[gmx-users] Problems building gromacs 4.6

colinbannister colin.bannister at nottingham.ac.uk
Fri Jun 7 12:20:32 CEST 2013

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)

[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 ?

Any assistance much appreciated!


cmake28.out <http://gromacs.5086.x6.nabble.com/file/n5008889/cmake28.out>  
make.out <http://gromacs.5086.x6.nabble.com/file/n5008889/make.out>  

View this message in context: http://gromacs.5086.x6.nabble.com/Problems-building-gromacs-4-6-tp5008889.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list