[gmx-users] Re: Re: mdrun -multi flag (Mark Abraham)

[bo.shuang]

Hi, Mark,

Thank you for help. It works. But now I have new fatal error:

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.


What does it mean about nodes? Thank you!

Bo

On Thu, Mar 1, 2012 at 7:42 PM, <gmx-users-request at gromacs.org> wrote:

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>   1. Re: mdrun -multi flag (Mark Abraham)
>   2. Re: dihedral distributions (Juliette N.)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 02 Mar 2012 10:17:12 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] mdrun -multi flag
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F500378.7030006 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2/03/2012 10:15 AM, bo.shuang wrote:
> > Hello, all,
> >
> > I am trying to do REMD simulation. So I used command:
> >
> > mdrun -s t2T.tpr -multi 2 -replex 1000
> >
> > And gromacs gives error report:
> > Fatal error:
> > mdrun -multi is not supported with the thread library.Please compile
> > GROMACS with MPI support
> > For more information and tips for troubleshooting, please check the
> > GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > Then I tried re-install mdrun:
> > ./configure --enable-mpi --program-suffix=_mpiq
> > make mdrun
> > make install-mdrun
> >
> > It looks fine, but I still cannot use multi flag, and it is still the
> > same error. I don't know what the problem is and what I should do
> > next. Thank you for help!
>
> With that program suffix, you need to use mdrun_mpiq
>
> Mark
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 1 Mar 2012 20:42:06 -0500
> From: "Juliette N." <joojoojooon at gmail.com>
> Subject: Re: [gmx-users] dihedral distributions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CAGDQh4os1KUuoGwLNcZnyxrf9SrA_+a8s0ekU2BUm6cojvZNsQ at mail.gmail.com
> >
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