I tried installing rdkit using conda install -c rdkit rdkit into the latest Anaconda2 in a RHEL5 linux cluster I have limited control over. I see exactly the same error when I try 'from rdkit import Chem.' I am running the same release of Anaconda2 on my PC and all is fine. If it is an LD_LIBRARY_PATH problem, I would be overjoyed to have rdkit working.

I see libboost_serialization.so.1.56.0 in Anaconda's lib directory. I set LD_LIBRARY_PATH to the Anaconda lib directory it did not help.

I had the impression my problem was my linux is just too old. But the suggestion was to build rdkit from scratch, and that does not seem to be helping in your case.

I am also using Python 2.7 (2.7.13).

If you get a solution, I would love to know what worked.

Jon T. Swanson, Ph.D.

ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304

(636) 329-0300


-------- Original Message --------
Subject: [Rdkit-discuss] Cannot import rdBase after installed rdkit by
source in a non-administrator linux cluster
From: 杨弘宾 <yanyangh...@163.com>
Date: Tue, March 28, 2017 10:56 am
To: rdkit-discuss <rdkit-discuss@lists.sourceforge.net>

Hi, rdkiters,

    Have you tried install rdkit from source? It's ok when I installed rdkit by conda in my PC. But when I tried installing it in a server in which I am only a user who cannot use "sudo" and the "python" is in a read-only directory.

Here is my cmake command:
`~applic/cmake/bin/cmake -D PYTHON_LIBRARY=/home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/home/yccai/Programs/Anaconda/include/python2.7 -D PYTHON_EXECUTABLE=/home/yccai/Programs/Anaconda/bin/python -D BOOST_ROOT=/home/yccai/Programs/Anaconda -D Boost_NO_SYSTEM_PATHS=ON ..`

And output:

-- The C compiler identification is GNU 4.1.2
-- The CXX compiler identification is GNU 4.1.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Found PythonInterp: /home/yccai/Programs/Anaconda/bin/python (found version "2.7.12")
-- Found PythonLibs: /home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a (found version "2.7.12")
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- python
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0")
Eigen3 not found, disabling the Descriptors3D build.
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- thread
-- system
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- regex
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hbyang/applic/rdkit-Release_2016_09_4/build 

There was no error in `make` and `make install`.

But when I used:
`from rdkit import rdBase`
error happened:
ImportError: /home/yccai/Programs/Anaconda/bin/../lib/libboost_serialization.so.1.56.0: undefined symbol: _ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchiveEEEE14m_is_destroyedE

I tried the older version of rdkit and got similar error (libboost_python.so.1.56.0).

I don't think the problem is in the boost in conda but..   So what can I do to install it (or find where is the problem)?

I want to use rdkit to draw molecules in my tool. Is there any alternative way to do so?


Hongbin Yang 

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