Doesn't appear like ::mol parallelized either. Only seeing the following
use 1 CPU in top.
ligandlibrary=# explain analyze select count(*) from ligands where
rdkit_mol@>'Br'::mol;
QUERY PLAN
-------------------------------------------------------------------------------------------------------------------------------------------------------------
Aggregate (cost=50959.06..50959.07 rows=1 width=8) (actual
time=791284.354..791284.354 rows=1 loops=1)
-> Bitmap Heap Scan on ligands (cost=3156.60..50926.74 rows=12927
width=0) (actual time=252201.744..790985.637 rows=667236 loops=1)
Recheck Cond: (rdkit_mol @> 'Br'::mol)
Rows Removed by Index Recheck: 13725739
Heap Blocks: exact=42169 lossy=1254494
-> Bitmap Index Scan on rdkit_substructure_idx
(cost=0.00..3153.37 rows=12927 width=0) (actual time=252166.576..252166.576
rows=14511013 loops=1)
Index Cond: (rdkit_mol @> 'Br'::mol)
Planning time: 0.109 ms
Execution time: 791284.588 ms
(9 rows)
Time: 791385.473 ms (13:11.385)
ligandlibrary=# select name, setting from pg_settings where name like
'dynamic_shared_memory_type';
name | setting
----------------------------+---------
dynamic_shared_memory_type | posix
(1 row)
Time: 41.439 ms
ligandlibrary=# select name, setting from pg_settings where name like
'max_parallel_workers_per_gather';
name | setting
---------------------------------+---------
max_parallel_workers_per_gather | 2
(1 row)
Time: 0.926 ms
ligandlibrary=#
Maybe some other flag I need to specify. Only 2 cores in this system at the
moment, maybe it only parallelizes when there's more than 2 cores?
Thanks,
Brian
On Fri, Jun 1, 2018 at 10:07 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> I think they should. Does a ::mol query on the same table parallelize? If
> it does but a ::qmol query does not maybe I forgot something in the SQL
> function definitions
>
> On Fri, 1 Jun 2018 at 15:43, Brian Cole <col...@gmail.com> wrote:
>
>> Hi Greg,
>>
>> Are SMARTS searches with the ::qmol type supposed to parallelize? They
>> don't appear to be either.
>>
>> -Brian
>>
>> On Fri, Jun 1, 2018 at 1:46 AM, Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>
>>> Hi Brian,
>>>
>>> When the new parallel queries came out I checked that they actually
>>> could be used and things seemed fine.
>>> The problem (and it's a sizable one) is that parallel queries don't use
>>> the index. Until parallel scans using GIST indices work, I don't think this
>>> is really going to help much.
>>>
>>> -greg
>>>
>>>
>>> On Fri, Jun 1, 2018 at 12:04 AM Brian Cole <col...@gmail.com> wrote:
>>>
>>>> It appears like Postgres 9.6+ supports parallel queries now to
>>>> accelerate slow queries:
>>>> https://www.postgresql.org/docs/10/static/parallel-query.html
>>>>
>>>> Has anyone successfully got this to accelerate substructure queries
>>>> with the RDKit Postgres cartridge?
>>>>
>>>> Thanks,
>>>> Brian
>>>>
>>>> ------------------------------------------------------------
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>>
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