[gmx-users] Problems building gromacs 4.6

Mark Abraham mark.j.abraham at gmail.com
Fri Jun 7 16:43:48 CEST 2013

On Fri, Jun 7, 2013 at 12:20 PM, colinbannister <
colin.bannister at nottingham.ac.uk> wrote:

> I am trying to build Gromacs 4.6 on a Linux machine, running Scientific
> Linux
> 6.2.  I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.
> Commands I issue to set environment, and run cmake (available as cmake28)
> are:
> [cczcb at login02 gromacs-build-nocuda]$ module load intel/compiler/64
> [cczcb at login02 gromacs-build-nocuda]$ module load intel-mpi/64/4.1.0
> [cczcb at login02 gromacs-build-nocuda]$ module load intel/mkl/64
> [cczcb at login02 gromacs-build-nocuda]$ export CC=mpicc
> [cczcb at login02 gromacs-build-nocuda]$ export CXX=mpicxx
> [cczcb at login02 gromacs-build-nocuda]$ mklvars_intel64.sh
> [cczcb at login02 gromacs-build-nocuda]$ cmake28 ../gromacs-4.6
> -DCMAKE_INSTALL_PREFIX=/home/cczcb/gromacs-install -DGMX_MPI=ON
> -DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/include
> -DMKL_LIBRARIES=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mkl/lib/intel64/libmkl_core.so
> This completes, but gives Segmentation fault messages at the end.  Output
> attached as 'cmake28.out'
> When I type 'make', it gets to 53% then gives a large number of 'undefined
> reference' errors, see 'make.out'.
> I have also tried only putting the libmkl_core.so library path as the
> setting for MKL_LIBRARIES.  This avoids the Segmentation faults, but again
> results in many undefined references, as you might expect.
> Any idea what could be happening here ?  Is Cmake messing up in parsing the
> command in some way ?  Is there a different approach I could use to build
> Gromacs ?

All that sounds very weird, and makes me wonder whether an MKL test program
would compile on your system. Since the value of MKL is very limited, I
would suggest compiling with FFTW for now.

GROMACS 4.6.2 streamlined the MKL build process greatly for icc >= 11, but
I would suggest waiting until GROMACS 4.6.3, because of a performance
regression with MPI builds that we are working on fixing.



> Any assistance much appreciated!
> Colin
> cmake28.out <http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out>
> make.out <http://gromacs.5086.x6.nabble.com/file/n5008889/make.out>
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