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

Erik Lindahl erik.lindahl at scilifelab.se
Fri Jan 31 08:53:44 CET 2014

Hi Raffaella,

First: You absolutely shouldn’t remove all acceleration in cases like this - that would hit your performance by ~50%. Instead, you can pick the greatest common divisor, which is SSE4.1.

Second, the segfault happens because we use a timing instruction. You can disable this by using the Cmake argument


Which creates a binary that will work on most x86 machines.

This will be more automated in 5.0, but by not using AVX_128_FMA on your new AMD nodes you will lose ~30% performance compared to what is possible, so you might want to consider installing at least two mdrun binaries (renamed to, say, mdrun_intel and mdrun_amd).



On 30 Jan 2014, at 23:35, 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 (http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc) 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?
> 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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