[gmx-users] Gromacs 4.6 crushes in PBS queue system

Bogdan Costescu bcostescu at gmail.com
Tue Feb 19 14:08:45 CET 2013

On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski
<tomek.wlodarski at gmail.com> wrote:
> The problem is that this is only message I got...

But that's an important error. GROMACS 4.6 depends a lot on the
compiler generated code, as opposed to 4.5 and previous which used
hand-written assembler code. The build procedure detects the
architecture and instructs the compiler to optimize for it. If the
computer on which you build GROMACS 4.6 has a different architecture
from the one on which the executables are run, you get exactly this
error. F.e. if your build computer is has Intel Sandy Bridge
CPUs and the compute nodes have AMD Magny Cours CPUs, the executable
won't run. You have to instruct the build procedure to use the proper
type of acceleration for the compute nodes where the executable will
be run.

> I also  get this Warning:
> --------------------------------------------------------------------------
> WARNING: Open MPI will create a shared memory backing file in a
> directory that appears to be mounted on a network filesystem.

OpenMPI users have found that shared memory performance was lower when
the shared memory backing file was created on a shared file system.
This mechanism is used by default when you run several MPI ranks on
the same computer. There's some documentation on the OpenMPI site on
the implications and how to control this.

> but this I got also with gromacs 4.5.5 which is running ok so I think this
> is not a problem in my case.

... so performance with GROMACS 4.5.5 might have also suffered from this :)

> Like Alexey notice the problem is that my nodes have different
> architecture.. but this was not a problem with gromacs 4.5.5

Indeed, for the reason I mentioned above. Check for example the
presence/absence of "avx" in the "flags" section.


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