/fftw/lib, I find that the freshly built libfftw3_mpi.so links to wrong version of fftw library.
$ ldd libfftw3_mpi.so |grep fftw
libfftw3.so.3 => /usr/lib64/libfftw3.so.3 (0x00007f7df0979000)
If I now try to set the LD_LIBRARY_PATH correctly pointing to this directory, it still prefers the wrong library:
$ export LD_LIBRARY_PATH=$HOME/install/fftw/lib
$ ldd libfftw3_mpi.so |grep fftw
libfftw3.so.3 => /usr/lib64/libfftw3.so.3 (0x00007f32b4794000)
Only if I explicitly use LD_PRELOAD, I can override this behavior. I don't think LD_PRELOAD is a proper solution though.
$ export LD_PRELOAD=$HOME/install/fftw/lib/libfftw3.so.3
$ ldd libfftw3_mpi.so |grep fftw
$HOME/install/fftw/lib/libfftw3.so.3 (0x00007f5ca3d14000)
Here is what I would have expecting, a small test done in Ubuntu desktop, where I installed fftw to /usr/lib first, and then override this search path with LD_LIBRARY_PATH.
$ export LD_LIBRARY_PATH=
$ ldd q0test_mpi |grep fftw3
libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3
$ export LD_LIBRARY_PATH=$HOME/install/fftw-3.3.4/lib
$ ldd q0test_mpi |grep fftw3
libfftw3.so.3 => $HOME/install/fftw-3.3.4/lib/libfftw3.so.3
In short: Why is libfft3_mpi library still finding the wrong dynamic fftw3 library? Where is this searchpath hard coded in a such way that it is prioritized over LD_LIBARY_PATH? Why is this is not the case in another computer?
I am using intel compilers 13.1.2, mkl 11.0.4.183 and openmpi 1.6.2 if this matters.
Edit: Thanks for all the answers. With help of those, we were able to isolate the problem to RPATH, and from there, the cluster support was able to figure out the problem. I accepted the first answer, but both answers were good.
The reason, why this was so hard to figure out, is that we did not know that the compilers were actually wrapper scripts, adding things to compiler command line. Here a part of a reply from the support:
[The] compilation goes through our compiler wrapper. We do RPATH-ing
by default as it helps most users in correctly running their jobs
without loading LD-LIBRARY_PATH etc. However we exclude certain
library paths from default RPATH which includes /lib, /lib64 /proj
/home etc. Earlier the /usr/lib64 was not excluded by mistake
(mostly). Now we have added that path in the exclusion list.
From http://man7.org/linux/man-pages/man8/ld.so.8.html
When resolving shared object dependencies, the dynamic linker first
inspects each dependency string to see if it contains a slash (this
can occur if a shared object pathname containing slashes was
specified at link time). If a slash is found, then the dependency
string is interpreted as a (relative or absolute) pathname, and the
shared object is loaded using that pathname.
If a shared object dependency does not contain a slash, then it is
searched for in the following order:
o (ELF only) Using the directories specified in the DT_RPATH dynamic
section attribute of the binary if present and DT_RUNPATH
attribute does not exist. Use of DT_RPATH is deprecated.
o Using the environment variable LD_LIBRARY_PATH. Except if the
executable is a set-user-ID/set-group-ID binary, in which case it
is ignored.
o (ELF only) Using the directories specified in the DT_RUNPATH
dynamic section attribute of the binary if present.
o From the cache file /etc/ld.so.cache, which contains a compiled
list of candidate shared objects previously found in the augmented
library path. If, however, the binary was linked with the -z
nodeflib linker option, shared objects in the default paths are
skipped. Shared objects installed in hardware capability
directories (see below) are preferred to other shared objects.
o In the default path /lib, and then /usr/lib. (On some 64-bit
archiectures, the default paths for 64-bit shared objects are
/lib64, and then /usr/lib64.) If the binary was linked with the
-z nodeflib linker option, this step is skipped.
with readelf readelf -d libfftw3_mpi.so you can check if your lib contains such a attribute in the dynamic section.
with export LD_DEBUG=libs you can debug the search path used to find your libs
with chrpath -r<new_path> <executable> the rpath can be changed
I see two possible reasons for this.
First, libfftw3_mpi.so may be linked with /usr/lib64/ as RPATH. In that case, providing LD_LIBRARY_PATH will have no effect. To check if it is your case, run readelf -d libfftw3_mpi.so | grep RPATH and see if it has /usr/lib64/ as a library path. If it does, use chrpath utility to change or remove it.
Alternatively, you may be running a system that does not support LD_LIBRARY_PATH at all (like HP-UX).
The problem I faced has been solved here:
Loading shared library in open-mpi/ mpi-run
I know not how, setting LD_LIBRARY_PATH or specifying -x LD_LIBRARY_PATH fixes the problem, when my installation itself specifies the necessary -L arguments. My installation is in ~/mpi/
I have also included my compile-link configs.
