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
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
S.vidhyasankar
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