All,
Paolo helped me off-list to resolve this (many thanks Paolo!).
There were a number of things wrong, partly in what I was doing (cmake
switches) and partly some problems in CMakeLists.txt that requires a
patch until the PR that Paolo has submitted is merged.
I'll spare you of all the details, but here is what seem to be a working
build:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
The downside of this is that I needed to switch from building based on
an image that has already built RDKit to one that does the complete
RDkit build (which adds an hour or so to the build process) as the
cartridge build is now part of the standard build, and so to build with
cartridge support you must have postgres present.
So I ask if its still somehow possible to decouple the building of core
RDKit from building (and installing) what's needed for postgres?
Tim
On 18/04/2016 19:43, Paolo Tosco wrote:
Dear Tim,
did you check that the Boost libraries you linked the RDKit against
are in the postgres user LD_LIBRARY_PATH? You might need to login as
root, then su postgres, and echo "export
LD_LIBRARY_PATH=</path/to/Boost/libs>" > ~/.bashrc. Then, as root,
restart the postgres service. That fixed the problem for me.
Kind regards,
p.
On 18/04/2016 09:18, Tim Dudgeon wrote:
I spoke too soon!
I'm still having problem with postgres cartridge.
psql -c 'create extension rdkit' rdkitdb
ERROR: could not load library
"/usr/lib/postgresql/9.4/lib/rdkit.so":
/usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol:
_ZTIN5boost6detail16thread_data_baseE
Is something else needed for cartridge?
The docker image is here:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
which is based on rdkit build that now works OK based on the earlier
discussions in this thread.
Tim
On 17/04/2016 13:43, Brian Kelley wrote:
Now that we made thread safe the default, you also need boost-system
( and boost-serialization for FilterCatalog serialization)
|Here is the apt get we use to configure docker files.|
|apt install -y wget flex bison build-essential python-numpy cmake
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev
libboost-thread-dev libboost-serialization-dev libboost-python-dev
libboost-regex-dev; |
It looks like I should add a PR to detect this at build time?
I admit to being confused why this builds but doesn't run...
See here for more details:
https://github.com/rdkit/rdkit/issues/762
----
Brian Kelley
On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
I've hit the same issue. Any thoughts on what the underlying issue
is (without reverting to using anaconda)?
An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit
Tim
On 20/11/2015 16:02, Greg Landrum wrote:
Hi Huw,
This is not directly responsive to your question, but if you're
working with anaconda, it is probably easier to just build and
install the RDKit using the conda-rdkit recipes here:
https://github.com/rdkit/conda-rdkit
The development branch there pulls from master.
-greg
On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones <huwdjo...@hotmail.com>
wrote:
Hi there,
I’ve been building the Python RDKit modules direct from the
GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e. git
clone https://github.com/rdkit/rdkit.git).
*I use the following aptitude packages for the build process:*
flex2.5.35-10.1ubuntu2
bison 2:3.0.2.dfsg-2
build-essential 11.6ubuntu6
cmake 2.8.12.2-0ubuntu3
libboost-dev 1.54.0.1ubuntu1
libboost-regex-dev 1.54.0.1ubuntu1
python-dev 2.7.5-5ubuntu3
libboost-python-dev 1.54.0.1ubuntu1
python-numpy 1:1.8.2-0ubuntu0.1
*The build process is as follows:*
git clone https://github.com/rdkit/rdkit.git rdkit-latest
source /opt/virtualenv/current/bin/activate
export RDBASE=/path/to/rdkit-latest
cd rdkit-latest
mkdir build
cd build
cmake ..
make -j 2
make install
cd ..
cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit
*I have recently been experiencing this error:*
Python 2.7.10 (default, Nov 20 2015, 07:14:39)
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more
information.
>>> from rdkit import rdBase
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError:
/opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1:
undefined symbol: _ZN5boost6python23throw_error_already_setEv
*It looks like this error starts appearing from this commit
onwards:*
https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331
Any ideas?
Many thanks as ever.
Huw Jones
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