[gmx-users] mdrun_d not running in parallel

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Mon Mar 8 12:49:40 CET 2010

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 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)

However when I give the commands 
grompp_d  -f em.mdp -c solvated.gro -o em.tpr -zero
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.

Where have I gone wrong?
Any suggestion will be of great help.
Thanks in advance.
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