Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

jon Wed, 29 Mar 2017 08:24:12 -0700

I tried installing rdkit from the bioconda channel as suggested. It worked perfectly. Thanks much!

Jon T. Swanson, Ph.D.

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

(636) 329-0300

-------- Original Message --------
Subject: Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit
by source in a non-administrator linux cluster
From: "Hongbin Yang" <yanyangh...@163.com>
Date: Wed, March 29, 2017 3:01 am
To: greg.landrum <greg.land...@gmail.com>
Cc: "Jonna.Stalring" <jonna.stalr...@astrazeneca.com>, rdkit-discuss
<rdkit-discuss@lists.sourceforge.net>, 蔡迎春 <1096425...@qq.com>

Hi, Greg,

Thanks for your suggestion. However, I cannot install it correctly by "original conda" as suggested in document.

> `conda create -c rdkit -n hbyang-rdkit-env rdkit`
> The same error occured just like what I installed from source:
/home/hbyang/.conda/envs/hbyang-rdkit-env/lib/python2.7/site-packages/rdkit/../../../libboost_serialization.so.1.56.0: undefined symbol: _ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchiveEEEE14m_is_de

Fortunately, I solved the problem referring to the previous mail-list https://sourceforge.net/p/rdkit/mailman/message/35103418/
> the linux packages that are available from the rdkit channel on anaconda.org are based on centos6
> rdkit packages compatible with the rhel5 distribution could be available from the bioconda channel

So I added the channel via `conda config --add channels bioconda` , installed rdkit by `conda install rdkit` and it worked. I found that it requires boost 1.57.0-4 and thus I guess that 1.56.0 is not well compatible with rhel5.
The cost is that I can not use the lastest version, but it's ok.

Hongbin Yang 杨弘宾

From: Greg Landrum
Date: 2017-03-29 14:01
To: 杨弘宾
CC: rdkit-discuss
Subject: Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster
A first thing that's important to know and that may make all of this easier:
You can install the rdkit using conda even if you don't have write access to the directory where anaconda python is installed.
If you follow the directions in the documentation and create an environment to use the RDKit in you should be able to install your own packages without any problems. Environments are (normally) created in a subdir of your home directory, where you will (hopefully) have write access.

If you cannot do that or, for some other reason, want to install the RDKit from source, I will try and provide more help on that.

-greg

On Tue, Mar 28, 2017 at 5:56 PM, 杨弘宾 <yanyangh...@163.com> wrote:

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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Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

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