[gmx-users] AVX libraries with GMX4.6.3

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 30 18:03:55 CEST 2013

With what compiler? (e.g. consult mdrun -version) There are many known
bugs in early point versions of each minor release of gcc, for
example. This is why the installation instructions stress getting the
latest version of your compiler.

Otherwise, what is your .mdp file and simulation system contents?


On Fri, Aug 30, 2013 at 5:48 PM, Ali Sinan Saglam
<asinansaglam at gmail.com> wrote:
> 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;
> (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
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