Re: Running a test simulation using GPU only (without any CPU core)

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 28 2016 - 10:40:38 CDT

On Thu, Apr 28, 2016 at 11:09 AM, Josh Vermaas <vermaas2_at_illinois.edu>
wrote:

> Hi Sourav,
>
> It is just not how NAMD works. ACEMD or AMBER can both run as you
> describe, in that there is no communication between GPU and CPU once the
> job has started. NAMD wasn't designed this way, and requires a CPU
> associated with the process to deal with bonded interactions.
>

‚Äč...and even in the case of a simulation software that does the entire
force field computation and time integration on the GPU, you still need a
CPU to *manage* the GPU and exchange status information, schedule and
dispatch individual GPU kernels to be run and so on. the GPU cannot run
independently.

axel.

>
>
> -Josh
>
>
> On 04/28/2016 10:04 AM, Sourav Ray wrote:
>
> Hello Brian
>
> Is there any alternative to CUDA version that might support a GPU only
> simulation? I checked the mailing list and couldn't find a relevant answer
> to this.
>
> Thanks and regards
> Sourav
>
> On Thu, Apr 28, 2016 at 8:30 PM, Brian Radak <bradak_at_anl.gov> wrote:
>
>> No. That's not how the NAMD-CUDA implementation is designed. Many
>> operations in normal MD are only ever performed on the CPUs.
>>
>> Brian
>>
>>
>> On 04/28/2016 09:40 AM, Sourav Ray wrote:
>>
>> Hello
>>
>> Is there any way I can use the NAMD-CUDA version to run simulations
>> without using any of the CPU cores and restricting the simulation to only
>> GPU unit? I tried the following command:
>>
>> NAMD_2.11_Linux-x86_64-multicore-CUDA/namd2 +p0 +devices 0 test.conf >
>> test.log
>>
>> It doesn't work and putting +p0 shows the following error:
>>
>> pthread_create: Resource temporarily unavailable
>> Segmentation fault (core dumped)
>>
>> Please let me know if there is a workaround.
>>
>> Thanks and regards
>> Sourav
>>
>>
>> --
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643
>> brian.radak_at_anl.gov
>>
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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