From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 20 2017 - 11:20:29 CDT
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
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