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.
-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
