Re: NAMD run on Intel hyperthreaded cores

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Tue Feb 06 2018 - 08:20:43 CST

Sorry, that's my mistake. It was actually 2 CPUs with 16 cores each and 2
threads per core.

Thaks for your reply.

On Tue, Feb 6, 2018 at 6:01 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Souvik,
>
> This CPU has 16 cores, the 32 cores are virtual. You may get similar
> throughput with just 16 threads. At any rate, 64 seems excessive.
>
> https://ark.intel.com/products/91766/Intel-Xeon-Processor-E5-2683-v4-40M-
> Cache-2_10-GHz
>
> Jerome
>
> On 6 February 2018 at 09:41, Souvik Sinha <souvik.sinha893_at_gmail.com>
> wrote:
>
>> Hi,
>> There is a cluster with nodes containing 32 cpu cores and each core is
>> doubly threaded and the processor is "Intel(R) Xeon(R) CPU E5-2683 v4". I
>> am currently using "NAMD_2.12_Linux-x86_64-multicore" binary in that
>> cluster. I am not exactly sure how to distribute hyperthreaded jobs. So, to
>> check the performance of hyperthreaded cores, the following commands are
>> tried and the resulting "Benchmark time" are given:
>>
>> charmrun namd2 +setcpuaffinity +pemap 0-31+32 +p64 <inputfile > :
>> Benchmark: 0.170056 days/ns
>>
>> charmrun namd2 +p64 <inputfile > : Benchmark: 0.168904 days/ns
>>
>>
>> charmrun namd2 +setcpuaffinity +pemap 0-31+32 +p32 <inputfile > :
>> Benchmark: 0.228512 days/ns
>>
>> charmrun namd2 +p32 <inputfile > : Benchmark: 0.157081 days/ns
>>
>> I can't see how this "+setcpuaffinity" is helping, as without defining
>> the mapping of PEs on threads is working fine (considering the Benchmark
>> time). Does multicore binary, by default, distribute processes on all
>> available threads (i.e. 64 in this case) and there is no need of
>> "+setcpuaffinity"? If that is true, then why with and
>> without "+setcpuaffinity", benchmark time differs significantly while
>> launching 32 processes?
>>
>> Please help me to understand this. Thank you.
>>
>> --
>> Souvik Sinha
>> Research Fellow
>> Bioinformatics Centre (SGD LAB)
>> Bose Institute
>>
>> Contact: 033 25693275
>>
>
>

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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