$ mpic++ -showme:version
mpic++: Open MPI 1.6.3 (Language: C++)
$ mpic++ -showme
g++ -I/home/vigneshwaren/mpi/include -pthread -L/home/vigneshwaren/mpi/lib
-lmpi_cxx -lmpi -ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl
$ mpic++ -showme:libdirs
/home/vigneshwaren/mpi/lib
$ mpic++ -showme:libs
mpi_cxx mpi dl m rt nsl util m dl % Notice mpi_cxx here %
When I compiled with mpic++ <file> and ran with mpirun a.out I got a (shared library) linker error
error while loading shared libraries: libmpi_cxx.so.1:
cannot open shared object file: No such file or directory
The error has been fixed by setting LD_LIBRARY_PATH. The question is how and why? What am i missing? Why is LD_LIBRARY_PATH required when my installation looks just fine.
libdl, libm, librt, libnsl and libutil are all essential system-wide libraries and they come as part of the very basic OS installation. libmpi and libmpi_cxx are part of the Open MPI installation and in your case are located in a non-standard location that must be explicitly included in the linker search path LD_LIBRARY_PATH.
It is possible to modify the configuration of the Open MPI compiler wrappers and make them pass the -rpath option to the linker. -rpath takes a library path and appends its to a list, stored inside the executable file, which tells the runtime link editor (a.k.a. the dynamic linker) where to search for libraries before it consults the LD_LIBRARY_PATH variable. For example, in your case the following option would suffice:
-Wl,-rpath,/home/vigneshwaren/mpi/lib
This would embed the path to the Open MPI libraries inside the executable and it would not matter if that path is part of LD_LIBRARY_PATH at run time or not.
To make the corresponding wrapper add that option to the list of compiler flags, you would have to modify the mpiXX-wrapper-data.txt file (where XX is cc, c++, CC, f90, etc.), located in mpi/share/openmpi/. For example, to make mpicc pass the option, you would have to modify /home/vigneshwaren/mpi/share/openmpi/mpicc-wrapper-data.txt and add the following to the line that starts with linker_flags=:
linker_flags= ... -Wl,-rpath,${prefix}/lib
${prefix} is automatically expanded by the wrapper to the current Open MPI installation path.
In my case, I just simply appends
export LD_LIBRARY_PATH=/PATH_TO_openmpi-version/lib:$LD_LIBRARY_PATH
For example
export LD_LIBRARY_PATH=/usr/local/openmpi-1.8.1/lib:$LD_LIBRARY_PATH
into $HOME/.bashrc file and then source it to active again source $HOME/.bashrc.
I installed mpich 3.2 using the following command on Ubuntu.
sudo apt-get install mpich
When I tried to run the mpi process using mpiexec, I got the same error.
/home/node1/examples/.libs/lt-cpi: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory
Configuring LD_LIBRARY_PATH didn't fix my problem.
I did a search for the file 'libmpi.so.0' on my machine but couldn't find it. Took me some time to figure out that 'libmpi.so.0' file is named as 'libmpi.so' on my machine. So I renamed it to 'libmpi.so.0'.
It solved my problem!
If you are having the same problem and you installed the library through apt-get, then do the following.
The file 'libmpi.so' should be in the location '/usr/lib/'. Rename the file to 'libmpi.so.0'
mv /usr/lib/libmpi.so /usr/lib/libmpi.so.0
After that MPI jobs should run without any problem.
If 'libmpi.so' is not found in '/usr/lib', you can get its location using the following command.
whereis libmpi.so
first, run this command
$ sudo apt-get install libcr-dev
if still have this problem then configure LD_LIBRARY_PATH like this:
export LD_LIBRARY_PATH=/usr/local/mpich-3.2.1/lib:$LD_LIBRARY_PATH
then add it to ~/.bashrc before this line:
[ -z "$PS1" ] && return
Simply running
$ ldconfig
appears to me as a better way to solve the problem (taken from a comment on this question). In particular, since it avoids misuse of the LD_LIBRARY_PATH environment variable. See here and here, for why I believe it's misused to solve the problem at hand.
I have a certain shared object library in a special directory which I
make sure special directory is in $LD_LIBRARY_PATH
make sure this directory has read and execute permisions for all
make sure appropriate library directory is in ld.so.conf and that root has done a ldconfig
(verify by checking for library using ldconfig -p as normaluser.
make sure it is has no soname problems (i.e. create a few symlinks if necessary)
Now, say I compile a program that needs that special library, a program packaged in a typical Open Source manner which ./configure && make, etc) and it says -lspecialibrary cannot be found, an error which a lack of any of the above checks would also probably throw.
A workaround I have done is to symlink the library to /usr/local/lib64 and suddenly the library has ben found. Also when compiling a relatively simple package, I manually add -L/path/to/spec/lib and that also has worked. But I regard those two methods as hacks, so I was looking for any clues as to why my list of checks aren't good enough to find a library.
(I particularly find the $LD_LIBRARY_PATH of shallow use. In fact I can exclude certain libraries from it, and they will still be found in a compilation process).
$LD_LIBRARY_PATH and ldconfig are only used to locate libraries when running programs that need libraries, i.e. they are used by the loader not the compiler. Your program depends on libspeciallibrary.so. When running your program $LD_LIBRARY_PATH and ldconfig are consulted to find libspeciallibary.so.
These methods are not used by your compiler to find libraries. For your compiler, the -L option is the right way to go. Since your package uses the autotools, you should set the $LDFLAGS environment variable:
LDFLAGS=-L/path/to/lib ./configure && make
This is also documented in the configure help:
./configure --help