[gmx-users] AVX libraries with GMX4.6.3

[Ali Sinan Saglam]

Hi,

I have been running some energy conservation tests with GMX4.6.3 and had
encountered some issues when using the AVX-256 instruction set.

I first noticed that my systems were freezing on a cluster that uses
Sandy-bridge CPUs and did not on a different cluster using SSE. After
realizing that the problems were not in my configuration and setup I
started compiling multiple copies of Gromacs and saw that only the AVX-256
compiled binaries showed this behavior.

After a few colleagues reproduced the same results, I'm now pretty sure
this is the case. Two colleagues started completely independently and
reproduced the same behavior on 2 different clusters and 2 desktop machines
(all sandy-brige, in all cases AVX yielded really weird temperatures,
sometimes exponential freezing sometimes heating etc.).

Gromacs was compiled with -DGMX_CPU_ACCELERATION=AVX or =SSE4.1 (or any
version of SSE) and that was the only difference between the two binaries.
The method of simulation was exactly the same outside of the mdrun that was
used. The temperature results from my simulations can be seen here;
https://www.dropbox.com/s/ul7g0fb4il17wxm/avx_sse_temp.png
Another example with a different person reproducing the results;
https://www.dropbox.com/s/x7mr3kcgmvd78ie/adam_avx_sse_temp.png

Cmake command was;
cmake SOURCE -DGMX_BUILD_OWN_FFTW=on -DGMX_OPENMM=off -DGMX_MPI=off
-DGMX_GPU=off -DGMX_THREAD_MPI=on  -DGMX_CPU_ACCELERATION=AVX (or SSE4.1)
(also tried THREAD_MPI=off, similar results)

Also all builds passed regression tests.

I just wondered if this is a known problem or are we making a mistake while
compiling?

Best,
Ali Sinan Saglam