View source for Error while loading shared libraries

== The symptoms ==
If you get a message of the likes of 
<pre>
./gcm_32x32x15_phystd_seq.e: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory
</pre>
or
<pre>
./gcm_32x32x15_phystd_seq.e: error while loading shared libraries: libnetcdff.so.5: cannot open shared object file: No such file or directory
</pre>
or 
<pre>
./gcm_32x32x15_phystd_seq.e: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory
</pre>
etc.

This is because your executable was build with dynamic libraries (the default nowadays) and that these are not found at run time. You should therefore ensure that you have the same environment setup when you run the model than when it was compiled. In practice this essentially means that you should source the arch.env file that was used to compile the model before running it. e.g.:
<syntaxhighlight lang="bash">
source ../LMDZ.COMMON/arch.env
./gcm_32x32x15_phystd_seq.e > gcm.out 2>&1
</syntaxhighlight>

== Additional comments (mostly for experts) ==
=== the ldd command ===
To find out if an executable knows where to find all the libraries it will need, just ask! Using the ldd command:
<syntaxhighlight lang="bash">
ldd gcm_32x32x15_phystd_seq.e
</syntaxhighlight>
which will return a list of the likes of:
<pre>
	linux-vdso.so.1 =>  (0x00007ffd67df3000)
	libblas.so.3 => /lib64/libblas.so.3 (0x00002b76b6116000)
	liblapack.so.3 => /lib64/liblapack.so.3 (0x00002b76b636f000)
...
</pre>
If a library is missing, this is mentioned there, e.g.:
<pre>
	libnetcdff.so.5 => not found
</pre>

=== the LD_LIBRARY_PATH environment variable ===
Apart from the default system directories (/lib64/, /usr/lib/, etc.) where a program will always look for libraries, one can use the '''LD_LIBRARY_PATH''' environment variable to specify (non-standard) paths where the program will look for. e.g: if your NetCDF library "lib" directory is in "/home/me/my_stuff/netcdf/lib" and you want you programs to find it you should update your '''LD_LIBRARY_PATH''':
<syntaxhighlight lang="bash">
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/me/my_stuff/netcdf/lib
</syntaxhighlight>

=== the "Wl,-rpath=" compilation option ===
One can "hard code" into an executable where it should look for when seeking dynamical libraries at run time via the "-Wl,-rpath=" option provided to the linker when compiling/linking the code.
Following up on previous example and assuming you're using the makelmdz_fcm script, this implies adapting the arch.fcm file '''%BASE_LD''' line:
<pre>
%BASE_LD -Wl,-rpath=/home/me/my_stuff/netcdf/lib
</pre>
Note however that this "hard coding" of the path into the executable '''is not recommended''' as if the library is later moved to a different directory then the executable won't find it anymore... You have been warned.

=== the ''patchelf'' utility ===
Sometimes ldd reveals that  some "system libraires" (e.g. located in /lib64) are used instead of the ones you provide. There is actually a tool '''patchelf''' which may be useful to modify, in a similar way to the ''-rpath'' mentioned above, but on an existing executable the paths where it will expect to find its shared libraries. See https://github.com/NixOS/patchelf

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