> > Message: 1 > Date: 8 Mar 2010 11:49:40 -0000 > From: "sarbani chattopadhyay" <[email protected]> > Subject: [gmx-users] mdrun_d not running in parallel > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > 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) > > > 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. > > Where have I gone wrong? > Any suggestion will be of great help. > Thanks in advance. > Sarbani > > ---------------------------------------------------------------------------------------------------
Try first installing the fftw with the option of --enable-mpi, as u did for gromacs. then again install the gromacs with options same as before. Sarath Kumar B, Research Scholar, Centre for Biotechnology, Anna University.
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