Re: [Rdkit-discuss] Postgres query performance

2017-12-11 Thread Greg Landrum
Another update here: I just uploaded an rdkit-postgresql95 build for the
mac. This is, again, using the older version of conda.

Installation instructions and caveats are the same as below. :-)

-greg


On Mon, Dec 11, 2017 at 6:56 AM, Greg Landrum 
wrote:

> This morning I managed to get at least something done. It should now be
> possible to install the cartridge for linux from the rdkit conda channel
> with the command:
> conda install -c rdkit rdkit-postgresql95
>
> caveats:
> - linux only. I built it on centos6, so it should work on just about any
> linux system though
> - requires you to use postgresql95 (also from the rdkit channel)
> - does not have pl/python installed
> - since I had to grab an early train this morning I haven't done much
> testing
>
> This is a long way from being optimal, but it should at least be
> functional. Please let me know if you get a chance to try it out.
>
> I *hope* that this will all get easier when we switch over to using the
> new compiler packages that are part of conda-build v3. I'm trying the first
> experiments with this now.
>
> -greg
>
>
> On Fri, Dec 8, 2017 at 4:07 PM, Greg Landrum 
> wrote:
>
>> At some point, in the not too distant future (I hope), there will be an
>> updated version of the cartridge.
>>
>> On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
>> wrote:
>>
>>> Thanks Riccardo.
>>>
>>> While I can see Rdkit 2017.09.2.0 is available on conda (
>>> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
>>> at 2016.03.4
>>>
>>> Can I update the rdkit installation and use it to update the Postgres
>>> extension? Or must I wait for a rdkit-postgres conda with the right version
>>> of Rdkit?
>>>
>>> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
>>> riccardo.viane...@gmail.com> wrote:
>>>
 Hi Rajarshi,

 On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha <
 rajarshi.g...@gmail.com> wrote:

> Hi, I'm working on an application that is trying to do arbitrary
> substructure queries across ChEMBL 23. I pretty much followed the
> instructions at http://www.rdkit.org/docs/Cartridge.html on a
> Postgres 9.2 instance with RDKit 2016.03.1 all running on a Linux box with
> 88GB of RAM.
>

 some 2016 releases were affected by a bug in the cartridge Makefile
 that disabled any compiler optimization. If possible, I would suggest
 trying a more recent version (>= 2016.09.1).

 Best,
 Riccardo


>>>
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>> NIH Center for Advancing Translational Science
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
--
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Re: [Rdkit-discuss] Postgres query performance

2017-12-11 Thread Rajarshi Guha
Thanks a lot - we'll give this a try

On Mon, Dec 11, 2017 at 12:56 AM, Greg Landrum 
wrote:

> This morning I managed to get at least something done. It should now be
> possible to install the cartridge for linux from the rdkit conda channel
> with the command:
> conda install -c rdkit rdkit-postgresql95
>
> caveats:
> - linux only. I built it on centos6, so it should work on just about any
> linux system though
> - requires you to use postgresql95 (also from the rdkit channel)
> - does not have pl/python installed
> - since I had to grab an early train this morning I haven't done much
> testing
>
> This is a long way from being optimal, but it should at least be
> functional. Please let me know if you get a chance to try it out.
>
> I *hope* that this will all get easier when we switch over to using the
> new compiler packages that are part of conda-build v3. I'm trying the first
> experiments with this now.
>
> -greg
>
>
> On Fri, Dec 8, 2017 at 4:07 PM, Greg Landrum 
> wrote:
>
>> At some point, in the not too distant future (I hope), there will be an
>> updated version of the cartridge.
>>
>> On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
>> wrote:
>>
>>> Thanks Riccardo.
>>>
>>> While I can see Rdkit 2017.09.2.0 is available on conda (
>>> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
>>> at 2016.03.4
>>>
>>> Can I update the rdkit installation and use it to update the Postgres
>>> extension? Or must I wait for a rdkit-postgres conda with the right version
>>> of Rdkit?
>>>
>>> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
>>> riccardo.viane...@gmail.com> wrote:
>>>
 Hi Rajarshi,

 On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha <
 rajarshi.g...@gmail.com> wrote:

> Hi, I'm working on an application that is trying to do arbitrary
> substructure queries across ChEMBL 23. I pretty much followed the
> instructions at http://www.rdkit.org/docs/Cartridge.html on a
> Postgres 9.2 instance with RDKit 2016.03.1 all running on a Linux box with
> 88GB of RAM.
>

 some 2016 releases were affected by a bug in the cartridge Makefile
 that disabled any compiler optimization. If possible, I would suggest
 trying a more recent version (>= 2016.09.1).

 Best,
 Riccardo


>>>
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>> NIH Center for Advancing Translational Science
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>


-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Postgres query performance

2017-12-10 Thread Greg Landrum
This morning I managed to get at least something done. It should now be
possible to install the cartridge for linux from the rdkit conda channel
with the command:
conda install -c rdkit rdkit-postgresql95

caveats:
- linux only. I built it on centos6, so it should work on just about any
linux system though
- requires you to use postgresql95 (also from the rdkit channel)
- does not have pl/python installed
- since I had to grab an early train this morning I haven't done much
testing

This is a long way from being optimal, but it should at least be
functional. Please let me know if you get a chance to try it out.

I *hope* that this will all get easier when we switch over to using the new
compiler packages that are part of conda-build v3. I'm trying the first
experiments with this now.

