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I am trying to run drmaa (a python module that controls jobs in SGE) under a CentOS 6.x. According to the drmaa-python (https://github.com/pygridtools/drmaa-python) one of the requirement is libdrmaa.so, which I acquired from gridengine-libdrmaa-dev package.

I stored a copy of libdrmaa.so under mydir/lib/.

I also put the DRMAA_LIBRARY_PATH environmental variable in .bashrc:

DRMAA_LIBRARY_PATH=mydir/lib/libdrmaa.so

And the error message showed when I ran main.py:

Traceback (most recent call last):
  File "mydir/main.py", line 3, in <module>
    from . import tools
ImportError: cannot import name 'tools'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "mydir/main.py", line 5, in <module>
    import tools
  File "mydir/tools.py", line 20, in <module>
    import drmaa
  File "mydir/anaconda3/lib/python3.6/site-packages/drmaa/\__init\__.py", line 63, in <module>
    from .session import JobInfo, JobTemplate, Session
  File "mydir/anaconda3/lib/python3.6/site-packages/drmaa/session.py", line 39, in <module>
    from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator,
  File "mydir/anaconda3/lib/python3.6/site-packages/drmaa/helpers.py", line 36, in <module>
    from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t,
  File "mydir/anaconda3/lib/python3.6/site- 
packages/drmaa/wrappers.py", line 56, in <module>
    _lib = CDLL(libpath, mode=RTLD_GLOBAL)
  File "mydir/anaconda3/lib/python3.6/ctypes/__init__.py", line 348, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /lib64/libc.so.6: version 'GLIBC_2.14' not found (required by mydir/lib/libdrmaa.so)

I suspected that the libdrmaa.so is using the default libc.so.6 with GLIBC lower than 2.14. Let's assume that I do not have sudo privilege and no superuser could upgrade the glibc for me. I installed glibc-2.19 under my home directory and ran main.py again. The error message remained the same.

After some research, I now can list the dependencies the libdrmaa.so is looking for:

$ ldd /usr/lib/libdrmaa.so 
linux-vdso.so.1 =>  (0x00007ffdd1199000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9d4ff97000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9d4fd93000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9d4f9c9000)
/lib64/ld-linux-x86-64.so.2 (0x00007f9d505a4000)

A program patchelf was developed to change the soft link without re-compiling the file (https://nixos.org/patchelf.html):

$patchelf --set-rpath mydir/glibc/lib/libc.so.6 libdrmaa.so
$patchelf --set-interpreter mydir/glibc/lib/ld-2.19.so libdrmaa.so
cannot find section .interp

This is where I got stuck. The rpath was successfully switched to my new libc.so.6, but there was no interpreter section for the libdrmaa.so. This is also why the patchelf --set-interpreter did not do anything to libdrmaa.so.

The dependencies of libdrmaa.so after patchelf:

$ ldd ~/lib/libdrmaa.so 
ldd: warning: you do not have execution permission for `mydir/lib/libdrmaa.so'
linux-vdso.so.1 =>  (0x00007ffde5799000)
libpthread.so.0 => mydir/glibc/lib/libpthread.so.0 (0x00007febbbba1000)
libdl.so.2 => mydir/glibc/lib/libdl.so.2 (0x00007febbb99c000)
libc.so.6 => mydir/glibc/lib/libc.so.6 (0x00007febbb5ef000)
/lib64/ld-linux-x86-64.so.2 (0x00000037dec00000)

Without the interpreter section (cannot find section .interp), I was not able to change the last line to new ld-linux-x86-64.so.2 that is updated to 2.19. Here's my questions:

  1. Am I able to change the /lib64/ld-linux-x86-64.so.2 to mydir/glibc/lib/ld-linux-x86-64.so.2 for the libdrmaa.so without re-compile libdrmaa.so?

  2. Could anyone find the source code for libdrmaa.so so that I could re-compile with the prefix I want it to be?

Or if this is much easier than I thought. Please do not hesitate to response with some solution here. Thanks ahead.

===============solution==============

After @EmployedRussian response, it got confirmed that libdrmaa.so does not have a interpreter section. Since my case is to use libdrmaa.so under python, the executable program I am supposed to patch is python! So after patching the rpath for the libdrmaa.so, I typed:

patchelf --set-interpreter mydir/glibc/lib/ld-2.19.so python

Then ran the main.py again. Now the python uses the new glibc I installed in my local directories and my python and libraries uses the local glibc dependencies.

I think this question seems to be a redundant one but it is not. libdrmaa.so is not an executable, and that is why I got stuck. That also said there is a fundamental knowledge gap for me as a beginner (and presumably for other beginners looking at this forum) that needs a more step-by-step solution. Hopefully this thread will help someone in the future.

cc3423Chung
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