[gmx-users] Problems building gromacs 4.6

[Colin Bannister]

Mark,

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.

Colin

-----Original Message-----
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 
> 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 
> -DGMX_FFT_LIBRARY=mkl
>
> -DMKL_INCLUDE_DIR=/cm/shared/apps/intel/composer_xe/2011_sp1.11.339/mk
> l/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/201
> 1_sp1.11.339/mkl/lib/intel64/libmkl_sequential.so;/cm/shared/apps/inte
> l/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.

Cheers,

Mark


>
> 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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> View this message in context:
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> 889.html Sent from the GROMACS Users Forum mailing list archive at 
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