[gmx-users] About gomacs MPI installation

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 31 14:37:43 CEST 2012

On 31/05/2012 10:17 PM, 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

As you will see in the 
http://www.gromacs.org/Documentation/Installation_Instructions, there is 
no need to do both "make mdrun" and "make" because the former does part 
of latter. Likewise for "make install-mdrun" and "make install". However 
it doesn't hurt.

> make install
> make install-mdrun
> It compiles nicely and successfully
> 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

You've installed GROMACS from source already. You have no need of a 
binary distribution in an .rpm or .deb. However that binary probably is 
linked to FFTW3, which your source installation was not, so PME will 
likely be much faster. You should probably get rid of the source 
installation, and do it again following 
http://www.gromacs.org/Documentation/Installation_Instructions, or use 
the binary distribution.

>   Otherwise is it enough to install only Debain   gromacs-openmpi to 
> install gromacs in paralleel

Probably it is.

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

Something named gromacs-openmpi, or successfully configured --with-mpi 
is very likely to run in parallel with MPI. That's the point of the name!

> 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)

No. See http://www.gromacs.org/Documentation/Installation_Instructions. 
Hyper-threading is useless for GROMACS, and you have configured with 
MPI, which prevents attempting to use threading of any sort.

> 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

mdrun -nt is not available with an MPI-configured mdrun, and likely 
exits with an error.


> Don't i Need mpirun command ?
> Thanks in Advance
> With regards
> S.vidhyasankar

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