[gmx-users] About gomacs MPI installation

[Justin A. Lemkul]

On 5/31/12 8:17 AM, vidhya sankar wrote:
> Dear justin
> Thank you for your previous reply
> Now i am trying to run the parallel gromacs simulation (gromacs 4.5.5) first of
> all i have successfully installed debain package of gromacs-openmpi
> for that i have configured and compiled using the following command
> ./configure --enable-mpi --enable-double --prefix=/usr/local/mpigromacs
> --program-suffix=_mpi_d
> then I issued the
> make
> make mdrun
> make install
> make install-mdrun
> It compiles nicely and successfully

If you have installed a Debian package, why are you re-compiling from source? 
Now you may have duplicate executables on your system.

> I have few doubt
> 1) should i need to install both rpm of openmpi (coresponding to my OS) and
> Debain of gromacs-openmpi ? (compatible to my Linux OS) Now i have both
> Otherwise is it enough to install only Debain gromacs-openmpi to install gromacs
> in paralleel
>

I would assume the Debian package contains everything you need; refer to its 
documentation.  Either you need a pre-built package or you need to compile from 
source, not both, unless the gromacs-openmpi package contains only mdrun, in 
which case you will need the other tools.

> 2) how to check Wheather Parallel installation of gromacs ? wheater is installed
> parallely or not?

If you have mdrun_mpi (or mdrun_mpi_d from source) and it executes in parallel 
via mpirun, then it is installed and working.

> I have installed on single Hyper threading supported intel pentium i5 (dual core
> processor,four thread)
> it means i amusing thread based parallelism not mpi based parallelism (i know
> the performance may be poor, though later i will extend this to clustering)

Use of threading and MPI are mutually exclusive.  If you invoke --enable-mpi, 
you are not using threading.  If your architecture supports threading, there is 
no need to compile with MPI support.  Configuration will detect necessary 
options and the resulting mdrun executable will have an argument called -nt, 
which allows you to execute the process using threads.

>
> please tell me The Above my understandings is correct or not
> if ther are any wrong things in the compilation procedure Please give me some
> tips to rectify error?
> I am very grateful to your valuable reply
>
>
> Also if the above procedure is correct
> Can i run the gromacs parallel simulation using the following command
> mdrun_mpi_d -nt 8 -s topol.tpr
>
> Don't i Need mpirun command ?
>

The above command is incorrect.  If compiled with MPI, there should be no -nt 
flag.  If you invoke MPI support when configuring, you need mpirun:

mpirun -np X mdrun_mpi -s topol.tpr

All of these issues are discussed in the manual and on the Gromacs website.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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