[gmx-users] Is version 5.0 generating portable binaries?

Mark Abraham mark.j.abraham at gmail.com
Fri Jan 31 02:40:56 CET 2014

On Jan 30, 2014 11:57 PM, "Raffaella D'Auria" <rdauria at ucla.edu> wrote:
> Hello All,
> I have just performed a fresh installation of gromacs version 4.6.5 on a
heterogeneous linux cluster (running centos 6.4) . After the installation I
see that the binaries, for say mdrun,  work on all the machines with
hardware similar to the one on which they were installed (namely AMD
processor such as: Quad-Core AMD Opteron Processor 2354) but produce an
"illegal instruction (core dumped)" when run on nodes with intel processors
(such as: Intel Xeon CPU E5335  @ 2.00GHz).
> As suggested in the documentation (
I have tried to compile with GMX_CPU_ACCELERATION set to "none" (I have
also turned down the optimization levels) with always the same result
(illegal instruction) across different hardware.
> Is this expected behavior? If so will the binaries of version 5.* have
the same portability problem?

In short, yes, and yes. While discussions like
http://redmine.gromacs.org/issues/1165 have taken place, nobody has decided
to commit time to solving this, because the only benefit comes when the
target machine architecture is variable, unknown, and there is no local
mechanism in place to call the correct mdrun. This painful situation is
partly created by choosing to have a  heterogeneous cluster... In 5.0 you
will be able to compile for SSE4.1 and avoid RDTSC with the distributable
build option, but this is wasting the capabilities of the AMD processors. A
second GROMACS install, together with a recommended run script that chooses
the mdrun binary based on the node name / whatever should be a reasonable


> One more thing the situation described above occurs with both the gnu
4.4.7 compiler and the intel 13.1.1.
> Any feedback would be greatly appreciated.
> Thanks,
> Raffaella.
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