On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski <tomek.wlodar...@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. Cheers, Bogdan -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