-greg


On Fri, Dec 8, 2017 at 4:07 PM, Greg Landrum  wrote:

> At some point, in the not too distant future (I hope), there will be an
> updated version of the cartridge.
>
> On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
> wrote:
>
>> Thanks Riccardo.
>>
>> While I can see Rdkit 2017.09.2.0 is available on conda (
>> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
>> at 2016.03.4
>>
>> Can I update the rdkit installation and use it to update the Postgres
>> extension? Or must I wait for a rdkit-postgres conda with the right version
>> of Rdkit?
>>
>> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
>> riccardo.viane...@gmail.com> wrote:
>>
>>> Hi Rajarshi,
>>>
>>> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha >> > wrote:
>>>
 Hi, I'm working on an application that is trying to do arbitrary
 substructure queries across ChEMBL 23. I pretty much followed the
 instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
 RAM.

>>>
>>> some 2016 releases were affected by a bug in the cartridge Makefile that
>>> disabled any compiler optimization. If possible, I would suggest trying a
>>> more recent version (>= 2016.09.1).
>>>
>>> Best,
>>> Riccardo
>>>
>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Rajarshi Guha
Thanks Greg.

Right now I have

rdkit 2017.09.2.0  py27h080088d_1rdkit

rdkit-postgresql  2016.03.3py27_1rdkit

But when I try to install the extension I get an error

chembl23=# create extension if not exists rdkit;

ERROR:  could not load library
"/home/rdkit/.conda/envs/ifx-rdkit-env/lib/postgresql/rdkit.so":
libAvalonLib.so.1: cannot open shared object file: No such file or directory

STATEMENT:  create extension if not exists rdkit;

ERROR:  could not load library
"/home/rdkit/.conda/envs/ifx-rdkit-env/lib/postgresql/rdkit.so":
libAvalonLib.so.1: cannot open shared object file: No such file or directory

Would this be related to the mismatch between the rdkit and rdkit-postgres
versions?

If so, what is the recommended way to get postgres to use the 2017 version
of rdkit?

On Fri, Dec 8, 2017 at 10:07 AM, Greg Landrum 
wrote:

> At some point, in the not too distant future (I hope), there will be an
> updated version of the cartridge.
>
> On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
> wrote:
>
>> Thanks Riccardo.
>>
>> While I can see Rdkit 2017.09.2.0 is available on conda (
>> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
>> at 2016.03.4
>>
>> Can I update the rdkit installation and use it to update the Postgres
>> extension? Or must I wait for a rdkit-postgres conda with the right version
>> of Rdkit?
>>
>> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
>> riccardo.viane...@gmail.com> wrote:
>>
>>> Hi Rajarshi,
>>>
>>> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha >> > wrote:
>>>
 Hi, I'm working on an application that is trying to do arbitrary
 substructure queries across ChEMBL 23. I pretty much followed the
 instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
 RAM.

>>>
>>> some 2016 releases were affected by a bug in the cartridge Makefile that
>>> disabled any compiler optimization. If possible, I would suggest trying a
>>> more recent version (>= 2016.09.1).
>>>
>>> Best,
>>> Riccardo
>>>
>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Greg Landrum
At some point, in the not too distant future (I hope), there will be an
updated version of the cartridge.

On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
wrote:

> Thanks Riccardo.
>
> While I can see Rdkit 2017.09.2.0 is available on conda (
> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
> at 2016.03.4
>
> Can I update the rdkit installation and use it to update the Postgres
> extension? Or must I wait for a rdkit-postgres conda with the right version
> of Rdkit?
>
> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
> riccardo.viane...@gmail.com> wrote:
>
>> Hi Rajarshi,
>>
>> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
>> wrote:
>>
>>> Hi, I'm working on an application that is trying to do arbitrary
>>> substructure queries across ChEMBL 23. I pretty much followed the
>>> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
>>> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
>>> RAM.
>>>
>>
>> some 2016 releases were affected by a bug in the cartridge Makefile that
>> disabled any compiler optimization. If possible, I would suggest trying a
>> more recent version (>= 2016.09.1).
>>
>> Best,
>> Riccardo
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Rajarshi Guha
Thanks Riccardo.

While I can see Rdkit 2017.09.2.0 is available on conda (
https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
at 2016.03.4

Can I update the rdkit installation and use it to update the Postgres
extension? Or must I wait for a rdkit-postgres conda with the right version
of Rdkit?

On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
riccardo.viane...@gmail.com> wrote:

> Hi Rajarshi,
>
> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
> wrote:
>
>> Hi, I'm working on an application that is trying to do arbitrary
>> substructure queries across ChEMBL 23. I pretty much followed the
>> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
>> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
>> RAM.
>>
>
> some 2016 releases were affected by a bug in the cartridge Makefile that
> disabled any compiler optimization. If possible, I would suggest trying a
> more recent version (>= 2016.09.1).
>
> Best,
> Riccardo
>
>


-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Postgres query performance

2017-11-30 Thread Riccardo Vianello
Hi Rajarshi,

On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
wrote:

> Hi, I'm working on an application that is trying to do arbitrary
> substructure queries across ChEMBL 23. I pretty much followed the
> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
> RAM.
>

some 2016 releases were affected by a bug in the cartridge Makefile that
disabled any compiler optimization. If possible, I would suggest trying a
more recent version (>= 2016.09.1).

Best,
Riccardo
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
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