----- Original Message ----- From: "Justin A. Lemkul" <[email protected]> Date: Monday, March 8, 2010 23:33 Subject: Re: [gmx-users] mdrun_d not running in parallel To: Discussion list for GROMACS users <[email protected]>
> > > 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) ./configure --enable-double --enable-mpi --program-suffix=_mpi_d is required for double precision floating-point and MPI named how you would like. Mark > 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. > > -Justin > > >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....@middle?> > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
