From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Jul 21 2017 - 12:20:38 CDT
Hi Giacomo,
I was trying to use Jim's build
named NAMD_2.12_Linux-x86_64-MVAPICH-Intel-Stampede. However, I got the
following error
error while loading shared libraries: libfftw3f.so.3: cannot open shared
object file: No such file or directory
Could you suggest which module I need to load for this?
On Thu, Jul 20, 2017 at 12:45 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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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