[gmx-users] Re: mpi enabled gromacs (

[Dr. Vitaly Chaban]

Look into the resulting md.log


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark



On Tue, Oct 23, 2012 at 1:52 PM, Rajiv Gandhi <grajiv03 at gmail.com> wrote:
> Thanks for your reply. Actually, i have installed gromacs in my cluster and
> then i configured with --enable-mpi --program-suffix=_mpi option by
> following make mdrun, make install-mdrun. It installed nicely and does works
> well. I want to know how would i check whether mpi works in gromacs? Is
> there any commands that i can check ? Thanks in advance,
>
> On Tue, Oct 23, 2012 at 7:05 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>>
>> > I have recomplied the -fPIC and its complied well. I have not used mpi
>> > cluster before so have some few doubts on it.
>>
>>
>> The -fPIC key stands for position independent code and has nothing to
>> do with parallelism itself.
>>
>>
>> > Could you please tell me how can i check whether my gromacs installed
>> > with
>> > enable_mpi. How do i check the cluster are connected in groamcs?
>>
>> ./configure --enable-mpi
>>
>> >Is that
>> > same procedure of running simulation steps with normal PC such as
>> > pdb2gmx,
>> > grompp, or should i need to specify the mpi like pdb2gmx_mpi, grompp_mpi
>> > ?
>>
>> NO.
>>
>> Dr. Vitaly V. Chaban
>> MEMPHYS - Center for Biomembrane Physics
>> Department of Physics, Chemistry and Pharmacy
>> University of Southern Denmark
>> Campusvej 55, 5230 Odense M, Denmark
>> --
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