Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

[Mark Abraham]

On 9/09/2011 1:46 AM, Marcin Zielinski wrote:
Hi there,
I've been having hard times the past days trying to build SP and DP 
binaries
of GROMACS 4.5.4 on our Power6 system, here at SARA, using IBM XL 
compilers,
LAPACK, BLAS, GSL and FFTW3.

At the end, I think I've succeeded and had to use two dirty hacks to 
avoid problems.
I'm waiting now for results confirmation from friend of mine.

First thing, small patch to cmake/FindLAPACK.cmake
-    set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas};-Wl,--end-group" ${_threads})
+    set(CMAKE_REQUIRED_LIBRARIES ${_flags} "-Wl,--start-group
${${LIBRARIES}} ${_blas} -Wl,--end-group" ${_threads})
(Note the removed semicolon. )

Thanks. Fixed for next version.


Create Your build directory, I had source dir and build dir in the 
same root dir.

Second thing, before issuing make (and after cmake) modify 
src/config.h inside Your build directory:
line 45: remove ## _ (should look like this: #define 
F77_FUNC(name,NAME)     name)
line 48: remove ## _ (should look like this: #define 
F77_FUNC_(name,NAME)    name)

If you set GMX_ACCELERATION=POWER6 this (and a few other things) should 
happen automatically.

Mark


After that, cmake command, for sp and tools only:
module load lapack fftw3/3.2.2 gsl/1.15 cmake

cmake \
      -DFFTW3F_INCLUDE_DIR=<path to fftw3>/include \
      -DFFTW3F_LIBRARIES=<path to fftw3>/lib/libfftw3f.a \
      -DGMX_EXTERNAL_BLAS=ON \
      -DBLAS_LIBRARIES=<path to gsl>/lib/libgslcblas.so \
      -DGMX_EXTERNAL_LAPACK=ON \
      -DLAPACK_LIBRARIES=<path to lapack>/lib/liblapack.a \
      -DGMX_GSL=ON \
      -DCMAKE_INSTALL_PREFIX=<install dir>/gromacs/4.5.4-sp \
      -DGMX_X11=OFF \
      -DCMAKE_CXX_COMPILER=mpCC \
      -DCMAKE_CXX_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
      -DCMAKE_CXX_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \
      -DCMAKE_C_COMPILER=mpcc \
      -DCMAKE_C_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
      -DCMAKE_C_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \
      -DCMAKE_F77_COMPILER=mpfort \
      -DCMAKE_F77_FLAGS="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 -qomp 
-qessl" \
      -DCMAKE_F77_FLAGS_RELEASE="-V -q64 -O3 -qarch=pwr6 -qtune=pwr6 
-qomp -qessl" \
      -DCMAKE_EXE_LINKER_FLAGS="-L<path to fftw3>/lib -L/usr/lib64 
-L<path to gsl>/lib -L/opt/ibmcmp/xlsmp/1.8/lib64 
-L/sara/sw/lapack/3.3.1-xlf12/lib -L/opt/ibmcmp/xlf/12.1/lib64 
-llapack -lgslcblas -lgsl -lesslsmp -lxlf90_r -lxlsmp -lxlfmath 
-lxlomp_ser " \
      -DCMAKE_SHARED_LINKER_FLAGS="-L<path to fftw3>/lib -L/usr/lib64 
-L<path to gsl>/lib -L<path to xlf>/xlsmp/1.8/lib64 -L<path to 
lapack>/lib -L<path to xlf>/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \
      -DCMAKE_MODULE_LINKER_FLAGS="-L<path to fftw3>/lib -L/usr/lib64 
-L<path to gsl>/lib -L<path to xlf>/xlsmp/1.8/lib64 -L<path to 
lapack>/lib -L<path to xlf>/xlf/12.1/lib64 -llapack -lgslcblas -lgsl 
-lesslsmp -lxlf90_r -lxlsmp -lxlfmath -lxlomp_ser" \
      -DGMX_MPI=OFF \
      ../gromacs-4.5.4

From here, there's a straight way for a parallel build for mdrun and 
same goes for double precision.
Hope this is going to help to anyone having similar problems as I did.

good luck,

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