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
--
========================================
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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