[gmx-users] Problems building gromacs 4.6
Colin.Bannister at nottingham.ac.uk
Fri Jun 7 17:22:06 CEST 2013
Thanks for the response. We use MKL for a lot of applications, and have had no problems, except with gromacs. I wonder if there is a bug in cmake, as surely getting a segmentation fault can never be right ?
If anyone else has any ideas, I'd be grateful for them - I will try a build with FFTW3 for now.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: 07 June 2013 15:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Problems building gromacs 4.6
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
> [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
> 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!
> make.out <http://gromacs.5086.x6.nabble.com/file/n5008889/make.out>
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