[gmx-users] mdrun_d not running in parallel

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 8 13:31:24 CET 2010

sarbani chattopadhyay wrote:
> Hi ,
> I had installed gromacs4.0.7 in double preicision in 64 bit Mac 10.6.1 
> computer with 8
> dual core processors.
> 1) I installed the fftw-3.0.1 in the following way
> ( in the directory)
> ./configure --enable float
> sudo make sudo make install
> make distclean
> ./configure --enable-threads
> make
> make install
> 2) I installed gromacs as
> ./configure --disable-float
> sudo make
> sudo make install
> 3) I installed lam-7.1.4 as
> ./configure --prefix=/usr/local/lam --without-fc
> sudo make
> sudo make install
> After that I went back to the gromacs directory
> and did
> make clean
> ./configure --enable-mpi --program-suffix=_mpi
> make mdrun
> sudo make install -mdrun
> In this way I couldn't get mdrun_mpi_d. However I read from the revision 
> notes that grompp
> and mdrun can run in parallel by themselves.( "-np" option is not there 
> in grompp_d)

The use of -np is entirely unrelated to precision.  Why couldn't you get the 
MPI-enabled mdrun?  I'm assuming there were some errors.

If you're referring to the following statement: "Parallel simulations can be 
started with grompp and mpirun -np mdrun without further options," it only 
refers to the fact that grompp no longer requires -np.  The only MPI-enabled 
program is mdrun, and must be configured against MPI libraries; it doesn't just 
magically work by itself.

> However when I give the commands
> grompp_d -f em.mdp -c solvated.gro -o em.tpr -zero
> lamboot
> nohup mpirun -np 8 mdrun_d -v -s em.tpr -deffnm em &
> the md.log file says nnodes=1. the simulation is not running in parallel.

Clearly.  The mdrun_d executable is a result of your double-precision, non-MPI 
installation (step 2 above).  If you want both MPI-enabled and double-precision, 
you need to --disable-float and --enable-mpi in the same configuration step.


> Where have I gone wrong?
> Any suggestion will be of great help.
> Thanks in advance.
> Sarbani
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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