On 9/03/2010 3:42 PM, Sarath Kumar wrote:
Message: 1
Date: 8 Mar 2010 11:49:40 -0000
From: "sarbani chattopadhyay" <[email protected]
<mailto:[email protected]>>
Subject: [gmx-users] mdrun_d not running in parallel
To: <[email protected] <mailto:[email protected]>>
Message-ID:
<[email protected]
<mailto:[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.
That configure flag is not relevant unless you are compiling FFTW 2.x to
link to GROMACS, though FFTW does plan to re-introduce such
functionality in the future.
Mark
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