[gmx-users] Re: mdrun_mpi executable not found

[Xiaohu Li]

Message: 4
> Date: Wed, 26 Jan 2011 12:53:17 -0500
> From: Justin Kat <justin.kat at mail.mcgill.ca>
> Subject: Re: [gmx-users] mdrun_mpi executable not found
> To: "jalemkul at vt.edu" <jalemkul at vt.edu>,        Discussion list for
> GROMACS
>        users <gmx-users at gromacs.org>
> Message-ID:
>        <AANLkTinJXi=7zN80eBnj01VkGggv6tzKst33qkTVy_P9 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you, I have been to that page probably a good 100 times by now.
>
> Was the 'No.' response with regards to my primary question? Or to the
> one within the parentheses?
>
> Suppose I remove my existing installation and reinstall, I am hoping
> to figure out when/where exactly should I specify
> --program-suffix=_mpi so as to not overwrite the pre-existing serial
> mdrun as I have mistakenly done so with my current installation.
>
>
> *./configure --enable-mpi --program-suffix=_mpi
> **make mdrun
> **make install-mdrun
> **make links*
>
> Lastly, if the above set of commands are incorrect, or will not carry
> out what I intend (to build a separate mdrun_mpi executable apart from
> the existing mdrun after a normal build), I am kindly requesting for a
> suitable revision.
>
> Have you tried
 ./configure --help
 to find out where the installation is?
by default gromacs will be installed at /usr/local/gromacs (according to
./configure --help).
If it's not installed there, do you have a openmpi or mpich compiler in your
path?
if not, then specify ./configure   --enable-mpi --program-suffix=_mpi
MPICC=<your own mpi compiler>

Xiaohu


>
>
> Thanks,
> Justin
>
>
> On 26/01/2011 8:50 AM, Justin Kat wrote:
> >* Alright. So meaning I should have instead issued:
> *>*
> *>* ./configure --enable-mpi --program-suffix=_mpi
>
>
> *>* make mdrun
> *>* make install-mdrun
> *>* make links
> *>*
> *>* to have installed an MPI-enabled executable called mdrun_mpi apart
> *>* from the existing mdrun executable? (Would I also need to append the
>
>
> *>* _mpi suffix when issuing the first two make and make install commands
> *>* above?
> *
> No. See http://www.gromacs.org/Downloads/Installation_Instructions
>
>
>
> Mark
>
> >*
> *>* Thanks,
> *>* Justin
> *>*
> *>* On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul <jalemkul at
> vt.edu <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>
>
> *
> - Show quoted text -
> >* <mailto:jalemkul at vt.edu <
> http://lists.gromacs.org/mailman/listinfo/gmx-users>>> wrote:
> *>*
> *>*
> *>*
> *>*     Justin Kat wrote:
>
> *>*     > Thank you for the reply!
>
> *>*     >
> *>*     > hmm mdrun_mpi does not appear in the list of executables in
> *>*     > /usr/local/gromacs/bin (and well therefore not in
> /usr/local/bin).
> *>*     >
>
>
> *>*     > Which set of installation commands that I used should have
> *>*     compiled the
> *>*     > mdrun_mpi executable? And how should I go about getting the
> *>*     mdrun_mpi
>
>
> *>*     > executable at this point?
> *>*     >
> *>*
> *>*     I see it now.  When you configured with --enable-mpi, you didn't
> *>*     specify
> *>*     --program-suffix=_mpi, so the installation procedure over-wrote
>
>
> *>*     your existing
> *>*     (serial) mdrun with an MPI-enabled one simply called "mdrun."  The
> *>*     configure
> *>*     output should have warned you about this.  You could, in theory,
>
>
> *>*     simply re-name
> *>*     your existing executable "mdrun_mpi" and then re-install a serial
> *>*     mdrun, if you
> *>*     need it.
> *>*
> *>*     -Justin
>
>
> *>*
> *>*     --
> *>*     ========================================
> *>*
> *>*     Justin A. Lemkul
> *>*     Ph.D. Candidate
> *>*     ICTAS Doctoral Scholar
>
>
> *>*     MILES-IGERT Trainee
> *>*     Department of Biochemistry
> *>*     Virginia Tech
> *>*     Blacksburg, VA
> *
> >*     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>
>
> *
> >*     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> *>*
> *>*     ========================================
>
>
> *>*     --
> *
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