Here's the github issue: https://github.com/rdkit/rdkit/issues/1886
On Sat, Jun 2, 2018 at 6:08 AM Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Brian,
>
> I just did a bit of looking here and either something has changed since my
> first experiments with 9.6 or I was remembering incorrectly. The functions
> exposed in the cartridge need to be marked as being "parallel safe" in
> order to be usable in a parallel query. At the moment none of them are.
> This would clearly be useful, so I'm going to start taking a look at
> adding the relevant flags.
>
> -greg
>
>
> On Fri, Jun 1, 2018 at 5:05 PM Brian Cole <col...@gmail.com> wrote:
>
>> 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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