[gmx-users] About gomacs MPI installation

vidhya sankar scvsankar_agr at yahoo.com
Thu May 31 14:17:26 CEST 2012

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

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

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 ?

Thanks in Advance 

With regards 
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