From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 20 2017 - 11:45:18 CDT
I don't have an account there currently, but why don't you look for nightly
builds in Jim's folder?
On Thu, Jul 20, 2017 at 12:29 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> Hi Giacomo,
>
> The reason I am not using the pre-compiled versions is because I need to
> run Gaussian accelerated MD which as far as I know if only available in the
> latest nightly build. Are you aware whether any of the pre-compiled
> versions on Stampede 2 can run GaMD?
>
> On Thu, Jul 20, 2017 at 12:20 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> > wrote:
>
>> Intel vs GNU may improve the single-core performance by a few percent
>> (and parallel performance by the same prefactor), but not so much the
>> parallel scaling.
>>
>> If you're not sure about the differences between these options, why don't
>> you try a precompiled version?
>>
>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtTexas
>>
>> In the paths shown in there the original version of NAMD is very old, but
>> in the same home folder (which is Jim Phillips') you will find up to date
>> versions as well.
>>
>> Giacomo
>>
>>
>>
>> On Thu, Jul 20, 2017 at 12:09 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>> wrote:
>>
>>> Hi Giacomo,
>>>
>>> Thanks for the response.. No, I don't need to use the SMP version, just
>>> MPI is fine for me. I had originally tried it like this
>>>
>>> env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
>>>
>>> That worked but the scaling was extremely poor. That's when I felt maybe
>>> using iccstatic would be better. Do you have any inputs for this?
>>>
>>>
>>> Chitrak.
>>>
>>> On Wed, Jul 19, 2017 at 9:14 PM, Giacomo Fiorin <
>>> giacomo.fiorin_at_gmail.com> wrote:
>>>
>>>> Hi Chitrak, I would specify manually only one of the compilers, or
>>>> neither one if possible. The architecture mpi-linux-x86_64 should already
>>>> take care of calling mpicxx, and you should load the relevant environment
>>>> module set the MPI library and wrapper to the Intel version.
>>>>
>>>> Also, check this from the NAMD release notes:
>>>>
>>>> *MPI-based SMP builds have worse performance than verbs or ibverbs and
>>>> are not recommended, particularly for GPU-accelerated builds.*
>>>>
>>>> So, stick to plain MPI if you must use SMP (for example because you
>>>> want to communicate more efficiently with the GPU), or otherwise skip MPI
>>>> use the IBverbs option for Charm++.
>>>>
>>>> Giacomo
>>>>
>>>> On Wed, Jul 19, 2017 at 6:47 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>>>> wrote:
>>>>
>>>>> Hi NAMD users
>>>>>
>>>>> I am trying to compile the latest nightly build version of NAMD on
>>>>> Stampede 2. For building charm 6.8 beta2 I used the following command that
>>>>> was recommended by the interactive session
>>>>>
>>>>> ./build charm++ mpi-linux-x86_64 iccstatic mpicxx smp -j16
>>>>> --with-production
>>>>>
>>>>>
>>>>> However, I am getting the following error:
>>>>>
>>>>> Error> Tried to specify two compilers: iccstatic and mpicxx
>>>>>
>>>>>
>>>>>
>>>>> How should I fix this?
>>>>>
>>>>>
>>>>> Best regards,
>>>>> Chitrak.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Giacomo Fiorin
>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>> http://goo.gl/Q3TBQU
>>>> https://github.com/giacomofiorin
>>>>
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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