apache doesn't respect LD_LIBRARY_PATH?

Question

In my web application I have this piece of code:

from rdkit import Chem

This causes it to crash under apache, in logs I can see:

[Fri Sep 06 10:35:44 2013] [error] [client 172.22.69.51] ImportError: libRDGeneral.so.1: cannot open shared object file: No such file or directory

It looks like this problem is caused by LD_LIBRARY_PATH but I set it in my wsgi.py file:

os.environ['LD_LIBRARY_PATH']='/usr/lib/oracle/11.2/client64/lib:/nfs/public/rw/chembl/utils/RDKit_2012_09_1/lib:/nfs/public/rw/chembl/utils/indigo/lib/Linux/x64/'

as well as in VirtualHost apache conf:

<VirtualHost *:8787>
    ...
SetEnv LD_LIBRARY_PATH /usr/lib/oracle/11.2/client64/lib:/nfs/public/rw/chembl/utils/RDKit_2012_09_1/lib:/nfs/public/rw/chembl/utils/indigo/lib/Linux/x64/
</VirtualHost>

I can run this without problems from command line on the same machine:

(chembl_webservices)-bash-4.1$ export PYTHONPATH=/nfs/public/rw/chembl/utils/RDKit_2012_09_1/
(chembl_webservices)-bash-4.1$ export LD_LIBRARY_PATH=/nfs/public/rw/chembl/utils/RDKit_2012_09_1/lib
(chembl_webservices)-bash-4.1$ /nfs/public/rw/chembl/utils/virtualenvs/ldc/envs/chembl_webservices/bin/python
Python 2.7.5 (default, Aug  5 2013, 17:00:57) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import rdkit
from rdkit import Chem

And of course I can make my script print actual value of LD_LIBRARY_PATH so I know it's set correctly, the file and path exists and privileges are fine:

ls /nfs/public/rw/chembl/utils/RDKit_2012_09_1/lib -lh
-rwxr-xr-x 1 cbl_adm cbl_pub 406K Aug  8 11:13 libRDGeneral.so.1.2012.09.1

I can run ldd libRDGeneral.so.1.2012.09.1 to see that all dependencies are met:

linux-vdso.so.1 =>  (0x00007fff397ff000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f096ecd5000)
libm.so.6 => /lib64/libm.so.6 (0x00007f096ea50000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f096e83a000)
libc.so.6 => /lib64/libc.so.6 (0x00007f096e4a7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f096f22d000)

So what's wrong? What else can I do? How can I debug it? Please help.

Answer 1

The LD_LIBRARY_PATH must be set in the environment outside of the Apache process when Apache is started. It cant be set inside of your web application after Apache has been started.

What you should do is recompile the rdkit module and set:

LD_RUN_PATH=/nfs/public/rw/chembl/utils/RDKit_2012_09_1/lib

in the environment when compiling it. Setting LD_RUN_PATH at compile time of the Python C extension module will cause that directory to be embedded in the Python C extension module so that it knows where to find the library at run time without LD_LIBRARY_PATH needing to be set.