[gmx-users] Compiling gromacs 4.6.5 on cray XT5m

Gmx QA gmxquestions at gmail.com
Tue May 13 09:13:23 CEST 2014

Dear users

I am having problems compiling gromacs 4.6.5 on a (rather ancient) Cray
XT5m machine.

My approach has been the following, but it stops during the make stage when
processing fftw.

1. Download gromacs-4.6.5 tar ball
tar -xvg gromacs-4.6.5.tar
cd gromacs-4.6.5
mkdir build
cd build

Then swap some modules
module swap PrgEnv-pgi PrgEnv-gnu
module swap gcc/4.4.4 gcc/4.6.1

I now have the following modules loaded:

~/gromacs-4.6.5/build> module list
Currently Loaded Modulefiles:
  1) modules/
  2) portals/2.2.0-1.0301.26633.6.9.ss
  3) nodestat/2.2-1.0301.25918.4.1.ss
  4) sdb/1.0-1.0301.25929.4.88.ss
  5) MySQL/5.0.64-1.0301.2899.20.1.ss
  7) Base-opts/1.0.2-1.0301.25878.4.1.ss
  8) xtpe-network-seastar
  9) PrgEnv-gnu/3.1.72
 10) atp/1.4.4
 11) xt-asyncpe/5.10
 12) pmi/2.1.4-1.0000.8596.15.1.ss
 13) xt-mpich2/5.3.5
 14) xt-libsci/10.5.02
 15) gcc/4.6.1

Then my cmake line is:

Which proceeds fine through the configuring stage, but then during make I
get this:

-- Performing Test GNU_SSE2_CFLAG
-- Performing Test GNU_SSE2_CFLAG - Success
-- Looking for emmintrin.h
-- Looking for emmintrin.h - found
-- Enabling SSE2 Gromacs acceleration
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- checking for module 'fftw3f'
--   package 'fftw3f' not found
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_r2r_1d in /opt/fftw/;/usr/lib/libm.so
-- Looking for fftwf_plan_r2r_1d in /opt/fftw/;/usr/lib/libm.so - not found
CMake Error at cmake/FindFFTW.cmake:97 (message):
  Could not find fftwf_plan_r2r_1d in
  /opt/fftw/;/usr/lib/libm.so, take a look at
  error message in
  /home/users/pela3247/gromacs-4.6.5/build/CMakeFiles/CMakeError.log to find
  out what went wrong.  If you are using a static lib (.a) make sure you
  specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
  CMakeLists.txt:895 (find_package)

-- Configuring incomplete, errors occurred!

Clearly there is something screwy with fftw, but I am not experienced
enough with cray to tell what it is. Trying to do what the message suggest
(adding -DFFTWF_LIBRARY=''') only results in exactly the same error.

Could you please provide some pointers to where I go wrong?


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