I just hit the same problem.
Setup:
- Centos7 with postgres already present.
- Install miniconda
- conda install -y -c rdkit rdkit-postgres95
The install ran OK with no errors. However I notice that it states that
these packages are installed:
rdkit: 2017.09.1-py27_1 rdkit
rdkit-postgresql95: 2016.09.4-py27_1 rdkit
Note that the versions are different. Is this expected?
Then when I run:
psql -c 'create extension rdkit' mydatabase
I get:
ERROR: could not open extension control file
"/opt/rh/rh-postgresql95/root/usr/share/pgsql/extension/rdkit.control":
No such file or directory
And indeed there is no such file. A search of the filesystem shows that
file is only present within the miniconda2 directory, so it seems that
the cartridge extensions were not deployed correctly.
The same happens if I try to use the rdkit-postgresql RPM packages.
Tim
On 28/10/2017 16:06, Drew Gibson via Rdkit-discuss wrote:
Hello,
I have installed anaconda3 on Ubuntu 16.04.3 LTS, and have installed
the |rdkit-postgresql95 |
conda environment.
When trying to install the cartridge on a new db, I get the message -
ERROR: could not open extension control file
"/home/drew/anaconda3/envs/rdkit/share/postgresql/extension/rdkit.control":
No such file or directory
Sequence of commands to install and set-up (error occurs after the
last command)...
NB, when I do the following with the standard rdkit-postgresql
package, I don't get the error.
// having installed anaconda3, install the rdkit-postgresql95 conda
environment
// rdkit: 2017.09.1-py35_1 rdkit
// rdkit-postgresql95: 2016.09.4-py35_1 rdkit
conda create -c rdkit -n rdkit rdkit-postgresql95
// create the directory for postgres data
mkdir ~/anaconda3/envs/rdkit/pgdata
// activate the environment
source activate rdkit
// navigate to the /bin directory
cd ~/anaconda3/envs/rdkit/bin
// run initdb
./initdb ~/anaconda3/envs/rdkit/pgdata
// initdb creates postgres.conf in the /pgdata folder -
// we can now edit to rdkit recommended settings.
"To improve performance while loading the database and building
the index, I changed a
couple of postgres configuration settings in postgresql.conf :"
synchronous_commit = off # immediate fsync at commit
full_page_writes = off # recover from partial page writes
"And to improve search performance, I allowed postgresql to use
more memory than the
extremely conservative default settings:"
shared_buffers = 2048MB # min 128kB (change requires
restart)
work_mem = 128MB # min 64kB
// reboot (to new config), activate the environment then start the DB
server from /bin
./pg_ctl -D /home/drew/anaconda3/envs/rdkit/pgdata -l logfile start
// navigate to the /bin directory and create chembl DB
./createdb chembl_23
// back out to command line and setup rdkit cartridge on db
./psql -c 'create extension rdkit' chembl_23
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