[gmx-users] Building gromacs on CRAY XC40

[Sabyasachi Sahoo]

I am trying to install gromacs 5.0.5, and I did the following like you said:

module load fftw
module swap PrgEnv-cray PrgEnv-gnu
../../CMake/bin/cmake -DGMX_BUILD_SHARED_EXE=off ..

(I had to build Cmake myself, since Cmake version installed on our
supercomputer is 2.6 and I built Cmake for the version 3.2)

And I get the following error:

CMake Error at cmake/gmxManageFFTLibraries.cmake:76 (MESSAGE):
  Cannot find FFTW 3 (with correct precision - libfftw3f for mixed-precision
  GROMACS or libfftw3 for double-precision GROMACS).  Either choose the
right
  precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
  advanced option to let GROMACS build FFTW 3 for you
  (-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack
  library (-DGMX_FFT_LIBRARY=fftpack)

This error comes, even though fftw is already installed. I also have
manually built FFTW by downloading the tar ball and building it, in the
hope that it may somehow locate that and use it. ( I have also referred to
this a bit, https://www.youtube.com/watch?v=vOJsmtFeSGk and
https://www.youtube.com/watch?v=BZNzYt_DUB0 ) Anyways I allow the gromacs
to build its own fftw by the following sequence of steps:

module load fftw
module swap PrgEnv-cray PrgEnv-gnu
../../CMake/bin/cmake -DGMX_BUILD_SHARED_EXE=off -DGMX_BUILD_OWN_FFTW=ON ..
make -j
make DESTDIR=$installpath install -j
source /in/the/installed/directory/GMXRC.csh

and its done!! Thanx a lot!!!

I was trying to install gromacs since about past one week, and it turns out
that the only thing I was missing out was on switching the Programming
environment:

module swap PrgEnv-cray PrgEnv-gnu

I owe you big time!


On Tue, Jul 7, 2015 at 10:58 AM, Roland Schulz <roland at utk.edu> wrote:

> Hi,
>
> your not saying what version you are trying to install. Assuming 5.0.5 it
> should just work with
> cmake -DGMX_BUILD_SHARED_EXE=off ..
>
> Make sure to select GCC or ICC as compiler with a command such as (might be
> different on your machine)
> module swap PrgEnv-pgi PrgEnv-gnu
>
> If it still doesn't work, send your exact steps and errors.
>
> Roland
>
> On Tue, Jul 7, 2015 at 1:02 AM, Sabyasachi Sahoo <ssahoo.iisc at gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I am trying to build gromacs on our latest supercomputer CRAY XC40, but I
> > am unable to do so because of lack of administrator privileges and
> > different programming environment, w.r.t. my previous experience on
> tyrone
> > supercomputers. I continuously get errors regarding something or the
> other,
> > but trying to solve that results in another error.
> >
> > I am sure many of you would have already build gromacs on cray machines,
> > and hence would be really grateful, if anyone can tell me the correct
> > sequence of steps to build gromacs.
> > I have extensively searched through the web, and documentation and
> nothing
> > seems to work. It be also really great if someone could give me the link
> to
> > the any thread that addresses this problem.
> >
> > Thanx in advance.
> >
> > --
> > Yours sincerely,
> > Sabyasachi Sahoo
> > --
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-- 
Yours sincerely,
Sabyasachi Sahoo
M. Tech - Computational Science
Supercomputer Education & Research Center
Indian Institute of Science - Bangalore