Hi Greg,
This is super feature, but are there any downsides? Why not to enable it by
default (provided the dependencies are met)?
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2015-07-03 16:54 GMT+02:00 Greg Landrum <[email protected]>:
> Hi Adam,
>
> Sorry I forgot to mention that.
> If you are building your own version of the RDKit, you will need to
> provide the flag RDK_THREADSAFE_SSS=ON to cmake. You can do this when you
> first call cmake or, if you have run it already, by runing ccmake in your
> build directory, modifying the value of the variable, re-generating the
> cmake files (hitting 'c' and then 'g') and then re-building.
>
> Best,
> -greg
>
>
> On Friday, July 3, 2015, az <[email protected]> wrote:
>
>> Thanks Greg
>>
>> One silly question. Should the parallelization work "right off the bat"
>> or do I need some special steps in building RDKit ? I'm betting the latter,
>> but can't find what I'm missing (numThreads=4 does nothing for me).
>>
>> Cheers,
>> Adam
>>
>> On 03-Jul-15 5:11, Greg Landrum wrote:
>>
>> Dear all,
>>
>> James' question about boost.thread dependencies reminded me that I seem
>> to have neglected to post anything about one of the useful additions to the
>> most recent RDKit release; I'll remedy that now.
>>
>> I added multi-threading support for a few more time-consuming functions
>> that are embarrassingly parallel: conformation generation, force field
>> minimization of multiple-conformer molecules, and Open3D alignment of
>> multiple-conformer molecules.
>>
>> Here's a quick demonstration of how this works.
>>
>> Start by creating a basic molecule:
>>
>> In [1]: from rdkit import Chem
>>
>> In [2]: from rdkit.Chem import AllChem
>>
>> In [3]: m =
>> Chem.MolFromSmiles('Cc1cc(C(=O)NCC(=O)N)c(C)n1c2ccc(F)cc2') # CHEMBL2113931
>>
>> In [4]: mh = Chem.AddHs(m)
>>
>>
>> Time how long it takes to generate 50 conformers using one thread:
>>
>> In [5]: %timeit AllChem.EmbedMultipleConfs(mh,50)
>> 1 loops, best of 3: 260 ms per loop
>>
>>
>> And using 4 threads:
>>
>> In [6]: %timeit AllChem.EmbedMultipleConfs(mh,50,numThreads=4)
>> 10 loops, best of 3: 77.6 ms per loop
>>
>>
>> Nice speed up there.
>>
>> Do a force-field minimization of all of those conformations with one
>> thread:
>>
>> In [7]: %timeit tm = Chem.Mol(mh);AllChem.UFFOptimizeMoleculeConfs(tm)
>> 1 loops, best of 3: 1.11 s per loop
>>
>>
>> And using 4 threads:
>>
>> In [8]: %timeit tm =
>> Chem.Mol(mh);AllChem.UFFOptimizeMoleculeConfs(tm,numThreads=4)
>> 1 loops, best of 3: 288 ms per loop
>>
>>
>> Another good improvement.
>>
>> Use the O3A code to align all the conformers to another molecule:
>>
>> In [16]: m2 =
>> Chem.MolFromSmiles(r'Cc1cc(\C=C\2/SC(=Nc3ccccc3)NC2=O)c(C)n1c4ccccc4') #
>> CHEMBL599702
>>
>> In [17]: m2h = Chem.AddHs(m2)
>>
>> In [18]: AllChem.EmbedMolecule(m2h)
>> Out[18]: 0
>>
>> In [19]: AllChem.UFFOptimizeMolecule(m2h)
>> Out[19]: 1
>>
>> In [20]: refParams = AllChem.MMFFGetMoleculeProperties(m2h)
>>
>> In [21]: prbParams = AllChem.MMFFGetMoleculeProperties(mh)
>>
>> In [23]: %timeit
>> tm=Chem.Mol(mh);AllChem.GetO3AForProbeConfs(tm,m2h,prbPyMMFFMolProperties=prbParams,refPyMMFFMolProperties=refParams)
>> 1 loops, best of 3: 1.13 s per loop
>>
>>
>> Do the same alignment with 4 threads:
>>
>> In [24]: %timeit
>> tm=Chem.Mol(mh);AllChem.GetO3AForProbeConfs(tm,m2h,prbPyMMFFMolProperties=prbParams,refPyMMFFMolProperties=refParams,numThreads=4)
>> 1 loops, best of 3: 304 ms per loop
>>
>>
>> I think this is a convenient (and very easy) way to take advantage of
>> one of the convenient features of modern compute hardware.
>>
>> Best,
>> -greg
>>
>>
>>
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