Hi, Andrew,
I did set the LD_LIBRARY_PATH and added the $conda/lib in it. Today,
I tried installing a new boost (1.60.0) myself with the following
commands:```./bootstrap.sh
./b2 install
``` Interestingly, I colud not `make` successfully this time, with the
several errors such as :```/home/hbyang/.local/lib/libboost_thread.so:
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&,
unsigned long)@GLIBCXX_3.4.21'
/home/hbyang/.local/lib/libboost_thread.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
``` Then I tried install by conda with `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_destroyedE
By the way, I found a similar problem reported at the end of the issue
[#762](https://github.com/rdkit/rdkit/issues/762 )
user-agent conda/4.3.4 requests/2.12.4 CPython/2.7.12 Linux/2.6.18-308.el5
CentOS/5.8 glibc/2.5
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
From: Andrew DalkeDate: 2017-03-29 03:35To: CC: rdkit-discussSubject: Re:
[Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a
non-administrator linux clusterOn Mar 28, 2017, at 17:56, 杨弘宾
<yanyangh...@163.com> wrote:
> 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.
Yes I have, and I find it rather difficult. (My system has Python 2.7 and
Python 3.5, for several versions of RDKit, so I can do regression testing
across multiple environments.)
I use Python virtual environments which helps, in that I effectively can
control a Python installation, but also adds its own layer of complexity.
> 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 think you are missing an LD_LIBRARY_PATH entry to point to your Boost
libraries.
Andrew
da...@dalkescientific.com
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