Myunggi Yi wrote:
Thank you for your answer, but I can't really get you.
I am using gromacs 3.3.3. <http://3.3.3.> on CentOS with AMD64 clusters
with infiniband connection.
I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi
(intel and gnu).
You are saying I don't have install fftw by myself, aren't you?
Then how can I compile? What is the best option for the performance?
I did the followings.
======================================
./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
make
make install
make clean
./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2
--program-suffix=_mpi
make mdrun
make install-mdrun
======================================
Is this wrong?
Seems reasonable, did it work?
Can I compile it with intel compiler?
It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4. There
are step-by-step instructions on how to install both FFTW and Gromacs on the
Gromacs website:
http://www.gromacs.org/content/view/23/33/
Following these directly will give you the standard installation, in serial and
parallel, and single and double precision, if you choose.
-Justin
I'm sorry. I have so many questions.
Please let me know how to compile it.
Thank you.
On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi,
Gromacs has it's own parallel FFT which only uses FFTW for the local
FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.
Roland
On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Dear gmx users,
fftw3 seems doesn't support MPI.
Why is the gromacs configuration default fftw3 not fftw2?
Which version should I use for parallel computing?
Thank you.
--
Best wishes,
Myunggi Yi
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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--
Best wishes,
Myunggi Yi
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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