ADL: autodock4.omp vs autodock4 (version 4.2.6 compiled from source code)

Kateryna Miroshnychenko kateryna.miroshnychenko at gmail.com
Tue Jan 20 09:17:22 PST 2015


Hi, Juan,
Thanks for the answer, but the question was on the Autodock4, not Autodock
Vina.
Autdock Vina and Autodock4 are based on different algorithms and I'm
interested in autodock4 currently.
Any information concerning the usage of  the parallel OpenMP implementation
of  autodock4 (autodock4.omp) would be greatly appreciated.

regards,
Kateryna

2015-01-20 18:58 GMT+02:00 js <facien03 at uchile.cl>:

> *Hi:**
> **Vina detects without problem the 4 threads (2 cores) in my laptop with
> an Intel I5. And it runs faster.**
> **.Regards,**
> **Juan**
> *
>
> On 1/20/2015 11:30 AM, Kateryna Miroshnychenko wrote:
>
>> Dear list subscribers,
>> I've compiled and installed autodock 4.2.6 from the source code and I've
>> got two autodock binaries: autodock4 and autodock4.omp. Test runs (make
>> check) went smoothly for both of them. The problem is that I don't see any
>> acceleration with autodock.omp (suppose that this is a parallelized openMP
>> version) compared to the autodock4 (serial).
>> My processor is Intel(R) Core(TM) i5-4200U CPU @ 1.60GHz. It has two cores
>> and four threads. System monitor shows that CPU usage is  only 25% for
>> autodock4.omp process (the same is for autodock4).
>> I haven't found any information concerning proper usage of autodock4.omp.
>> The help message for it is the same as for autodock4.
>> What am I missing? Any examples of autodock.omp usage would be helpful.
>>
>> with best regards,
>> Kateryna
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>>
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