Re: Compiling NAMD on stampede 2.

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jul 21 2017 - 12:47:07 CDT

I think the library name can give you some hints on that.

On Fri, Jul 21, 2017 at 1:20 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> 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
>>
>
>

-- 
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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