MPI - error loading shared libraries

Question

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.

Gerhardine

Answer 1

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.

Mylander

Be sure your LD_LIBRARY_PATH isn't being overwitten in your .bashrc like mine was with CUDA. You want something like export LD_LIBRARY_PATH=/lib64/openmpi/lib:$LD_LIBRARY_PATH – Priceless

Answer 2

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.

Autophyte

to find it (e.g. on a large cluster) use whereis openmpi. Worked for me. – Tuft

Answer 3

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

Nara

Answer 4

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

Common

Answer 5

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.

Flower

That is valid for system wide install and requires config and root access. This does not work for non root users and/or when multiple versions are installed. – Tetanic